Quantitative-PCR Validation of 154 Genomic Segments Called As Cnvs in Five Replicat

Supplementary Table 1

status number of regions calls in A calls in B calls in C calls in D calls in E average non validated 31 5 6 5 1 0 3.4 validated 123 78 77 74 52 43 64.8 total 154 83 83 79 53 43 68.2 false positive rate * 3.2% 3.9% 3.2% 0.6% 0.0% 2.2% false negative rate # 29.2% 29.9% 31.8% 46.1% 51.9% 37.8% % false positive calls $ 6.0% 7.2% 6.3% 1.9% 0.0% 5.0%

Supplementary Table 1: Quantitative-PCR validation of 154 genomic segments called as CNVs in five replicate comparisons of NA15510 versus NA10851 on WGTP array Replicate experiments A to E are ranked by global SDe (A: 0.033; B: 0.033; C: 0.036; D: 0.039; E: 0.053). *: false positive rate = number of called but not validated regions / total number of tested regions #: false negative rate = number of non called but validated regions / total number of tested regions $: % false positive calls = number of called but not validated regions / total number of calls

False positive estimates for 500K EA CNV calls

Total Rep1 Rep2 Rep3 Avg (unique) Validated 33 28 32 31 38 Not validated 2 2 2 2 5 Total 35 30 34 33 43 % False positive 5.71% 6.67% 5.88% 6.09% - % False negative 13.16% 26.32% 15.79% 18.42% -

Supplementary Table 2A : Quantitative PCR validation of 43 unique CNV regions called as CNVs in three replicate comparisons of NA15510 versus NA10851 using the 500K EA array. % False positive: Calculated for each replicate independently. Formula = # non-validated CNVs per replicate /total CNVs called per replicate % False negative = (# total unique validated CNVs - number of validated replicate CNVs) / # total unique validated CNVs For these experiments, each CNV called in each of the three replicates was tested using quantitative PCR or Mass Spectrometry as an independent validation method (see also Supplementary Table 4). Each pair-wise comparison gives rise to 2 false positive CNV calls, or approximately 6% of the calls. The percentage of false negative calls is estimated by calculating the % of validated CNVs that are captured in each replicate relative to the total number found in all three replicates. This is likely an underestimation of the false negative rate, since this calculation only considers CNVs from the 500K EA platform that have been called with our final algorithm parameters.

Total Rep1 Rep2 Rep3 Avg (unique) Validated 13 13 18 14.67 18 Not validated 1 0 0 0.33 1 Total 14 13 18 15 19 % False positive 7.14% 0.00% 0.00% 2.38% - % False negative 27.8% 27.8% 0.0% 24.1% -

Supplementary Table 2B : Quantitative PCR validation of 19 unique CNV regions called as CNVs in three replicate comparisons of NA15510 versus the HapMap reference set using the 500K EA array. This table uses the same calculations as above using validation data from CNVs called from NA15510 compared to the 270 HapMap samples. The total number of CNVs detected by each replicate is lower in the population wide comparisons because CNVs are being detected only in the test sample, whereas in the pair-wise comparisons, CNVs are being detected both in the test and reference sample.

Supplementary Table 3. Overlap of CNVs called from NA15510 with Tuzun et al., (2005)

A) Tuzun deletions detectable by 500K EA platform using 4 SNP criteria

median SNPs in 500K EA NA15510 500K EA NA15510 500K EA NA10851 vs WGTP NA15510 vs Tuzun call chr begin_span end_span size size window minimum SNPs vs NA10851 vs HapMap HapMap NA10851 Deletion 20 14700001 14897555 165991 36 35 loss loss Not called loss Deletion 16 34236453 34590205 329311 30 30 Not called gain gain Not called Deletion 15 32472522 32628056 149270 13 13 Not called loss loss Not called Deletion 22 21476328 21576188 72623 13 12 gain Ig locus Ig locus gain Deletion 11 55115601 55226935 85414 8 6 loss homozygous deletion Not called loss Deletion 1 149363029 149421545 32480 8 0 Not called Not called Not called loss Deletion 7 141501682 141557369 22083 7.5 2 Not called Not called Not called Not called Deletion 8 1327422 1358228 13004 7 0 Not called Not called Not called Not called Deletion 12 57006943 57032578 12415 7 2 Not called Not called Not called Not called Deletion 11 4915812 4941949 10197 5.5 1 Not called Not called Not called Not called Deletion 16 83201418 83232168 18892 5.5 3 loss loss Not called Not called Deletion 19 59408310 59460933 21523 5 2 loss loss Not called Not called Deletion 8 126662647 126708435 10798 4 1 Not called Not called Not called Not called Deletion 17 11157980 11202026 11860 4 0 Not called Not called Not called Not called Deletion 1 112402144 112423342 12173 4 2 Not called Not called loss Not called Deletion 11 5738669 5768809 22662 4 3 Not called loss loss Not called Deletion 16 76916517 76969258 14067 4 0 Not called Not called Not called Not called Deletion 4 9874892 9914828 22358 4 0 Not called Not called Not called Not called Deletion 1 149559508 149586671 11100 4 0 Not called Not called loss Not called

B) Tuzun deletions detectable by WGTP using a 50kb size requirement WGTP NA15510 500K EA NA15510 500K EA NA15510 500K EA NA10851 Tuzun call chr begin_span end_span size vs NA10851 vs NA10851 vs HapMap vs HapMap Notes Deletion 20 14700001 14897555 165991 loss loss loss no call - Deletion 14 105301889 105469293 136594 gain no call Ig locus Ig locus Ig locus homozygous Deletion 11 55115601 55226935 85414 loss loss deletion no call - Deletion 22 21476328 21576188 72623 gain gain Ig locus Ig locus Ig locus Deletion 16 34236453 34590205 329311 no call no call gain gain Same CNV genotype for NA15510 and NA10851 Deletion 17 41724262 41981453 218711 no call no call Not called no call Potential insertion in human genome reference DNA: Deletion 15 32472522 32628056 149270 no call no call loss loss Same CNV genotype for NA15510 and NA10851 Deletion 3 163991649 164115393 112179 no call no call no call no call Potential insertion in human genome reference DNA: Deletion 7 101825756 101930685 96208 no call no call no call no call No BAC clones in region Deletion 1 25318324 25417454 67848 no call no call no call no call False negative WGTP

Supplementary Table 3: Overlap of CNVs called from NA15510 with Tuzun et al., (2005) for A) 500K EA calls and B) WGTP calls

A) For the 500K EA platform, there are 5 Tuzun deletion regions identified by fosmid end sequencing that are detectable, having a minimum of 4 SNPs in any given size region. To calculate the median and mimimum number of SNPs, a sliding window was used for the known size of the deletion within the genomic span as defined by Tuzun et al., 2005. All 5 detectable regions are called by 500K EA in either the pair-wise comparison with NA10851 or in the population wide comparison with all 270 HapMap samples, 14 additional deletions contain a median of at least 4 SNPs, and 3 of these are called in pair-wise or population wide comparisons. B) For the WGTP platform, 10 deletions identified by fosmid end sequencing should be large enough for BAC array CGH, with a size larger than 50kb. 4 of these 10 regions are called, 2 of the non-called retions contain a CNV in the reference sample, and 2 of the non-called regions are likely artefacts of the fosmid end sequencing method, since these regions harbor duplication or complex CNVs in the HapMap population (see Supplementary Table 8). Only one of these non-called regions may be a true false negative. Supplementary Table 4: Validation data for CNVs called by WGTP and 500K EA

CNVs called by WGTP Quantitative PCR validation by SYBR Green real-time PCR (NA10851 vs NA15510) for WGTP 0=not validated Sanger Called by qPCR 1=confirmed CGH Called by Affy Affy result 2=mapping Region Chr Start End Result Affy 060308 validation 060308 problem new Chr new Start new End Forward primer Reverse primer Qty NA15510 (rel to 1) SD NA15510 Chr1tp-25F10 1 12757377 12790369 Loss No No Loss 1 1 12757377 12842343 ACAATCTTCTCTCTGGCCTCTG AGGGTGTTTACCCACAAAAATG 0.421 0.099

Chr1tp-6D2 1 103923046 104164023 Loss No No Loss 1 1 103898814 104049621 GGAAGAATATAGATGCCAACCC TCAGCTGAACTGGATCATTTGT 0.798 0.068

Chr1tp-38C8 1 120245520 120395759 Gain No No Gain 1 1 120245520 120395759 GCAGACATATTGCACCCAGATA TTCCAGTGTTTAACGCTTCTGA 1.590 0.276

Chr1tp-36B8 1 141918516 142199768 Gain No No Gain 1 1 141851837 141979099 AGTGGAAGCAGAGACTCCAGAC AAGGAAGCACATAACCTCCAAA 1.207 0.088

Chr1tp-7D2 1 142391276 142548088 Gain Gain Gain Gain Gain 1 1 142391276 142548088 ACTGGCTCTCCTCACAAAGTTC ATAAGGGGGAAGAAAACCAAAA 1.860 0.194

Chr1tp-20E3 1 142678316 142882622 Gain No No Gain 1 1 142678316 142882622 AGGTAGGGGTGATGCTAGTCAA AAAAACAAAACCAGGGACAAGA 1.297 0.069

Chr1tp-7H5 1 145888591 146093292 Gain Gain Gain Gain Gain 1 1 145888591 146093292 CCCAAGGGAGAAAAGAGTAGGT AGGAGAGTTTCTGCAGTCTTGG 1.245 0.049

Chr3tp-19E4 3 19709162 19895852 Gain Gain Gain Gain 1 3 19709162 19895852 CCCTTCTCATCTCTCACCAAAC CATCTAACCAGATGCCATTTCA 1.453 0.087

Chr3tp-14B12 3 20240591 20399098 Gain Gain Gain Gain 1 3 20240591 20399098 TTGCTGGAAATGAAAACAAATG TACAGGACAGTGCTCTGGAAGA 1.329 0.164

Chr3tp-3C7 3 98699482 98904950 Loss No No Loss 1 3 98699482 98904950 GCCATTTGATTCCTAGGTTCTG TATGGGAAAGCCTGACATTTCT 0.862 0.052

Chr3tp-9H6 3 196908420 197078010 Loss No No No change 1 3 196908420 197078010 GACCTAAACAAGATGGCCTGTC AAGTTCCACCTCACGTTGTCTT GGTGTTTCTGATATGCAGGTGA ACAGGGCTTGAAGAAGTTACCA NS NS TCTAGGACTGCGATGGTGTATG GTATCGCCCTGATAGATTCCTG Chr3tp-10B7 3 196920033 197108192 Loss No No No change 1 3 196920033 197108192 GACCTAAACAAGATGGCCTGTC AAGTTCCACCTCACGTTGTCTT GGTGTTTCTGATATGCAGGTGA ACAGGGCTTGAAGAAGTTACCA NS NS TCTAGGACTGCGATGGTGTATG GTATCGCCCTGATAGATTCCTG Chr4tp-9A2 4 9000913 9120591 Gain No No Gain 1 4 9000913 9120591 AATCCCTAGAGCCAGGATCTTC AAATTGTAATGCTGCCGAAAGT 1.800 0.261

Chr5tp-17H9 5 17465585 17597910 Loss No No Loss 1 5 17465573 17597918 GGGTCTGTTTGTGCAGGAAT TTCATCCAGGTAAGGGCAAC 0.640 0.078

Chr5tp-21E1 5 93886642 94067957 Loss No No Loss 1 5 93886642 94067957 CCATCATCACCTCAACTCAAAA CGGGGTAACAGGTTATGTGATT 0.563 0.079

Chr5tp-6E12 5 105318590 105505763 Loss No No Loss 1 5 105318590 105505763 TTTCAAGATGCTTACTGCCTCA TCTTGCCTAACCTTCCCTATCA 0.505 0.119

Chr6tp-2C12 6 143336 346084 Gain Gain Gain Gain Gain 1 6 143357 346084 CCTGCTACCACAGACTCACTTG AACCATGTCCTCCCTAGACTCA 1.187 0.091

Chr7tp-20B12 7 41617589 41797479 Gain No No No change 0 7 41617589 41797479 TGCCTTGTATCAGATCAACCAC CTGCTCTCCCAAGACACTCTTT NS NS GCTATGGGAAAGGTTCTGAATG GAAGGGGTACAGATTGACTTCG NS NS CAACCTGGAAAATGCTGTCATA TTGAAGTGAAAGAACCCCTGAT NS NS Chr7tp-19H7 7 64424689 64515187 Loss No No Loss 1 7 64424689 64515187 TACAGTTCATGCCCAGATGTTC GCGAAGCTTCTTGAGTTTTGTT 0.705 0.033

Chr7tp-21C5 7 99217194 99399792 Gain Gain No Gain Gain 1 7 99217194 99399792 ATGCTTAGTCCCACCAGATGAT TGAGATGCTTTTGAAGGAGACA 1.496 0.103

Chr8tp-3C12 8 47728697 47901824 Loss No No Loss 1 8 47728697 47901824 GAGCCATTCTGAAGCTCTCATT ATGTGGAACTGCCCATAGAAGT 0.798 0.056

Chr8tp-2F7 8 86592730 86763703 Gain No No Gain 1 8 86592730 86763703 AAACAACAAAGGGTTGGAGAGA ACAATTTCTGCCATTTCGATCT 1.283 0.127

Chr9tp-4C7 9 11303383 11457020 Loss No No Loss 1 9 11303383 11457111 TGTCCAGAATTTTGCATAGTGG CAGGCTTCGTTTCTCTCAAAGT 0.771 0.068

Chr10tp-13F5 10 47796101 47971413 Loss No No Loss 1 10 47796101 47801347 Chr10tp-6F3 10 47799348 47972563 Loss No No Loss 1 10 47799348 47972148 ACTGCCCTTAGCATTACTCTGC AGTCTCTGTCAGATGTGCGTGT 0.485 0.022

Chr10tp-5H2 10 56078040 56236185 Loss Loss No Loss Loss 1 10 56078033 56236143 GTTCTTGCCCAGGTCCATATAA AAATGGCAAACTGGACAGAAGT 0.359 0.050

Chr10tp-13D5 10 125047207 125217217 Loss No No Loss 1 10 125047207 125217217 GGTAAGCCCCTCTTTGAAAGTT CTCTGTACCAACACCATCCTCA 0.819 0.073

Chr10tp-3D5 10 127443890 127606660 Loss No No Loss 1 10 127443890 127606660 GACTGTGAGCCCACAAAACATA CAATTCAGAACAGCAAGGACTG 0.815 0.077

Chr13tp-1E4 13 56525617 56718127 Gain No No No change 0 13 56523625 56717361 Chr13tp-4D7 13 56600596 56729961 Gain No No No change 0 13 56600591 56729961 TCGGTTTTTATCAGTCGGTTCT TGATTGACTCCCCCTAAGAAGA NS NS TAGGAACAGGCGACTTCGTATT CTTATGGATGACAGACCCCAAT NS NS Chr14tp-2D11 14 31928231 32086193 Loss No No Loss 1 14 31928231 32086193 GGAGTAGCTGACAGAAGCGAAT GCCAGATAAACAACAGCCTACC 0.588 0.031

Chr14tp-4A9 14 73030050 73196823 Gain No No Gain 1 14 73030050 73196823 TAGGTCAGGATGACCACAACTG ATAGTGCCCTGTCTCTGGGTAA 1.243 0.055

Chr15tp-11F2 15 35892662 36092625 Loss No No Loss 1 15 35892662 36092625 GCCGAAGACCTAAGAGAACTCA TAGGAGATGGAAGAGGTGGTGT 0.673 0.062

Chr15tp-4B5 15 94433027 94616040 Loss No No Loss 1 15 94433027 94616040 GTGGCTGATCCCTTCTCAATAC TAAATCCACAGCTTCTGCTTCA 0.561 0.066

Chr15tp-10H9 15 95786870 95954157 Loss No No Loss 1 15 95786870 95954157 CTAAAAGGACCAAAACCAGCAC TCATGAATTTCACCCAAGTCAG 0.750 0.066

Chr16tp-3B11 16 22338076 22508688 Gain No No Gain 1 16 22338076 22508688 Chr16tp-8B1 16 22503592 22679810 Gain No No Gain 1 16 22503592 22679810 TGAGCCTTACTTAGCCTGGAAG GCAGGAAGCAAAAGATCCTAGA 1.257 0.049

Chr16tp-9C2 16 32422680 32576837 Gain No No No change 0 16 32446676 32576815 ATGTCCTGATTCAGCCTTTGTT TAATACTACCCCCTCTCCAGCA NS NS TCTCTCTGGCCTTCCTGTAGAC CAGAATGTGACCATCATGCTTT NS NS Chr16tp-2F9 16 33282424 33452774 Gain No No Gain 1 16 33282424 33452774 Chr16tp-13A2 16 33333009 33508862 Gain No No Gain 2 - - - Chr16tp-9B7 16 33362222 33555929 Gain No No Gain 1 16 33362222 33555929 ATTATATCCATTGGGCAACAGG GGATTCTGGTCAAGGTAGATGC 1.217 0.085

Chr17tp-11D5 17 21850381 22014559 Loss No No Loss 1 17 21850381 22014559 CTCCCCTGGACTGATAGTGTTC CCAGCCCCCTAAAAGAGATAGT 0.414 0.040

Chr17tp-11A1 17 31309398 31466733 Gain Gain Gain Gain 1 17 31309398 31466733 CTTGATCTTTGGGAAACTGACC GACACAAATCAAATCCCTCCAT 1.289 0.063

Chr20tp-2F12 20 25894247 26015566 Loss No No Loss 1 20 25894247 26015566 AGGTCCTTGGCAGTGATACCTA GGACGTTGAGAAGAATTTCCAG 0.485 0.035 Quantitative PCR performed using Quantitative Multiplex PCR with Short Fluorescent Fragments (QMPSF) (NA10851 vs NA15510) for WGTP 0=not validated Sanger Called by qPCR 1=confirmed CGH Called by Affy Affy result 2=mapping Region Chr Start End Result Affy 060308 validation 060308 problem new Chr new Start new End Forward primer Reverse primer p-value (t-test) Chr1tp-23H1 1 108504425 108699273 Gain No No Gain 1 1 108504425 108699273 CCTAACTTGCTAGGCATTGTACCT TTCAATTCACTCTTTGTCAGAAGC NS CCTAAACAGAATTTCATGGCATC ATTACTTTGGTCACGTTGGTGAT 0.0005

Chr1tp-8H9 1 163348043 163508931 Gain No No Gain 1 1 163348043 163508931 GAACTTTCTATGGGGGCTTCTT GAAGAGTTTGAGCCCCATTCTA NS CAAACCCAAGATTTGTTCCACT ATACTGCTCAGGACCACAATGA 0.021

Chr1tp-11C10 1 199211892 199384880 Loss No No Loss 1 1 199210505 199386132 GGAAGTTTCTGTGTGCATTTCA CGTTTTGAAGAATGTTGGATCA 0.0001 CATTAAGGGAACATGGAAGCTC TTGTGTCTGCAGAATCAGTGTG NS

Chr1tp-12D10 1 212165460 212327574 Loss No No No change 0 1 212165460 212327574 TATCCTGGGCTCTTTATCCTGA ATAAAGGATCTCGGCAGTTCAA NS TGGTCAGCTTTCAGATTTAGCA GAGTGACACCTTCCTCCTGAAC NS CACTAAGTTTCCAGGGCATAGG CTGTCAACTGATGGCTTGCTAC NS

Chr2tp-28A12 2 7875760 8029407 Loss No No No change 0 2 7875760 8029407 CTCATCTCTGCCTTCCTCAACT CAGATAACCAAGGCCACCTAGA NS ATGCAGAACAGGAGTCTGGTG AATCACATCAGTTGCAGCCTTG NS AGCTCTCACCTCACAAGGTCTC GTGCCAAGAAGAGTCACCAGAT NS

Chr2tp-4E12 2 87428555 87579864 Gain No No No change 0 2 87428555 87579864 TCTAGCATCCAAAGCAAACTCA TTGCCAGTTTAGAAGAGCAACA NS TCACCGTATGACTCTTGTGAGG GTCTCAGTTTCCCCAACTGTCT NS

Chr2tp-28H7 2 87958554 88112870 Gain No No Gain 1 2 87958554 88112870 GCTCCAGGTAAAGAGCACAAGT ACAAGCTTCTCCCTATGTGAGC NS GTTTCCCTAATAGGTGCCTTCC GCACACACGATTCTGTTTCAAT 0.022

Chr2tp-28B12 2 88979593 89141717 Gain Gain Gain Gain 1 2 88979593 89141717 CAGCCACTACCTGAAGAAACCT TAACCACAAAGCCCTCATTTCT Assay failed

Chr2tp-4C7 2 89792857 89962428 Gain Gain Gain Gain Gain 1 2 89792857 89962428 CTGAGCTGAGCTGTACTGTTGG GTATCGGTTTACATGGGTCAGG 0.007 ATAAGGCTGTCCTGCTTTCTTG TTTCCATAGGAATCCAGCAAGT NS

Chr2tp-10D5 2 89859003 90016977 Gain Gain Gain Gain Gain 1 2 89859003 90016977 TTCCATGGCTAATCCGTATCTT CTGCATACACAGCTTTCACACA 0.005 TGCAATGTGCTAGCCAAGTTTA GCCATGGAACAATAGAGAAGTG 0.0006

Chr2tp-12B8 2 97112914 97303968 Loss No No Loss 1 2 97112914 97303968 ATCTGAAGAGGATCCACAGAGC AAAGGGGTACTTCTCCACATCC 0.007 GCTTTATTCACTTGCCATCTCC TCCCTAATGGCAAACCTAAGAA NS

Chr2tp-7E6 2 127547173 127722744 Gain No No Gain 1 2 127547173 127722744 GCCTTTGAAGTCCCTGACATAC CCAGTCCATCTTCTTCTGCTCT 0.022 TCCTCTTCTTGGGCATAATGTT GCTTATGTTGGTCCTTGTCCTC NS

Chr2tp-18G8 2 131780250 131953801 Loss No No Loss 1 2 131780178 131953801 GCTGTGTTCATCCATTCTTTCA GCCCAGCAGATAAACATGAAGT 0.0074 AAGGGATTTAATCTGGTCAATG CTAGCTGCCCTGCAATAGAACT 0.0002

Chr2tp-17A4 2 156852993 157055606 Gain No No No change 0 2 156852987 157032312 CCAGCAAGCTGATCTCTCTACA TCCTCTTGGTCTGCCTCATAAT NS TGAGTTCTTTGCCTGTTTCTGA GCTTTACTCTAAGGGCATGGTG NS GAGAGCTGCTTCTGCAAGTGTA TGCTTCCATGTTGTCTTTATGG NS

Chr2tp-1H7 2 195293720 195479196 Loss No No No change 2 #N/A #N/A #N/A GGTGGTGAATCCCATACTCATT TCATAAACCATTGGTGTGGTGT NS ATCCATGGGACCTATGTTTCTG CTGCCTTCAGTGAGAGAGGAAT NS GATGAAAATGTGAAACCGCATA CCAGGCACTCGTAATGTGATT NS

Chr2tp-2H5 2 199210758 199378534 Gain No No No change 0 2 199210758 199378534 TTAGCAGAACACCAGCTCACAT AGAATTCAGGTTCCACTCAAGG NS AAAGAGCTCCACATTCCATCAT GTGCTACCAGTCCCTTCACTTC NS

Chr3tp-15C2 3 19416349 19587692 Gain Gain Gain Gain Gain 1 3 19416349 19587692 TTTTGACCTGTTGGGAAACATT AATTTGGGGAAAATGACTCAGA 0.0021 ATGGAACCCTTGTGAATGTAGG CAACAACATCTCTCAGCCTCAC 0.0025

Chr3tp-4F11 3 19800244 19957065 Gain Gain Gain Gain 1 3 19800244 19957065 TTCAAGTCTATCCTCATTGTTGG TTAACCAAGGAACTTGTTGGAA 0.0079 CAACTAGGACTTGAGACATCAGGA TTATTGGCTGCATTAGGATGTG 0.0023 CTTCACACTGTCTTGGCTGCT TCATCAGTTCCAATCTCCTTCC 0.0008

Chr3tp-26D6 3 20554037 20750375 Gain Gain Gain Gain 1 3 20554037 20750375 AGGTGTGGTAGGGTGGATTATG ATGAGCCTAATCGTTCACCTGT NS GGAAGGTCTCAGTAACGTTTGG AATTTTCAGGAGGCAACTTTCA 0.011 TCTATTCCTGCAAAGGAGAAGC TGGAAGCAACTCAGAATCAGAA 0.040

Chr3tp-17E12 3 38134056 38316283 Gain No No No change 0 3 38134056 38316283 TCCTTGAAAGGTTTGTTGTCCT ATCAATCCATGTTTCCCTTTTG NS GTTGTCTGGGGTAGTGAGGAAG GGAGACTGATAAAGGCAGCAGT NS

Chr3tp-22B11 3 77173797 77330525 Loss No No No change 0 3 77173797 77330525 AATATTCTCGCTCCGTGTTTGT AGACACAGCGAGGTAGGAAGAC NS TTACCTACCTTGCAATCCTGCT GTAGAAAGCTGCTGAGGGAGAA NS

Chr3tp-15B4 3 139009885 139181611 Loss No No No change 0 3 139009885 139181611 CCCCAGTAGCCCATTTGTAATA CCACTTTCTTCACTCCCAATTC NS CCCAGGAAGATTAGAGATGGTG TGAAGCTATTTGCTGGGGTTAT NS

Chr3tp-5C11 3 196868577 197042673 Loss No No Loss 1 3 196868577 197042673 CAAGCTAACAGGAGCCAGAAGT CACCTCACGTTGTCTTCATCAT 0.0002 AGGCAGATTTCAGCTTTGTAGG CAAATTGCACATTCGTAACCTC 0.031

Chr4tp-1E5 4 21733485 21891882 Loss No No Loss 1 4 21733485 21891882 TACCTTGCCACAGAGCAGTATG ACAGAGGATTGCTGGTATGCTT 0.021 CAGGACCATAATGACATGCTAA TGGTTCAGACATAGTCACACCTG 0.032 TCCAGAGGCAGAGAATATGTCC CATGGAAGCCAAGTAGGTCTCT NS

Chr4tp-1H7 4 34608504 34779109 Gain Gain Gain Gain Gain 1 4 34608481 34779109 TACCAGCCAAACAGAATCAATG TGTTGCTAATAAGCCAGCTCAA <0.0001

Chr4tp-5E8 4 49329870 49501045 Loss No No Loss 1 4 49329870 49501045 ACCTTGATCTGAAAAGGCATGT GTAAGGAGAAACGGATGTTTGC 0.015

Chr4tp-23H6 4 70277448 70448849 Gain Gain Gain Gain Gain 1 4 70277448 70448849 AATCATGTCTTGCATTGACCAG AAACGACTTTTGGTCTTGTGGT <0.0001

Chr4tp-24E2 4 93738673 93914296 Gain No No No change 2 #N/A #N/A #N/A GCCTCTGCTAGATTTGAGCAAT TCAGGTCAGTGGCTTTTGTCTA NS GAATGCATGGAGCATTACAAGA CTTTGACATCAGCCATAAGCAC NS AGATGTAGCACCAAATCCCCTA GTTCTTGGCAACAAACATCAAA NS

Chr4tp-3G10 4 144705898 144872906 Gain No No Gain 1 4 144705898 144872906 TTTGCAGTCAGAGCAGTACCAT ATGTGTGAGAATGACCGATGAG 0.035 TGGAAGATTATTGCATGTGGAG GGTTCATTGTATGCATTGATGG NS

Chr4tp-9F9 4 169237638 169426377 Gain Gain Gain Gain Gain 1 4 169237638 169426423 ACAAGCCACCTTAAAACCTGAA CTTGAAAACCAAATCACCAACA 0.0017 GGTGATGTATCAGCAGGTTTCA GGTGATTTGAAGGTCAAGAAGG 0.0023 ATTGTCAAGGTGCATGTGACTC ACTTGTTTTGCACGTGAAGTTG 0.0059

Chr4tp-3G3 4 190867229 191030241 Gain No No Gain 1 4 190867229 191030241 Chr4tp-24D8 4 190906276 191070120 Gain No No Gain 1 4 190906276 191070245 ATCCTGATGTCGCCTGATAAAT AATGAATGACACCTCGGATCTT 0.036 TTTAGGAGTGGGAAGCAAGAAG CAACAGCTACTGTGAACCAAGG 0.044

Chr5tp-24D2 5 673163 895224 Gain Gain No Gain 1 5 673163 895224 TAGGTGACCCTGGAAGCATATT CCACAGGAGAATGAGCTAACCT 0.0028 TGTGGACATCACTAGGAAGAGG CAAACAAACAGCCAGAAACTGA 0.012

Chr5tp-3H4 5 8191735 8341004 Loss No No Loss 1 5 8191735 8341004 AAAGAACATTGCTGGGACTCAT TGGGATCACAGGATTCACATAG NS AATGAACGTTGAACACAGGATG TCTCATTACATGGTGGAACCAA NS AGAAACTGCACATTCAAAGCAA TTCACAAGCAACCTGAGAAAGA 0.029

Chr5tp-16B1 5 69475945 69679055 Gain No No Gain 1 5 69475945 69679055 TGCTAGAAAGCCCTGTGTAGGT CCTGCCCTCTTTACTGTTTCTC 0.004 GAGGAGGTCCTTCTTGTTCACT TGCATTCATTCCTGCTTAGATG NS 0=not validated Sanger Called by qPCR 1=confirmed CGH Called by Affy Affy result 2=mapping Region Chr Start End Result Affy 060308 validation 060308 problem new Chr new Start new End Forward primer Reverse primer p-value (t-test) Chr5tp-2F6 5 86696707 86874513 Gain No No Gain 2 #N/A #N/A #N/A AGAGAGCAGGGAACAAGAGATG GCAGTTTGTTTGATTGGTTCAA NS TGGTGAATGATTCTCATTTTGC AACCTCATTTTTCCAAGGTTGA 0.019 GACCATTTTCAAAGAGGGTGAG TGGGAGCAGATAGAAGCCTAAA NS

Chr5tp-13B3 5 135739990 135916051 Loss No No Loss 1 5 135739990 135916051 AGCTCCTATGATTGGTGTTGCT AAATGGAATGAGGGAGAGATCA NS CAGAACTCGATGCTGCTTACAC AAACAAAGGCAACCATGATACC 0.0010

Chr5tp-24C7 5 140137200 140307304 Gain No No Loss 0 5 140137124 140307304 GCACTCCCATACAAAGGAACTC CGAAATTGGCTTCCAAAATAAG 0.0081 ACTACTCGTTGGTGTTGGACAG GGGTTGTTCTCCTTCACGAATA 0.011 GTAAGCGATAGGAAGGCTGATG CAACTGAATGAATGGGATGGTA <0.0001

Chr6tp-1F9 6 1372371 1547233 Loss No No Loss 1 6 1372371 1547259 AGATGCACGGGACACTTTACTT GAAACTGTTGCCTAATGGAAGG 0.014 CCACCTTAAACATTGCTGATGA TGCTCATTTTGATTGTTTCCAC NS

Chr6tp-11A11 6 78947195 79116378 Gain Gain Gain Gain Gain 1 6 78947195 79116378 AAGGTTTCGAAGAACAAGTTGC ATTGAAAGACGGTGTTCTTGGT 0.0025

Chr6tp-12H6 6 120657990 120793506 Gain No No No change 0 6 120657990 120793506 GAGAATGGCTTGAGAAAGTTGG GGAACCTGGTAAACACATAGGG NS GGGTATGATGTTGAGAGGCAAT TTGCTTGGTGATTCTGTTATGG NS GATTGCTCACTTGATGCTTCTG CCCTTTGACTAGAGACCAATGC NS

Chr6tp-13D7 6 167866346 168055393 Loss No No Loss 2 #N/A #N/A #N/A CCAGGAACTGAACAAGAAGGAC AGTGTTCCCAGCACTGGTTAAT 0.0066

Chr7tp-19C9 7 40895000 41063383 Loss No No No change 0 7 40895000 41063410 TTGAAAAGGAGTGGAATGTCCT GAGAGAGCACCTTATTGGGATG NS ATGATGGCCTGATCCTTTTAGA GCGTGGACATTAACACGACTAA NS TAGGCCTAAAGGCAATCACATT CAGGATGATGAGAGCTTGACAG NS

Chr7tp-17H6 7 75169293 75327473 Gain No No 0 7 75169293 75327473 TCCTGGGTACTCTGGCTATTGT CATACCCTACTGTTGCCTGACA Assay failed

Chr7tp-23C3 7 77145836 77313414 Gain No No No change 0 7 77145836 77313414 CCTAGGAAAAGCCCCTAGTTGT TCATTTCCCATTTTGAGAATCC NS TCGTGACATTCTGTCCTGAGTC GGAAAATTCCCTTCTTCTTGGT NS

Chr7tp-24C6 7 80893135 81075858 Loss No No No change 0 7 80893135 81075858 TCAAGGGTTGATTTTTCCAGAT CCAGGAAATGTCTTGTGTCTCA NS TTGGTTTTCCACTAGTCCCAAT CTCCATCTGGGGATGGTATTTA NS TTGCTTAATGCAGGAGTCTTCA GGGAACGGGCTACTTCTAAAAT NS

Chr7tp-21F7 7 109329274 109487548 Loss No No No change 0 7 109329274 109487548 TTTTGTCAGAGTTCCCCAATCT TGTGGACTGGGACCTTATCTCT NS AGTTTGCCTCAGAGCTTCATTC TGAATTTTGATCTGTCCACCAG NS

Chr7tp-12E6 7 133094440 133281052 Gain No No Gain 1 7 133094440 133281052 CATCAAGGTATGTGGCTCATTG GCCTTAGCTTCTGTCTGTGGAT No product in reference CATCCATTACCACGCATAAAGA GAAACTGAGGTGCAGATGACTG NS

Chr7tp-7A11 7 143479367 143635318 Loss No No Loss 1 7 143479367 143635318 GGAATTCAGCATTATCCCTGAG AATCGCATAGTCACACACATCC <0.0001 TTAGCCCAAATGACCTGAATCT TAGCTCAGCTCCACATACCAAA 0.0003

Chr8tp-16F1 8 3329651 3488923 Loss No No Loss 1 8 3329651 3488923 TCTGTGTGTGTATGAGCGAGTG TCATCAAATCCTGTGTTGAACC 0.036

Chr8tp-20A1 8 51049146 51223381 Loss No No Loss 1 8 51049146 51223381 Chr8tp-6C3 8 51113198 51300548 Loss No No Loss 1 8 51113198 51300548 TTTCTTCTCCTGAACCCACAAT CATTCCACGGCTACATGACTT No product in target sample CTTGAAGAGAGCATCTGGGACT TCTGAGAAATGAACCCAAACCT <0.0001

Chr8tp-9E2 8 77525972 77677515 Gain No No No change 2 #N/A #N/A #N/A GGAGCAGGCTAGCATTATGAA GTGCACGTAGCTGTTCCTCTC NS AATTGTCACAGGCATAGCAGGT TTCCTGCCTTGTTATAGGATGAA NS

Chr8tp-10H8 8 121716573 121904901 Loss No No No change 0 8 121716682 121891712 CTGAAACTGGAATGCTGACAAG TCCTTGCCTTCTAATCTCTTGC NS GTTGTTTCCACACCACTCAGAA GGGTTATGCCTGGAGAGTTATG NS AACCTCCTGTCCTTAAATGCAA GGCACTGGGAAAACAAAGATAG NS

Chr8tp-7G10 8 123959179 124126040 Gain No No No change 0 8 123959179 124126040 CGTTGGTTCAAGGAGAACAGAT TGCCTACTTTTACCCTGGTCAC NS GCAGGGGCCTTTAGTTATTCTT CAGGATTTGGTCCTTTTACTGG NS CAACACGCTAACTTACCCTTCC GCTCAGTTGCCTTCCTGTTACT NS

Chr8tp-19F5 8 128295494 128452932 Gain No No Gain 1 8 128295494 128452932 CTGTTTGCTACTTTGACCATGC ACACTGATGTCTGCCAGAGAGA 0.0098 CAAGGAGCTAAAGGATGCAAGT AGCAAGCAGTTATTGACACGAA NS

Chr9tp-13C12 9 38859439 39036984 Loss No No Loss 1 9 38859439 39036984 TCACCTAGTTGGGGAGTGCTAT CTCATCTTCTCTGCCAACTGTG 0.010 TTAACTGTCCTGGCCTCTTTGT TATGATGCTGGTTTATGGATGG 0.0006

Chr9tp-3D8 9 40012313 40155117 Loss No No Loss 1 9 40012313 40155117 AACATTGGCCAAGACTGAAGAT GAGAGTCCCATGGAATGGATTA 0.021 TTTCTTTAGGGTGGGCAAATTA CAGTTCTAGAAAGCTGCTCAGATG 0.007

Chr9tp-13C11 9 41065891 41216390 Loss No No Loss 1 9 41065891 41216390 AGACAAGAACGTGAGCGTGAT GCAGAACTTTCAGCATCCTCTT NS AATGGCTGCTCTTTGAAGACTC AGATTGGGACCCTAAACCCTAA 0.007

Chr9tp-13E5 9 43409087 43595741 Loss No No Loss 1 9 43409087 43595741 AAGTACCAGTTCCCATTCCTGA AGAGGGTGAACAATTTCTGCTC 0.0003

Chr9tp-13D8 9 43456697 43711107 Loss No No Loss 1 9 43456697 43711107 TTTCTTTGTAGATCCTCCCAGTTA AACCACCTGTTAGTGCTACCAAA 0.0042 CTTCCTCTCTTGACCTCACGTT TAGGCAAGTTCATCAGCATTTG 0.0019

Chr9tp-1D6 9 45632363 45798788 Loss No No No change 0 9 45632363 45798788 AGGAACAGATAATTGCCTGCAT CTGGCTAGAGAATGCTTCTGGT NS TCCCATGAACTACGTTCAATCA CTCTGGCCACTGTTTTAGAAGG NS

Chr10tp-13F8 10 46046163 46263181 Loss No no Loss 1 10 46046581 46263057 ACCTTTACGGATTTGAGTGAGC GCCTTAGCTTTCAGTTCCTCAG <0.0001

Chr10tp-1F10 10 46232533 46416508 Loss Loss Loss Loss 1 10 46232533 46416508 ATTGGGTCTCATGTTTCGTTTT AGGCTCAGAAGTTCCACAGAAG <0.0001 GCCAGGTGCAAATACACACTAC GTGAAAGCATGTGGCTATGGTA 0.0006 AGGCATAGCTGTCTGTTCCATT AATTCAAAGCCCAGCATTAGC 0.0002

Chr10tp-14A1 10 46272296 46428959 Loss Loss Loss Loss 1 10 46272296 46428959 GCAGACATCTTCCCTATGGTTC CCTGGAATCCTGCTCATAAGAC 0.0040

Chr10tp-3H3 10 46560330 46738511 Loss Loss Loss Loss Loss 1 10 46560330 46738511 TGAACAGAGGAGACAAGTCCAG TAGGATGCCCAGGGATGTATAG NS ACCTTTACGGATTTGAGTGAGC GCCTTAGCTTTCAGTTCCTCAG 0.018

Chr10tp-12F5 10 56823397 56992090 Gain No No No change 2 #N/A #N/A #N/A AATCCAGCTGTCATTCCACTTT GTAGGCTCTGGCAATAGATGCT NS AAGGCATGTGAACAAATGTGAG CCGTGCAATCTACAACTAAGCA NS AGTTTGCACTGCTGTACCTCAA CCAAATGCTTGTATGCGTATGT NS

Chr10tp-2G9 10 88715605 88898563 Loss No No Loss 1 10 88715605 88898563 Chr10tp-14A5 10 88878227 89041452 Loss No No Loss 1 10 88878227 89041452 GGCAGAAGAGGTGAGTGAAACT GCTAGATTCTCCTTGCTCTCCA 0.0072 AGGGTAGCCCATTTCAGTTACA CCCTTTCCAGCTTTACTCAGAA NS

Chr10tp-4G7 10 102553726 102699193 Loss No No Loss 1 10 102553726 102699193 CAAGGTTCCCAAGAATCAGAAG TGTTATTTGCAGAACAGGGATG 0.042 CAACATTCCCTGGTGTTATCCT GTGTCCTAGGCAGGGATGTTAC 0.0008 TTTCCTTTCCCATTCTGTGAGT TGTCTCCCAAATACATCACGAC NS

Chr11tp-11F9 11 58291823 58461382 Gain No No No change 0 11 58291823 58461382 GCAACTGGGATAATTTCTGAGG GTCTCAGTCTCAGCCCTTGTTC NS TATTCCTAGGCTCAAGGAGCAG CAGAGAGAGATCATGGCAAATG NS

Chr11tp-17D1 11 60671936 60837233 Gain No No Gain 1 11 60671936 60837233 ATCTTTGGTGGCATTGACTCTT ATTCTGGAAAGCTGATTGGCTA 0.014

Chr11tp-14H12 11 90424582 90559703 Gain No No No change 0 11 90424582 90559703 GAGCAATTCCGAGTGTCACATA GAGGGAGTTTGACTTGAAATGG NS TGAAAAGCTTAGGGAGACAAGAA ACTGACATTGTGATTTGGCAGT NS 0=not validated Sanger Called by qPCR 1=confirmed CGH Called by Affy Affy result 2=mapping Region Chr Start End Result Affy 060308 validation 060308 problem new Chr new Start new End Forward primer Reverse primer p-value (t-test) Chr11tp-13G11 11 92274276 92447910 Loss No No Loss 1 11 92274276 92447910 GTTGAAAGATGTTTGGGAAAGG TCAACATTTTGAATGCTTACCG 0.0030 AGCAGGTGGCAAAGCTAGTAAC GTTGGCACTTAGGATAGGTTGG NS

Chr12tp-19F12 12 2224169 2413734 Loss No No No change 0 12 2224169 2413734 CTGTCTCTTTATGCCCTTGTCC AGAAGGTGAGACCATCACAGGT NS

Chr12tp-17G1 12 19977999 20143369 Loss No No Loss 1 12 19977999 20143369 CATGCCTTAATACAACGTTTGG GCAGGACAATTCACTTCAAACA NS GAATTCAGAAGATCCTGGCAAC TCAGCTCATCATCACAAATTCC NS ATAATCGGTTGCTGTTGGTTCT ACTTCCATGGTTCAGGAAAAGA <0.0001

Chr12tp-3E1 12 56116000 56288135 Gain No No Gain 1 12 56116000 56288135 CTTAATGTCCCCAAGGTCAGAG AAAACCTGTAAGGTGGAAAGCA 0.00050

Chr12tp-9H4 12 116942623 117103163 Gain No No Gain 1 12 116942623 117103163 AACTCTGATTGGTCCAGGTCAT AGAATGGCTTGCTTTGTGTCTT NS TAACTGAGGTTCCCGTGTTCTT GAACAGGAGTGTAACCCAGGAG Additional product of different size CCTGTTCCAGTGAAGCTGTAAG GTCTAGTGGTTAATGGCCAACC Additional product of different size

Chr13tp-4B2 13 30406380 30571189 Loss No No No change 0 13 30406380 30571189 TGTTTAATGGGCTGTTGCTATG GTTTGGGATGTCCTTACAGCTC NS AGCTCTGTCCTAAGCTCTGTGG GAATATGGATGAAGGGAGCAAA NS

Chr14tp-3B6 14 18732531 18920839 Loss No No Loss 1 14 18732531 18920839 TGAAGCTTTATCTTGCTGTCCA AGGAAAGCATTCACTCTTGAGG <0.0001 TGTCAGAGCTCATCACGCTAAT GAGATACCTGCCAGATGAGTCAC 0.038

Chr14tp-1F2 14 30251821 30406994 Gain No No Gain 1 14 30251821 30406994 TACATTAGCTGGAGCCTTCCAC ACTCTGATGGCAAACCTTGAAT 0.049 TTCTGACCACATTTCACACTCC ATTTGGGAGGAACATAACAACG NS

Chr14tp-5D3 14 84403506 84587542 Loss No No Loss 1 14 84403506 84587542 TAATGACCGTATCCTCCATGTG TCTCTGCTTCATGTTTCTCTCG NS GGCCTTTGTTTATTGCTGAGAC GAGGTTTTCAGACCTTTGTTGG NS CTGCTGGCTCCTTTATCTCCTA TGACCCCTCTTCTGGTTACACT 0.025

Chr14tp-12C3 14 105476363 105645656 Gain No No Gain 1 14 105476363 105645656 Chr14tp-10B2 14 105545220 105701352 Gain No No Gain 1 14 105545220 105701373 TCTGTGCATAGCCTGTGTTACC TCTCTCCTGTGTTCTCTCCACA NS GGAACCCACACTTGAATAGCTC TGGAGATTTCTAACCCTGCTACA 0.0001

Chr15tp-11A6 15 18419709 18576834 Gain No No Gain 1 15 18419709 18576834 GGACTCTGTGACACTGTGGGTA CACAGACACTGTCCACCTAAGC NS TGGATTGCTCACCTCTGTTATG CTGGGATCTCCTCTCTGTGTCT 0.0004

Chr15tp-5C2 15 18747225 18935829 Gain Gain Gain Gain 1 15 18747225 18935829 TATGCTTTCAGGCATACAGTGG TTCTCTGGAGCCGAGATTAGAC 0.013 GCTTCCTGGATGGTATAGGATG TGTGTTTCTGGTAAAGCTGGAA 0.0032

Chr15tp-11G2 15 19050502 19257408 Gain Gain Gain Gain 1 15 19050502 19257408 TCTCCTGATACTGCCTAACACAA ACCCAGCCATCTGGATACATAC 0.0001 TCAAGTCTTGTGGCTTCACACT ATTCTGTGTTGGGTTCTGCTTT 0.021

Chr15tp-1E1 15 39838609 39977984 Gain No No No change 0 15 39838609 39977984 TTCTGGTTTACATTGCCCTCTT ACTTGCTGCTCCAGGTCTTTAC NS CGGACTCTCCCTACCACTACAC GCCAGGGAATGAATGAGAGTTA NS

Chr15tp-11F4 15 71136328 71320377 Loss No No Loss 1 15 71136328 71320377 AACGCATTCAGTCAGGGTAGAT CCACTCTTGTCTTCAACATGGA NS TGCAGCAGAAGGTAGTGACAGT CAGGGGTAGGCAATATCCATTA 0.0020 ACCCTGGCTCTTGGTATCTGTA TCTCCCTAAGTCATCCCAGAAA NS

Chr15tp-8E2 15 77142292 77305824 Loss No No Loss 2 #N/A #N/A #N/A TGCTATACGATTAAGGAAGAGTGG AAGATGACTGATAGGCACAATCATA 0.0006 AAGTGGCAAGAGGTGGTGAT CAGCTTGAGCAAGAGAGGACTA 0.020 GTCTTGCTTCGAGCTGGTATCT GCTGTGCTCTAGCTGTCTCAAC NS

Chr15tp-1G8 15 93987934 94138221 Loss No No No change 2 #N/A #N/A #N/A TGTGACATGCAGTGAACCTAGA AATAGAATGGTGCCATTGAAGG NS TGATAGATTCTGCCAACTCCTG TCTAAGGCTAGTCACGGTCTCC NS AATGTGGCATGTGCAGTCTC CTACTGTCCAAGGCCTCTGAGT NS

Chr16tp-9B5 16 9148951 9335290 Loss No No No change 0 16 9148951 9335290 TGATCATGACGTGTATCTGCTG TCATTACCTGGGACCTATCTGG NS AGCCTTTGATGAAAGAGACTGG GATGGTGACTGATGAAGGAACA NS

Chr16tp-12F7 16 21408063 21559206 Gain No No Gain 1 16 21408063 21559206 AGGTGCATCTCTCCGTAGACTC CTGAGCCCAATACAAAGTTTCC NS AGGAGCTTCCATCTTGTCTCAG ACCAATGTAAGTTGGCAGGAAT 0.0024

Chr16tp-3A1 16 21521452 21698983 Gain No No No change 1 16 21521452 21698983 Chr16tp-13B1 16 21655277 21833734 Gain No No No change 1 16 21655237 21833734 CCAGGGCCTCATCTAGTTTCTA CATCAATTAGTCCCAGCAATCA NS ATCTCCTGCTCATAGGTTTGGA GGGAAGTTGACTCATTCTTTGC NS

Chr16tp-3F5 16 29981456 30174443 Gain No No Gain 1 16 29981456 30174443 TATATGTCCATGCTCTGCTCCA AAGTCACCTACCTGCTGGCTAC 0.0079

Chr16tp-13A1 16 32722382 32898544 Gain No No Gain 1 16 32722382 32898544 GCCTGAGCAGGTTAGATGGTTA CAAGTCTCACTGACAACCTCCA NS CTCTTCTGACCTGCTGAACCTT CTGCACTCACCACAGCTACACT 0.015

Chr16tp-9A7 16 32738162 32902091 Gain No No Gain 1 16 32738162 32902091 ATCCTGTGAGGGGACACAAG GGAAGTCCCAAATCCTGACA NS GCATGATTGTCACCCTGAACTA ATCTGTGCCCCTTAACTGAGAA NS AAATCTGTCCCCTCACCTATCA CATTTATATGGCTCCCCTACCA 0.022

Chr16tp-13B3 16 33295215 33456498 Gain No No No change 1 16 33295151 33456507 TGCTTCGTTTGCAGAATTTAGA TTTCAGCCCACAGGATAGAAAG NS AGCATTTTGGAAGGCTCAGA CTGTGTGCCATTCAGACACC NS

Chr16tp-8C5 16 33544442 33715261 Gain No No Gain 1 16 33544442 33715261 GTGTGAGAAGCACAAGATCAGC GTAGTCAAAATTCCAGGGCTTG 0.0031 ATGTGGCTCACACGTTAGACTG TTGAAGGAAGAAGGCAAGAGAC 0.026

Chr16tp-12E12 16 84697584 84868496 Gain No No Gain 2 #N/A #N/A #N/A TCCCCTTGTGAAACTGAATCTT GATAAGGACCAGGAAGTGCATC 0.047

Chr16tp-12D4 16 87800695 87958839 Gain No No Gain 1 16 87800695 87958839 CACAGGATCCACCTCCTATTCT GCCCAAGTCCCTCTTGAAAT 0.005

Chr17tp-6F3 17 11620264 11804393 Loss No No No change 0 17 11626167 11801249 TGTTTAAGCTTGGCCCTACATT ACATGGACACACAGCAGATACC NS AAGAATGGTTGCCAGGAAGTAA CCTAATGGTATAGCCAGGCATC NS GCAGACAAACTCAAATGTCAGC GCTGTGCTCATCTATCTTGCAC NS

Chr17tp-6B10 17 18788241 19132640 Loss No No Loss 1 17 18788241 19132640 TCTCATCTGAGAGCACTTCGAG ACTTGCTAGACGAGAGGACAGG 0.010 CAACTTTCCTCCTTCCAGACC CATAGGTTGATGCCAGCAGATA 0.0004 CTCAGAGGAGATCTTGGCAATC CAGGAGCTGTACCTCATGTCAC 0.014

Chr17tp-10G9 17 31401925 31593135 Gain Gain Gain Gain Gain 1 17 31401905 31593135 CAAATGCCTTTGCCTAGTCTCT GCAAATCAGCCTTCAATGTGTA 0.0015 AAAGGACTCCCTTCTGTTCCTT AGGTAGAACTGGaCCTGCCATA 0.0004

Chr17tp-11D4 17 33376424 33649105 Gain No No Gain 1 17 33376424 33649105 TACAGCATTTGCCTTTAGCTTT GTGCGCATTTGCTGTAATGTT 0.025 AAAGTGCCTGGATTTAGATGGA ATAAACTGGCCAGATGCTGTCT NS

Chr17tp-1E6 17 49380817 49574410 Gain No No No change 0 17 49380817 49574410 GGAAGGTGTTTCTACCAGGTTC ACATCAAGCTGGGGATAAAGAA NS TTCACCAGCAAATGTTAACCAC TAGGTAAATGGGATGGAGTTGG NS

Chr18tp-8D9 18 32401474 32557139 Loss No No Loss 1 18 32401474 32557139 CTCCACTCAGAAGGAAGCTGTT TTTAAATGGCTTGTGTGTCCTG NS ATGTGCCAGGGTAGAGATGAAT CTTTGAAACCCCAAGCTAACTG 0.019

Chr18tp-8C1 18 61788350 61951442 Loss No No Loss 1 18 61788347 61951445 Chr18tp-2F1 18 61819037 61987071 Loss No No Loss 1 18 61819037 61987071 ACTATCCAGGAAGTGCAATGGT AAACTGATTGTCAAGCCCAAGT No product in target sample TGAGTCATCTTCCTACCTACACCA GCATAATTAAAGTGGGCAGCAT NS

Chr19tp-6D9 19 45983467 46152643 Loss No No Loss 1 19 45983467 46152643 TTCAAAGATTTTCAGCCTCCTC TTCAGGTTTGTGTTGACAGCTT <0.0001 0=not validated Sanger Called by qPCR 1=confirmed CGH Called by Affy Affy result 2=mapping Region Chr Start End Result Affy 060308 validation 060308 problem new Chr new Start new End Forward primer Reverse primer p-value (t-test) Chr19tp-6H5 19 55228822 55344796 Loss No No Loss 1 19 55228822 55344796 AATTCATCTCCTGGAAGCCATA GTCCCGGAATGTAGATGTGAAT NS AGTGCCTCGAGGATGTTACACT ACTTGGAGAATCCAGGAATCAA 0.0045 TGACAGAGTCTTCACCCAGAGA CTTCCCGCAGTAATCACATACA 0.042

Chr20tp-1H11 20 14757045 14926976 Loss Loss Loss Loss Loss 1 20 14757045 14926976 CATGCCCTGTCTTTAACTTTCC AACACCCTCTGGCCTATTTACA 0.0003 GCCATTTCAATTCCATTTTGAT TTGCCCGACTTTTCCTAAATAA <0.0001 GCTGTGTTAAATATGGCAACCA TGCTGCATTCTTTCTATGATGA NS

Chr20tp-2H2 20 61685172 61846811 Loss No No Loss 1 20 61685172 61846811 GCTAGGGTTTGAAGTTCACTGG CCCAGCTGCTTGTACCTTCTAC 0.0001 AAATCTAGCAGGTCAGCCTCAG CCATCACCATAGAGACCTGTGA 0.025 GCACGTGTCCACTTTTAATCAG ACCGTGGAGGAAGTACAGTGTC 0.011

Chr21tp-2H11 21 10032184 10197104 Loss No No Loss 1 21 10032184 10197104 TTTGCATGTTGTTTACTGAGGTC AGAAGAACTTTCATGCACAGCA NS AGGAAATGGAAGCAAAGAGTTG TAACAGCTGTATGCATGTGTGC 0.025

Chr21tp-2B8 21 23756431 23900451 Gain No No Gain 2 #N/A #N/A #N/A CAGCATGAAGAAGAAACTGTGG TGTAAACACCAAAGGACACAGC NS CCAATTTGCAGTATTTAGCATCC CCCTTTCAAAGATAAGCCATC NS TTCTGGACAACCAAGAACAGAG CTGCTGTCTCACTTCCTTCTCA 0.0051

Chr21tp-1D6 21 28068637 28217906 Loss No No No change 0 21 28068637 28217906 AAGGCTGTTAGTCACAAGCACA TGCCATTCATAAGTGTTGGGTA NS CAAAGTTTACAATGCCTCCAGA AGGAACTCCTTTTCCATTCCAT NS

Chr22tp-6B5 22 14509865 14549165 Loss No No Loss 1 22 14509865 14549165 CACAGATAGACAGCCCATACCA GAATTTGATTGCAGTTCCTTCC 0.0015 GCATGAGTTCAAGAGCAGAATG GGACTAGAGAGCCAGGAAGACA NS

Chr22tp-6E2 22 20983001 21021756 Gain Gain Gain Gain 1 22 20983001 21021756 Chr22tp-6F11 22 21008880 21045994 Gain Gain Gain Gain 1 22 21008880 21045994 CAGAAGTCTAGCATGTGCAACC GGGGAAGTAAACCAGGGATAAG 0.0003 TCAGTGTCCAACCTACACCATC CAGGTGAGTCTGACTGATGCTC NS

Chr22tp-4D5 22 44975462 45018495 Loss No No Loss 1 22 44975462 45018495 TCTCTAACCTCCCACCAGTGAT CATTGGCAAATGTCTCTACTGC 0.011

Quantitative PCR performed using QMPSF on singletons called by the WGTP array 0=not validated Sanger Called by qPCR 1=confirmed CGH Called by Affy Affy result 2=mapping Region Chr Start End Result Affy 060308 validation 060308 problem new Chr new Start new End Forward primer Reverse primer p-value (t-test) test sample Fold change chr1tp-1G5 1 21967826 22158163 Loss No No No Loss 1 1 21967826 22158163 CCTAACTTCCACCTCCATTCAG TTTCTGGCCTAGGAGTAGCTTG 0.0049 NA12057 0.76

chr1tp-28H7 1 72893632 73019191 Gain No No No No change 0 1 72893632 73019191 AATGTTCCTGTGAGGGATTCAC ATTCAGTTATGGCAGCCAGATT NS NA18632 NS

chr1tp-10G4 1 191987583 192311869 Gain No No No Gain 1 1 191987583 192311869 GGCCATGCAGTAATAAGTGTGA TCCCATTCTTATCACCACACAA 0.0063 NA19154 1.25

chr3tp-6A4_chr3tp-3D10 3 165085150 165392762 Gain No No No Gain 1 3 165085150 165392762 CGCAAAGAATATGATGGAAACA TTAATTCATGCCTCAAATGCAC 0.045 NA19130 1.2

chr4tp-7D9 4 12173443 12335659 Loss No No No No change 0 4 12173443 12335659 CTGGGAATACTCCATCCTCTTG TTCTCCCAGATTCAATCCAGTT NS NA12814 NS

chr5tp-13E6 5 12839320 13039901 Gain No No No Gain 1 5 12839320 13039901 ACTGGCATTCACCATTAACTCC CCAAGATGTGGTGAGATGATTG <0.0001 NA18561 1.23

chr7tp-4D8 7 972335 1463188 Loss No No No Loss 1 7 972335 1463188 GGGTGACTGGAACGTGAGAC CAAGGTTTAGCCCAGGAAGG 0.0079 NA18861 0.28

chr7tp-12E4 7 35597465 35893678 Gain No No No Gain 1 7 35597465 35893678 TCAGCTAATTCACATGCAACAA ATTGAAGGTTCTTCCTCATCCA 0.0062 NA19131 1.64

chr7tp-23F4 7 68857154 69038812 Gain No No No No change 0 7 68857154 69038812 GTGCTGTGCAGAGGACTGTTAC GTCCATAGAAGTGACGACACCA NS NA19099 NS

chr8tp-9H3 8 93612868 93782102 Loss No No No Loss 1 8 93612868 93782102 AAAGATGCAACCATCAACTCCT ACCTGTAAGCAGCAAATCCAAG 0.0061 NA12763 0.8

chr9tp-3C8_chr9tp-3H4 9 130767119 131058115 Loss No No No Loss 1 9 130767119 131058115 GTCCTTGTCCTCACGGTAGAGA ACAGCTATGGACACACAGCAAC 0.0090 NA10857 0.72

chr10tp-7B10_chr10tp13B9 10 56503548 56781399 Loss No No No Loss 1 10 56503548 56781399 GATGGTTGTCGATAGACTTGGA GCCACTAACACTGGATGAATGA 0.0001 NA18861 0.65

chr10tp-12F12 10 110448976 110633486 Gain No No No Gain 1 10 110448976 110633486 ATCACAGCCACTTAACCACAGA CCAAAGTTGAGTTCATGGTGAG 0.033 NA10856 1.21

chr11tp-16H4 11 122784404 123050005 Loss No No No No change 0 11 122784404 123050005 CTGAGAGAACGCCAACCATAG CAGCTTCCTGAACAGCTACACA NS NA07048 NS

chr13tp-3B5 13 113086429 113259065 Loss No No No Loss 1 13 113086429 113259065 CTCGTTCTGCCTTAGTGACCTT GACAGGAACCTGCTTTCTGAAC 0.0001 NA12814 0.56

chr15tp-11F6 15 89632853 89841316 Gain No No No Gain 1 15 89632853 89841316 AGCTATTGCTCAGCTGGTTAGG GAGAGGCTGGAGATAGACAGGA 0.0066 NA18563 1.3

chr15tp-3E8 15 93267979 93447142 Loss No No No No change 0 15 93267979 93447142 GCTTAGGTATGGGTTGAAGACG CCCATGTAAGTATGGACCCACT NS NA18552 NS

chr18tp-6B4 18 19024429 19181612 Loss No No No No change 0 18 19024429 19181612 GTGAATGTGCAAGTGTCTGAG CTAAGGGTGGAGGATGTCAAAC NS NA18503 NS

chr21tp-3H11 21 15834516 16018549 Gain No No No Gain 1 21 15834516 16018549 ATAGACTCTGCGGGATGATTGT TATGCACGAGACATCTTTGGAC 0.032 NA19007 1.23

Quantitative PCR performed using SYBR on singletons called by the WGTP array 0=not validated Sanger Called by qPCR 1=confirmed CGH Called by Affy Affy result 2=mapping Region Chr Start End Result Affy 060308 validation 060308 problem Fold change Forward primer Reverse primer p-value (t-test) test sample Ref sample NA18959_Chr2_1 chr2 104052123 104218620 Gain No No No no change1 1.06 TGCCAGAGCGCTGACTGA TTGTGCCGGACAATGTTGTAC 0.0400 NA18959 NA10851 gain 1.13 0.0430 NA18959 NA6994

NA19130_Chr5_5 chr5 32281118 32774401 Loss No No No loss 1 0.84 GATTTCTTTACCTTGCTACTTTCTTCT TCCGGGACATAGCATCCAA 0.0016 NA19130 NA10851 loss 0.83 0.0003 NA19130 NA6994

NA12006_Chr9_1 chr9 16631966 16799203 Loss No No No opposite 0 1.29 GGAGTACTGGATGAGTAAATGTAAACCATTTGTGTGCTGAATGGATCA 0.0068 NA12006 NA10851 no change 1.01 NS NA12006 NA6994

Quantitative PCR performed using SYBR on singletons called by the WGTP array with different lots between WGTP and 500KEA

0=not validated Sanger Called by qPCR 1=confirmed Fold CGH Called by Affy Affy result 2=mapping change Fold change Region Chr Start End Result Affy 060308 validation 060308 problem lot1 lot2 Forward primer Reverse primer p-value (t-test) test sample ref sample NA19173_Chr1_4 1 21481490 21687720 Loss No No No Loss 1 0.89 0.97 CAGCCCCCAGCACATTG CCCTGGAGAAGGCAGCAA NS NA19173 NA10851 0.63 0.56 TGGTCTCAAACTCCTGACTTCAAG CACACCTATAATCCCAACATTTTCG 0.01(lot1) and 0.04 (lot2) Lot1 and Lot2 Lot3 1 0.98 TGAGGCTCACGGAAGCTAGTAAG GAGTCCTGGGACCGTCTCTTG NS NA18500_Chr10_4 10 98779953 98952462 Loss No No No No change0 1.2 1.13 TGCCCCTGACTCCAATCACT CGTGTGAGGGCGGTGAA NS NA18500 NA10851 1.06 1.05 TTGCTGCCTGGGTTTACATG GTGAAGTGATGTGGTTAAAGTGACAA NS Lot1 and Lot2 Lot3 1.14 1 CACCCTGCCAGGACTCACA GTGGAACGTGGTGCTTTTGA NS NA19129_Chr14_3 14 47329907 47516073 Gain No No No Gain 1 1.07 1.13 GCTGTCCCTAACTCTAATCCATTACC GAGCAGTTTCAGATAGGCAAGGA NS NA19129 NA10851 1.11 1.03 TGTGTGTCTGTGTTTGTGTGCAT AGAGCCTACCACATGGCAGAGA NS Lot1 and Lot2 Lot3 1.3 1.6 GGAAGCTGAAGAGGGATGATAGC TGTAGTTTTTTAGAGACAGGGTTTTGC <0.0001 both lots Supplementary Table 4B: CNVs called by 500K EA

Quantitative validation of 500K EA CNVs called for NA15510 vs NA10851: SYBR real-time PCR or MassSpec*

# times 500K EA overlap with called in 3 mean validation Fold change overlap with overlap with Tuzun et al., Region Chr Start End reps Ratio result (15510/10851) t-test Forward primer (or rsID for MassSpec) Reverse primer WGTP seg dups 2005 DGV** cnp1 1 16780906 17016443 3 0.77 loss 0.61 0.004 CCTGAAATGCCGGGTTTACA GAAGTGGGTTCCTAGGTCTCTGTTT √√ Locus 0005 cnp2 1 30406466 30408889 1 0.78 loss 0.46 0.001 TTGGGCAGACCTCCTCTCTTATC CTTTCTGAAGGCAGGAGTTCTCTAA cnp3 1 142434077 142479046 2 1.16 gain 1.35 0.049 GCCTCTCCTTCTTGCCCATAA GCTAGGTGTCTCACATAAGCGTAAAAG √ Locus 0018 cnp4 1 145115762 145954489 3 1.33 gain 1.47 0.042 GGAACGCTGGGTGGACTTC CGCTGCCGCCTGGAT √√ Locus1474 cnp5 1 146022913 146713021 2 1.11 gain 1.28 0.018 AGGCCAGCACCCAAACC GGAGGAAGTTCTGCATGAAAGC √√ cnp6 2 89878936 95122604 1 1.36 gain 1.34 0.018 AGGTGACTGGCCTGGATGAG CCTCGATGCCCTTCAGAAAC √√Locus0031 cnp7 2 132649300 132963017 1 0.78 no change 1.14 NS GGGTTGCTTGGCCGTATTT CTGTCAGAACTGTAGCCGCTACCT √ cnp8 3 19487176 20587963 3 1.25 gain 1.32 0.03 TGTGTGTGAAAACTCCCCTTGA TGGCTGGAAGTTGAGCAGACT √ cnp9 4 34587749 34638958 3 1.34 gain 2.14 0.001 CTGATGGCACAGCTTCAAGATG GAAATCTCAGTCTCTCCCCATACG √ Locus0063 cnp10 4 69203585 69318438 2 1.40 gain 2058.67 0 TAAGGCATGAGGGAGCAGAAA TGATCAGCACAAACCACGGATA √√ Locus1625 cnp11 4 70315100 70364045 1 1.40 gain 1.16 0.037 GAACTCAAGTCAGAATAATTCTCAATCAA CACATTACACGCCTGGTGAAGA √√ Locus0573 cnp12 4 169193199 169354046 3 1.34 gain 1.91 0.022 CACTGAGCCTCACAGCAATTG GGAGAGCTTAATATTGTGAGGATGAA √ Locus1663 cnp13 4 172708642 172741856 1 1.28 no change 0.98 NS AGCGTATGATGTTGCTGCTCTATT TGGTCTGCTGGAGGCTCATT cnp14 6 214735 312109 2 1.21 gain 1.31 0.025 GGGCACAGTGAAAGGTGGAA TGACTGTGCTCCTGCTTCTCA √ cnp15 6 29951142 30006876 3 1.32 gain 2.55 0.045 CCCGAAGGCGATGTATTGAT AGTTGGGAGAGGGAGAAGAGAAA √ cnp16 6 31385149 31557248 3 0.76 loss 0.53 0.004 CGTTGTCTGTCCTGGAAGGAA CGGCCGCCCCATTAAA √ cnp17 6 79036117 79084209 3 1.32 gain 2.63 <.0001 CCTCAGTCTATCAGAGGTCCTTAACG AATCAATATGGGACAGGACAAGCT √ Locus0116 cnp18 7 3383544 3387478 3 1.38 gain 2.18 0.022 AAGGCATTGGTGGGACGAT CTGTGCAGGCCATACTGTCAGT cnp19 8 5588817 5591708 3 1.38 gain 3.1 0.0007 TTCCATAGCGAACGTGACACA GAAAATTGGTGCCGGTCATT cnp20 8 12285367 12446597 3 0.77 homozygous loss 0 <.0001 AGGCTTGCTCCCACTGACAAT CCTGTTCTCCATACAGTGCCATT √ Locus 0142 cnp21 8 39394152 39440685 3 1.31 gain 1.89 0.027 CTGGGTCCCTAGGACATTTGAC CTCCATAACAGAGAGCAGGTCTGA √ cnp22 10 6693757 6704160 3 1.35 gain 1.44 0.015 GGAGATAATGGATGAGCTTGTAGAGA TAGGCATGGGCACATTGACAT Locus1769 cnp23 10 46507480 47212082 3 0.80 loss 0.64 0.002 AGCGATTGGCCACACATTG CAACAGGGTCACCCCAGTTC √√ Locus0174 cnp24 11 18905796 18913266 3 1.40 gain 5.17 <.0001 CCCAATAACCCTCAGCCTGAA AGCCAGTGTTTGCAGCCAAT √√Locus0470 cnp25 11 49670299 49697457 3 1.29 gain 1.45 0.01 GCCTCTTCCTGACTGGCAGAT TATGTATGGGCTGCAAACAGGTT √ Locus0473 cnp26 11 55130549 55209410 2 0.71 homozygous loss 0 <.0001 GGAGGCCACATCTGCACTGT CTGGCCTGTCCAGCATCTCT √√Locus0186 cnp27 12 9532468 9599758 3 1.36 gain 3.54 <.0001 TGGGTCCTTCACCTACCATCAT GTCATTGTGATGGAGCAGCAAT √ cnp28 12 130781173 130786816 1 0.77 no change 0.94 NS AATTATCCACGTAACTGCCCAAA TGGGTGGTGACTTGAACCTACA √ cnp29 13 69634065 69670716 3 1.37 gain 1.94 0.011 CAGATGAGTAGGCAACGCAGTCT GGATCTAATTTATGTGTTTCCTTTTGTG cnp30 13 107099660 107126149 1 0.72 loss 0.64 0.013 CCTCACTCCCGCTCCACTATT GTGATGAGTGGGTCAAGGGTAAG cnp31 15 18758300 20329239 3 1.33 gain 1.55 0.001 GCTCCATAGGTGCACAATCACA TACCTATAAAATTCTGTATGCAACATTGATAT √√ √Locus0233 cnp32 15 20422689 20545323 1 1.12 no change 0.96 NS GTTTGCCATGTTGTCATTTTGG CGGAGTCAACCTGGGTGAGT Locus0233 cnp33 15 82744317 82889733 1 0.78 loss 0.88 0.001 AGGGTGTGACCTTTTCACTGTTC CTGCTGGCTGTGTTCTCTATGG √√Locus 0498 cnp34 16 83213092 83228651 3 0.75 loss 0.52 0.003 GAGCAAACGCGGCTAGTTCTA CTCCTCCTGAGCATCTTCCCTAA √ Locus0519 cnp35 17 9183884 9207567 3 1.34 gain 1.47 0.009 CAGGGATCATTGATTTTACATGTGA CCTGGGTCGGGAGAGAAGA √ Locus0521 cnp36 17 31471515 31494924 3 1.34 gain 2.92 <.0001 GGCGTCGGGCAATACAGA GCATTGGCACATGTCAGAGTCT √√ cnp37 18 62059541 62062341 1 0.73 loss 0 <.0001 GCTGTAGCCAGAGCAGCTGACT TGCCTAGGTGTTTCTGGCCTAA cnp38 19 59422014 59435029 3 0.76 loss 0.01 <.0001 CACGTGGTGATAGTGG TTATGGA TTGCCCAGGAACATGGTTTC √√Locus0540 cnp39 19 59906607 59991881 2 1.30 no change 0.91 NS CCTCCACGGGCAGGTTT CTGAGGTGTCCCCTGATTGC √ Locus0621 cnp40 19 63590775 63610149 2 1.26 gain 1.59 0.0103 rs4584938 (MassSpec validation only) cnp41 20 14710971 14856035 3 0.76 loss 0.53 0.001 TCCTTGGGATTTGGTTGTCAA CTTAATGCGGTCGCTGTGAA √√Locus0542 cnp42 21 22577771 22586139 3 0.74 loss 0.24 <.0001 ACACTGTGCTTTATGCATCCTTTTA ACATTAGCAGCTATCATTCGTCAAA cnp43 21 22596775 22624888 1 0.90 loss 0.89 0.0008 CCATTTTTTCCTCTCAAGCAGAA CAGTCACTTGAAATGAGTTCAGAAGTC *MassSpec validation involves gains only **DGV = Database of Genomic Variants (http://projects.tcag.ca/variation/)

Quantitative validation of 500K EA CNVs for NA15510 vs HapMap: SYBR real-time PCR # times called in 3 Call by Test sample Reference Also called in Region Chr Start End reps 500K EA qPCR result Fold change t-test Forward primer Reverse primer ID sample ID pair-wise? HM_CNP1 1 16609393 16708996 1 gain gain 1.23 0.0090 GGGTGGTTATTTTGGTGAATTTTTTA ATCATGAAGCAAACAAACAAAACCAAAC NA15510 NA12005 no 1.51 0.0026 NA15510 NA12144 no 1.94 0.0002 NA15510 NA18966 no HM_CNP2 1 158326814 158416227 3 gain gain 0.96 NS TGAAAAGAATGCAGCTCAAGTGA CACAGCCTTCCGCAAAGG NA15510 NA10851 no 2.85 0.0001 NA15510 NA18564 no 2.01 0.001 NA15510 NA18858 no 1.84 0.0036 NA15510 NA19101 no HM_CNP3 1 239405036 239477544 1 loss loss 0.67 0.0001 GTAGCTTGGGAAACGTATTTTAGGA TTACTGCGGTTCTCTGCATTTCT NA15510 NA10851 no 0.77 0.0005 NA15510 NA19103 no 0.7 0.0011 NA15510 NA19138 no 0.73 0.0019 NA15510 NA19171 no 0.7 0.0001 NA15510 NA19207 no HM_CNP4 3 19487176 20587963 3 gain gain 1.32 0.03 TGTGTGTGAAAACTCCCCTTGA TGGCTGGAAGTTGAGCAGACT NA15510 NA10851 same as cnp8 HM_CNP5 3 20700747 20738781 1 gain not validated 0.86 0.03 CTGTGCGGCAGGGTAGAAAG TCTCAATCTCCCTGCTGGAAA NA15510 NA10851 no 0.86 0.02 NA15510 NA18942 no 0.81 0.0029 NA15510 NA07022 no 0.91 NS NA15510 NA07056 no 0.79 0.01 NA15510 NA10838 no HM_CNP6 6 214735 312109 2 gain gain 1.31 0.025 GGGCACAGTGAAAGGTGGAA TGACTGTGCTCCTGCTTCTCA NA15510 NA10851 same as cnp14 HM_CNP7 6 31385149 31557248 3 loss loss 0.53 0.004 CGTTGTCTGTCCTGGAAGGAA CGGCCGCCCCATTAAA NA15510 NA10851 same as cnp16 HM_CNP8 8 12285367 12446597 3 loss homozygous loss 0 <.0001 AGGCTTGCTCCCACTGACAAT CCTGTTCTCCATACAGTGCCATT NA15510 NA10851 same as cnp20 HM_CNP9 11 5743360 5765806 3 loss omozygous delet 3.72 NS TTCTGTCTTTTGGATAATGGTGTCA TGGAGAAATACCAGGGAAGATCA NA15510 NA10851 no 0 0.0002 NA15510 NA12005 no 0 0.0002 NA15510 NA12815 no HM_CNP10 11 55130549 55209410 2 loss homozygous loss 0 <.0001 GGAGGCCACATCTGCACTGT CTGGCCTGTCCAGCATCTCT NA15510 NA10851 same as cnp26 HM_CNP11 14 19424016 19488329 1 gain gain 0.97 NS GACGTCCAGAGATGCCTTACAGA GTAGCAAGAACAACTTCCCTGACA NA15510 NA10851 no 1.31 <0.0001 NA15510 NA12005 no 1.4 <0.0001 NA15510 NA18502 no 1.36 <0.0001 NA15510 NA18858 no 1.28 <0.0001 NA15510 NA18859 no HM_CNP12 15 18758300 20329239 3 gain gain 1.55 0.001 GCTCCATAGGTGCACAATCACA TACCTATAAAATTCTGTATGCAACATTGATAT NA15510 NA10851 same as cnp33 HM_CNP13 15 32498326 32680396 3 loss loss 0.79 0.0012 CATTCTAACCTGGAGCTGCACAT AAGCATTAGACGAAACCAGTGAGA NA15510 NA10851 no 0.41 <0.0001 NA15510 NA12005 no 0.43 <0.0001 NA15510 NA12144 no 0.46 <0.0001 NA15510 NA19101 no 0.41 <0.0001 NA15510 NA19139 no HM_CNP14 16 34307201 34647872 3 gain gain 0.88 0.0032 AGCCTGTGACCCCCTGAGA CTCCCTTGCTGGCCAAAGT NA15510 NA10851 no 1.4 <0.0001 NA15510 NA12005 no 1.31 <0.0001 NA15510 NA12144 no 1.29 <0.0001 NA15510 NA18500 no 1.38 <0.0001 NA15510 NA19101 no HM_CNP15 16 83213092 83228651 3 loss loss 0.52 0.003 GAGCAAACGCGGCTAGTTCTA CTCCTCCTGAGCATCTTCCCTAA NA15510 NA10851 same as cnp34 HM_CNP16 17 9183884 9207567 3 gain gain 1.47 0.009 CAGGGATCATTGATTTTACATGTGA CCTGGGTCGGGAGAGAAGA NA15510 NA10851 same as cnp35 HM_CNP17 19 59422014 59435029 3 loss loss 0.01 <.0001 CACGTGGTGATAGTGG TTATGGA TTGCCCAGGAACATGGTTTC NA15510 NA10851 same as cnp38 HM_CNP18 20 14710971 14856035 3 loss loss 0.53 0.001 TCCTTGGGATTTGGTTGTCAA CTTAATGCGGTCGCTGTGAA NA15510 NA10851 same as cnp41 HM_CNP19 21 22577771 22586139 3 loss loss 0.24 <.0001 ACACTGTGCTTTATGCATCCTTTTA ACATTAGCAGCTATCATTCGTCAAA NA15510 NA10851 same as cnp42

Quantitative PCR validation using SYBR or MassSpec of singletons called by the 500K EA array

500K EA event Call by Call by validation Test sample Reference CNPID Chr Start End 500K EA WGTP result Fold change t-test Forward primer (or rsID for MassSpec) Reverse primer ID sampleID 93 2 1410597 1484084 gain no confirmed 1.97 0.0072 rs2070882 NA18856 NA18913, NA19154, NA18517 100 2 14296389 14319566 gain no confirmed 1.52 0.0002 GCAGCAGCAATGGCAGAGA GTCAATGCTCTGTGGCTGTAGCT NA12144 NA10851 188 3 42335110 42343886 loss no confirmed 0.52 <0.0001 TGACGCCCTTTGCTCTGAA GCGAGAGGAGACATGACGTTT NA19171 NA10851 229 3 164344341 164432687 loss no confirmed 0.66 0.04 CTCCATAATTCAGACCACAGTGAAA TAGATGCCCAGGAAGAGTCAGAA NA18968 NA10851 0.4 <0.0001 TGTTCACAGTCTCACACAGAATTATTACTT CTAGGAAATGTGACCACAAACACTTT NA18526 NA10851, NA18997 286 4 87774470 88046712 Loss no confirmed 0.52 <0.0001 GCCAGACACCCTAATAGAACGTATAAA TGATCTGAAAAATCCCTTTGCA NA18526 NA10851, NA18997 1.09 NS CGTCCTAGCTGTCAATGGAGTTAG TCAGTGTTTCCACAGCTTGCTT NA18526 NA10851, NA18997 291 4 114711846 114719490 loss no confirmed 0.5 0.0001 GGGCGGATCGTCTTGATTAA GACTCATCCGCGTCTGGAA NA12005 NA10851 337 5 40909835 41045039 Loss no confirmed 0.44 <0.0001 CCCCTTTCCCAGTACCTTATCC TTCCAAGAGCTCATTAGAGAAAGTGA NA18566 NA10851 1.54 <0.0001 GGAAAGCTGGGTGGAGTTACAG CCAGTGGTTCTCTTTCTTTCTTCAA NA18592 NA10851, NA18997 473 7 39833420 40042823 Gain no confirmed 1.46 0.0001 CAGGGTGTGCTGCCATCTT ACTGACCAGGTGCCACATTTG NA18592 NA10851, NA18997 1.35 0.0003 GCTTAGAAAACCAAAAGGGCATT ACATGATCCAAACATGGGAAGTT NA18592 NA10851, NA18997 474 7 40157270 40270518 Gain no confirmed 1.39 <0.0001 CAAATGTCTGTCTCTCTCTCAGCTTT CTACCCGATCAGGATGAAGCA NA12872 NA10851 497 7 122392587 122483286 gain no confirmed 1.75 0.0002 rs1343904 NA19238 NA18862, NA19120, NA18501 569 8 90162190 90164239 loss no confirmed 0.61 0.0004 TGCAGAGAAATTGGCATGCT GCGTATACAACATTGGTAGGTCTCA NA18971 NA10851 584 8 139050457 139114328 gain no confirmed 1.45 0.0003 GCTACACCTGGAAGGCTTTCAC GCTGCTAGGCCTTCTTCACTTG NA18967 NA10851 615 9 19116476 19151145 gain no confirmed 1.87 0.0001 rs4977499 NA19208 NA19094,NA19129,NA19222 0.57 <0.0001 GCTCACGTTGTTGCATGCA TTTGAGGAGAGCAACATTTTATTGTT NA7000 NA10851, NA18997 622 9 25211244 25374959 Loss no confirmed 0.5 <0.0001 CATGTTTCCTCAGGGCCTGTA GGAGTCATGTTGGCTGCTCAA NA7000 NA10851, NA18997 0.51 <0.0001 GCTTGCAGGCTTGCTTTCTTA AGCATCTCCATATCTCCCACAAA NA7000 NA10851, NA18997 726 11 5373198 5448609 loss no no change 1.04 NS GGGATCTGCAGTTGTCTATAACCATAC GGCATTGTCCTCTATGGAGTTGT NA18966 NA10851 746 11 37079701 37100001 loss no confirmed 0.54 <0.0001 AATACATCCACGAGGAAGATAGGAGTT ATCAGGTAGCCTACACTGTCAGGAA NA18564 NA10851 760 11 61505378 61650609 Gain no confirmed 1.43 <0.0001 ACTGCTTGGCAGCCACACT GAGGCAATGGCAGGTGAAA NA18940 NA10851 766 11 80076875 80080035 loss no no change 0.99 NS ACCACCCCTCTCTACGTTCCAT CATGCAGTGGGTTCAGAGAAATC NA18860 NA10851 782 11 97120050 97249540 Loss no confirmed 0.47 <0.0001 CAGTATGCAGGCTCCTCATTCTC TTCCTCCTCTACTACATGAACATTCCT NA18964 NA10851 0.76 <0.0001 TTAGCAGGACGCAGTGGTGTA TCCATGCATGTGACTGACTAAAGA NA18540 NA10851, NA18997 787 11 102541001 102720677 Loss no confirmed 0.81 0.0055 GGTTTTTAGCAGTCAGCGTAACATT ACACAAGAGCAAATTCAGCATGA NA18540 NA10851, NA18997 1.05 NS TCCTGAGGCAAACACAATAATCTATT TCTTTACCAGTAGAATCCTCAATGTTTT NA18540 NA10851, NA18997 839 12 73396068 73500176 Gain no no change 1.07 NS TGAACATATGGAGTAAAAACATAAGCAGATGGGTACTATCGAAAAGAAATCATTGAA NA19094 NA10851 908 14 52872802 52890807 loss no confirmed 0.51 0.0002 ACCAGTGTCTGCTGATACCGAAT ACCCTGTCGCCAACTGGTT NA18997 NA10851 1022 16 53310669 53336408 loss no confirmed 0.51 0.0001 GGGAAGGCCAGACTCCTTAACTA GACCGGAAAGATGAGTTGGTTT NA18942 NA10851 1124 19 60229274 60342499 Gain no no change 0.95 NS CCCTCCTTGTGCCTCAGTCTA TGACTCCATGCAAAACTCTTGTTC NA18620 NA10851 1158 21 39779393 39888026 Gain no confirmed 1.44 <0.0001 CTCAGCACCACCTGCCATAA CGCTTGGTGGGTATTGCTAGA NA12156 NA10851

Quantitative validation using SYBR or MassSpec on CNVs called by 500K EA array in more than one individual or by both platforms 500K EA event Call by validation Test sample Reference CNPID chr start end gain/loss WGTP result Fold change t-test p-value Forward primer (or rsID for MassSpec) Reverse primer ID sample IDs 2 1 1548033 1725888 Loss (2) Loss confirmed 0 (no product) <0.0001 AAAAACAAGAACATCTCCCACACA TTTCACCCAACAAATGATCTTAAGG NA12248 NA10851 51 1 149495781 149552299 Gain (1) Gain confirmed 2.50 0.0002 rs6687202 NA19193 NA19221,NA18507,NA19144 89 1 244079375 244648357 Gain (1) Gain confirmed 1.82 0.0005 rs7525488 NA19127 NA18500,NA19204,NA19210 156 2 183354176 183590436 Gain (1) Gain confirmed 1.57 0.0002 rs11892516 NA19139 NA19171,NA19128,NA19203 189 3 45991468 46095404 Loss (2) no no change 0.98 NS CACGTGAGTTCGGAATAATCACA CCTCGACACCATCTTCCACAA NA18508 NA10851 NA18994 Gain (1) 1.68 <0.0001 CAAGTCCCCAAGGTCTGTCTCT GGCTACGCCTCTGCTAAGGA NA18532 NA18994 269 4 42950671 43051416 no confirmed Loss (9) 0.98 NS CAAGTCCCCAAGGTCTGTCTCT GGCTACGCCTCTGCTAAGGA NA18532 NA10851 CNV does not confirm using 108 275 4 68619630 68857679 Gain (1) Gain confirmed 1.52 0.0013 rs10866201 NA18517 NA19131,NA18515,NA19132 376 6 162334 356954 Gain (120) Gain confirmed 1.16 0.0329 TTGGCACCAGCGACAGTAGAT GCGTTCCCACTTTTCTAGAATTCT NA15510 NA10851 428 6 114671437 115749378 Gain (1) Gain confirmed 1.67 0.0001 rs1337335 NA19092 NA18863,NA18862,NA19171 548 8 16303512 16949896 Gain (2) Gain confirmed 2.25 <0.0001 TGCTCCTGATACATGAAACGTTAAG AGCCATGATGTAATGTTGAAATGTG NA12802 NA10851 567 8 63318677 63422736 Loss (2) no confirmed 0.56 <0.0001 CTAGGGCTTAGAGATGCTGTTTCC TGCTATGTTCTCCTGACCCATTT NA19132 NA10851 NA18994 640 9 78658863 78703638 Loss (3) no confirmed 0.49 <0.0001 CATTCTCAAGGCAGATAGACCTTTTC TCTCTCCACTGTGCAAAATCTACCT NA18503 NA10851, NA06994 658 10 2682793 3124681 Gain (1) Gain confirmed 1.63 0.0001 rs1556637 NA19201 NA18505,NA19144,NA18912 702 10 77206052 77406628 Gain (1) Gain confirmed 1.86 0.0006 TCAAATTTCTAGGCCACTCATCATAA TCACTCACCTACCACAAGGAGGTA NA12872 NA10851, NA06994 711 10 102193061 102265632 Gain (2) Gain confirmed 1.66 0.0002 GAGGAGAAGATCCCAGACATTCA GGCTGGAACCACGGTGTTA NA06994 NA10851, NA12005 723 11 4119053 4282368 Gain (1) Gain confirmed 1.76 0.0041 rs11824618 NA19144 NA19193,NA19201,NA19130 Gain (2) 832 12 59797263 59888595 no confirmed 0.47 <0.0001 TCAGCTGAGAGGTCTCTGAGGAA GGGATTAGCTTTTCACTCTGACAAA NA19137 NA10851 NA18994 Loss (1) 870 13 65903813 66017201 Loss (3) no confirmed 0.89 0.0076 GCTTGTGCACCTCAAATTTATACATATT ACAGCTTTGTTCAACTCATTACCAA NA18999 NA10851 NA18994 914 14 77174650 77282215 Gain (1) Gain confirmed 2.19 0.0004 rs12050437 NA19203 NA19152,NA19142,NA18960 995 15 98175492 98422157 Gain (1) Gain confirmed 2.00 0.0003 rs1347477 NA19141 NA18504,NA19131,NA19138 998 16 4995942 5310411 Gain (1) Gain confirmed 1.60 0.0004 rs3760030 NA18855 NA18504,NA19202,NA18870 1046 17 31429427 32016863 Gain (112) Gain confirmed 1.73 0.0001 CCCATCTTCTCAGGGAGTGACT TCGGGCTGCCGCTTAAC NA18515 NA10851 1047 17 32018706 32104672 Gain (3) no no change 0.98 NS TGGGCATACATCACCCACAT AGTCCTATCAAGACACAGTGAAATGG NA19100 NA10851, NA12005, NA18861 1.46 0.0013 CCCACCCCCGACCACTA GGTGCAGGCCTGGTGACTT NA10838 NA10851 1055 17 44093882 44118402 Gain (1) Gain confirmed 1.37 <0.0001 CCCACCCCCGACCACTA GGTGCAGGCCTGGTGACTT NA12004 NA10851 1072 18 32364761 32735865 Gain (1) Gain confirmed 1.41 0.0013 TTGCTGTAAGCATTAGCCATGATAA CCAATGCCACACAGATCAGAA NA18971 NA10851, NA12004 1140 20 36367793 36539571 Gain (1) Gain confirmed 1.57 0.0005 rs6014705 NA18852 NA19138,NA19171,NA19201 Supplementary Table 4C: UCE regions validation data Validation of UCE elements overlapping with HapMap CNVs Merged CNVID_uce platform original call qPCR results fold change t-test Test samples Reference forward primer reverse primer CNV11_uc3 chr1 10676768 10989413 WGTP loss loss confirmed in uce 0.56 0.0466 NA10846 NA10851 AAGTTCAAAGAAGAGACTGAGATGGTATC TGGCAGAGTTCTGACTGTTTCC loss confirmed in uce 0.59 0.0025 NA18970 NA10851

CNV11_uc9 WGTP loss no change in uce 1.07 NS NA18504 NA10851 GGGAGAAATGCGAAATTATATATGG ATGGGTGAGGAGAGAGTTTTGG no change in uce 1.13 NS NA18558 NA10851

CNV170_uc67 chr2 104052123 104218620 WGTP gain gain relative to 10851 1.22 0.0014 NA18959 NA10851 TCATATTCAGCGGTTTTGATCAA TGCCAGCGGTGCTAAATTTA no change in uce relative to 185 0.98 NS NA18959 NA18504 no change in uce relative to 120 0.99 NS NA18959 NA12005 no change in uce relative to 19 1.08 NS NA18959 NA19100

CNV170 chr2 104052123 104218620 WGTP gain gain/ trend confirmed in CNV 1.06 0.0400 NA18959 NA10851 TGCCAGAGCGCTGACTGA TTGTGCCGGACAATGTTGTAC gain/ trend confirmed in CNV 1.13 0.0430 NA18959 NA6994

CNV429_uc151 chr5 32281118 32774401 WGTP loss no change in uce 1.06 NS NA19130 NA10851 CGTCCGGTGGGTCTTTCA CATTTTGCCAATTCAATCCATTT no change in uce 0.89 NS NA19130 NA18504

CNV429 chr5 32281118 32774401 WGTP loss loss confirmed in CNV 0.84 0.0016 NA19130 NA10851 GATTTCTTTACCTTGCTACTTTCTTCTGT TCCGGGACATAGCATCCAA loss confirmed in CNV 0.83 0.0003 NA19130 NA6994

CNV590_uc204 chr7 972336 1463188 WGTP loss no loss in uce (opposite result) 1.12 0.0235 NA18861 NA10851 GGCGGCTTGTAAATTAGAGCTAAG CCACATCGTAAACGAGAAAAGATG no loss in uce (opposite result) 1.14 0.0235 NA18861 NA19100

CNV590 chr7 972336 1463188 WGTP loss loss confirmed in CNV* 0.28 0.0079 NA18861 NA10851 GGGTGACTGGAACGTGAGAC CAAGGTTTAGCCCAGGAAGG using QMPSF

CNV764_uc252 chr9 16631966 16799203 WGTP loss no change in uce 0.99 NS NA12006 NA10851 CTGTTCGCGTGTCATGTGTAGA GAGCGAGGGACAGCAGTGA no change in uce 0.90 NS NA12006 NA18504

CNV764 chr9 16631966 16799203 WGTP loss opposite to expected 1.29 0.0068 NA12006 NA10851 GGAGTACTGGATGAGTAAATGTAAACTAAGGCATTTGTGTGCTGAATGGATCA no change in CNV 1.01 NS NA12006 NA6994

CNV790_uc260 chr9 78664404 78703638 500K EA loss no change in uce 0.98 0.3433 NA18503 NA10851 TAGGTAGAAATCACAGGCTCAATGA TCAGCGGCTGCCAATCA no change in uce 0.95 0.1753 NA18503 NA6994

CNV790 chr9 78664404 78703638 500K EA loss loss confirmed in CNV 0.49 <0.0001 NA18503 NA10851 CATTCTCAAGGCAGATAGACCTTTTC TCTCTCCACTGTGCAAAATCTACCT loss confirmed in CNV 0.45 <0.0001 NA18503 NA6994

CNV859_uc287 chr10 77090565 77440455 both gain no change in uce 0.99 NS NA12872 NA10851 CTCCCCCTTCAATATCAGATGAA CATGGCAACAAAGGTGCATT no change in uce 0.95 NS NA12872 NA6994

CNV859 chr10 77090565 77440455 both gain gain confirmed in CNV 1.86 0.0006 NA12872 NA10851 TCAAATTTCTAGGCCACTCATCATAA TCACTCACCTACCACAAGGAGGTA gain confirmed in CNV 1.56 0.0027 NA12872 NA6994

CNV870_uc293 chr10 102141840 102370625 both gain gain confirmed in uce 1.40 0.0009 NA06994 NA10851 ACCTCTCTCCGCGGCAGTAT GCCCAAGCAGTGGCTGAA gain confirmed in uce 1.16 0.0132 NA06994 NA12005

CNV870 gain confirmed in CNV 1.66 0.0002 NA06994 NA10851 GAGGAGAAGATCCCAGACATTCA GGCTGGAACCACGGTGTTA gain confirmed in CNV 1.68 0.0019 NA06994 NA12005

CNV1224_uc410 chr17 32049873 32104672 both loss for WGTP no change in uce 1.03 NS NA12005_loss NA10851 TCAACCTCAGGCCCCAATC CAAGTGCATCTTATTAGGCGACAA gain for 500K EA no change in uce 0.99 NS NA12005_loss NA18959 no change in uce 1.07 NS NA19100_gain NA10851 no change in uce 0.92 0.0206 NA19100_gain NA18959

CNV1224_500K_region chr17 32049873 32104672 500K EA gain no change in CNV 1.06 0.0500 NA19100_gain NA10851 TGGGCATACATCACCCACAT AGTCCTATCAAGACACAGTGAAATGG no change0.98 NS NA19100_gain NA12005 no change 1.00 NS NA19100_gain NA15510 no change 1.01 NS NA19100_gain NA18861

CNV1224_WGTP_region chr17 32049873 32104672 WGTP loss no change in CNV 1.37 NS NA12005_loss NA10851 no change in CNV 1.04 NS NA12005_loss NA19100 no change in CNV 1.01 NS NA12005_loss NA15510 no change in CNV 1.01 NS NA12005_loss NA18861

CNV1232_uc415 chr17 43957672 44191836 both gain no change in uce 0.91 NS NA10838 NA10851 AACGGGACGCTAAAGCAAAA CAAAGGTAGAGGCTTATGACGGTTT no change in uce 0.94 NS NA12004 NA10851 CNV1232_common gain confirmed in CNV 1.46 0.0013 NA10838 NA10851 CCCACCCCCGACCACTA GGTGCAGGCCTGGTGACTT gain confirmed in CNV 1.37 <0.0001 NA12004 NA10851

CNV1260_uc429 chr18 32304033 32735865 both gain no change in uce 1.06 NS NA18971 NA10851 GATGTTTCTGTCAGCCTTGGAAA ACGATGTCAAATAAGTGGATGTGAA no change in uce 1.14 NS NA18971 NA12004 CNV1260_common gain confirmed in CNV 1.41 0.0013 NA18971 NA10851 TTGCTGTAAGCATTAGCCATGATAA CCAATGCCACACAGATCAGAA gain confirmed in CNV 1.64 0.0006 NA18971 NA12004 PCR validation of homozygous deletions called by the 500K EA array

500K EA # samples with Test Sample Reference event homozygous sample2 sample3 Ref2 Ref3 IDs sample IDs CNPID Chr Start End Call by 500K EA Validation results deletion Forward primer Reverse primer 30 1 94846203 94863834homozygous loss confirmed 1 TGCGTTTCTCTCAGGACCTT CGCTGAGTGAAAGAATGCTG 19141 19238 19239 19240 72 1 193555270 193618427homozygous loss confirmed 1 AGGCTCACTTCCTGCAAATC CCCGACCACTGTTTGGATA 18870 19238 19239 19240 IgL-K 2 88991630 89125346homozygous loss confirmed 0 GGAAACACAGGGAGGATCAG GCAGGGAATAATTTGCAGGA 12248 19238 19239 19240 133 2 89740700 89951815homozygous loss confirmed 3 GGAGCAATGGAGCCACTTAG TGGATTGAAGAACACACACCA 18505 19137 18500 19238 19239 19240 252 4 11342661 11348511homozygous loss not confirmed 0 AAAATCTGCCCCATTTTGGT TCCCTGCAGGAAGTAGCAGT 19172 19128 19238 19239 19240 268 4 34604640 34638958homozygous loss confirmed 10 TCATGCTTTCTTGCTTTGGAT TTTAAGGAGATGCATGTTTCCA 18529 19098 19200 19238 19239 19240 329 5 17649730 17675214homozygous loss confirmed 1 CGGCTTCAGTGTGAAACCAT GATCGTTGAAGCAGCCTTTT 18515 19238 19239 19240 390 6 29967224 30014028homozygous loss confirmed 13 AACTCTGAAGGCAGGTGTCC GCTTTGACACAGCACCAAGA 18960 18972 19000 19238 19239 19240 398 6 31377008 31385472homozygous loss not confirmed 0 GGCTTGGCAAGAGGATCTTA ATGCAGAATCCCACGAACTT 18976 19238 19239 19240 418 6 77496587 77509523homozygous loss confirmed 9 TTGTCCCTGCTTTCAGTGTG GGGCACCTGAAGCCTTTTA 12802 12815 18852 19238 19239 19240 419 6 79036117 79084209homozygous loss confirmed 5 TGCTTGAGGGATGGTTTCTC GAGCCATGGGAGATCTGAAT 7019 7056 18998 19238 19239 19240 542 8 13659506 13696428homozygous loss confirmed 1 GAAGCAGAAATCCCATAAGCA TCCAAAGGCTTTCTGAATGG 19205 19238 19239 19240 557 8 39326152 39440685homozygous loss confirmed 21 CCCATGTAGTCCCTTTGGAG AGCAGAATGGGGATGATGAA 18526 18942 18967 19238 19239 19240 590 9 582757 597816homozygous loss confirmed 1 AAACACCTGAAGCCTTTGTTTT CAAGCCCTGGTCCTCTGTAA 18862 19238 19239 19240 641 9 101796515 101801974homozygous loss confirmed 3 CCCGTAACATGTCTTCCTTTG TTTCCAAGAATGAACCAACAG 7056 18956 18961 19238 19239 19240 694 10 58575853 58606498homozygous loss confirmed 1 TGGGCATATTGAAAGATGGA GGCCATTTCCTTGACTGTGT 18972 19238 19239 19240 696 10 59242689 59439185homozygous loss confirmed 1 TCTAAATTTAATTGTCAAGGCTGAGA AGCTACTTTTGTCAGTGCCTTT 18572 19238 19239 19240 727 11 5743360 5765806homozygous loss confirmed 11 TCAGCACTTGTGCAAACTCTC CGGAAAGCAGGGTGATAGAG 18872 19101 19159 19238 19239 19240 732 11 18905796 18915387homozygous loss confirmed 1 AATGCTTTCCATGGGTGAAA GGACTTTGAGAGCAACACTGC 12057 19238 19239 19240 755 11 55130549 55176235homozygous loss confirmed 16 GATGGCCTATGACCGCTATG ATTTGGGCCACAAAATGGTA 18992 18997 18998 19238 19239 19240 765 11 79650581 79660804homozygous loss confirmed 1 TCAAGATGGGGTTTTCTTGG GGATCAAATGGAGAGCAAGC 18500 19238 19239 19240 780 11 93321085 93327323homozygous loss not confirmed 0 TTCTGAACCATGGGAAACTG CTCTGCTGCCCTAACTCCAC 19119 19238 19239 19240 789 11 104428916 104436371homozygous loss confirmed 1 CACACCACTTCAACCCTCCT CTGGACCCACATATGCACAG 19130 19238 19239 19240 813 12 27539678 27542418homozygous loss confirmed 1 AGAGCATGTGCTGCCTCTTT AAAAGGCCTGAAGATTTCCAA 19160 19238 19239 19240 901 14 40684540 40706033homozygous loss confirmed 7 CCAATATGGGATGTGGGATG CAAAGCAATCTGACCAGCAG 12760 12761 18965 19238 19239 19240 904 14 43576461 43600178homozygous loss confirmed 1 AGCAACAGGCTGAGAACGAT GGTTTGTTGGCATTTTCCAC 18622 19238 19239 19240 IgH 14 105786534 106061045homozygous loss not confirmed 0 GCAAAGCAGTGGAGAGGAGA ATCACACCCCTGATGCTTTC 7029 12865 19000 19238 19239 19240 968 15 22622873 22629835homozygous loss not confirmed 0 CACACGTAACCATGCCTTGTA TCAGGCGACACAAATCTTCA 19172 19238 19239 19240 972 15 32537861 32602617homozygous loss confirmed 3 TCTGCATTTGTGACCCCTTT CTGAATTCTGCCCATTTAAGG 18582 18500 18521 19238 19239 19240 1034 16 79536934 79539177homozygous loss confirmed 1 CGCTCATCTGCTCTCTGCTA TGTTGGACAACATGTTCTTGG 12248 19238 19239 19240 1084 18 64897804 64903434homozygous loss confirmed 2 CCACATTCTCTGCACTTTGAA GCATTTTCTCCTAAGCAAGTCAA 18964 18976 19238 19239 19240 1091 19 20424240 20490118homozygous loss confirmed 1 TGATGTGGATCTTATGCTGTTCTT GCCATGGGCAGAGTTTTTAT 19171 19238 19239 19240 1120 19 59422014 59435029homozygous loss confirmed 2 GACGTGCTTATCTGCCCAGT gGGCTCTGCAAATGAAAATG 18858 18872 19238 19239 19240 1122 19 59991881 60007809homozygous loss confirmed 1 GCCTCAAGCCAGACATCTTC GAGAGCAGACAAGCCACACA 19137 19238 19239 19240 1134 20 15259431 15265978homozygous loss confirmed 1 AGACAATCAAGTGGGGGAAA CCCAGCTCTTCATCCACACT 18507 19238 19239 19240 1153 21 22577771 22586139homozygous loss confirmed 22 acaTGGGGTTAGGAGAGGAT TGCCTACAGCTACAGAAGTAAAACA 18972 18973 19000 19238 19239 19240 IgL-L 22 21025208 21078408homozygous loss confirmed 0 GCTCCAGTCTGAGGATGAGG GTTTGTCCCTTGGCTGGTTA 10846 19238 19239 19240 IgL-L 22 21082323 21569023homozygous loss confirmed 0 TTGCAATCCATCTTGCATTC CCACAAGTGACAGGGACTGA 19154 6994 10846 19238 19239 19240 X2-4 23 7211131 7355904homozygous loss confirmed 1 CCTTGGTTGATAGCTACAAATTACA GAATGGAGAGATGGCCAAAA 12248 19238 19239 19240 X2-6 23 47627524 47700051homozygous loss confirmed 1 TGCTGTGCCCTTTTCTTACC CCTCAGGGTTGATGTCTGGT 18856 19238 19239 19240 X2-8 23 75918345 75923773homozygous loss confirmed 1 TGGCCAGTTAGCATCTTGAA AGGCAGAATGTTAAATCAGGAA 12864 19238 19239 19240 Supplementary Table 5

Chromosomal Sample WGTP 500KEA Karyotype LTA Imbalance NA07019 partial dup(5q), partial del (7q) √ √ 46,XX NA07034 del(7)(p14.1p14.1) √ √ 46,XY √ NA07055 del(2)(q23.1q24.3) √ √ 46,XX,t(4;6)(q21;q2?6)[2]/46,XX[4] NA07345 del(4)(q32.1q32.1) √ 46,XX √ del(9)(p24.1p24.1) √ √ √ NA07348 del(4)(q35.2q35.2) √ √ 45,X,-X[4]/46,XX[2] √ del(X) √ NA10831 del(7)(q21.11q21.11) √ √ 46,XX,add(21)(q22)[4]/46,XX[10] √ del(21) √ NA10854 del(X) √ 46,X,-X,+9[3]/45,X,-X[3] NA10856 partial dup(13q) √ √ 46,XY NA10859 del(8)(p23.2) √ 46,XX √ del(X) √ NA11839 del(10)(p15.3q21.1) √ √ 47,XY,+12[7]/46,XY[3] del(14)(q11.2q11.2) √ √ √ NA11882 dup(19)(q13.41q13.43) √ √ 46,XX NA12056 dup(16)(q23.2q24.3), √ √ 46,XY NA12057 del(1)(q44) √ 47,XX,+12[10]/46,XX[1] √ NA12145 del(X) √ 46,XX NA12248 dup(9),dup(12),dup(14),dup(22) √ √ 50,XY,+9,+12,+14,+22[1]/50,sl,add(8)(q24)[3]/ NA12707 del(16)(q11.2q24.3) √ √ 46,XY NA12875 dup(2) √ √ 47,XX,+2[6]/46,XX[1] NA12891 del(15)(q25.2q25.2) √ √ 46,XY √ del(19)(q13.12q13.12) √ √ √ NA18507 del(7)(p11.1p11.1) √ 46,XY √ dup(X) √ NA18516 del(X) √ 46,XY NA18522 dup(12) √ 46,XY NA18524 dup(X) √ 46,XY NA18529 del(16)(q11.2q24.3 ) √ √ 46,XX,inv(6)(p11q27)[7]/46,sl,-16,+mar[3] NA18540 dup(4),dup(7),dup(9),dup(14), √ √ 50,X,-X,+4,+7,+9,+14,+21[5]/46,XX[1] NA18562 dup(X) √ 46,XY NA18635 dup(X) √ 46,XY NA18852 del(3)(q24q24) √ 46,XX √ del(13)(q32.2q32.2) √ √ √ NA18855 del(18)(q22.1q22.1) √ 47~51,XX,+X[2],+5[4],+9[1],+11[9],+12[5],+17[3][cp9] √ NA18859 del(4)(p16.3p16.3) √ 46,XY √ NA18862 dup(12) √ √ 46,XY,add(3)(q29)[6]/46,XY[16] NA18956 dup(4)(q31.3q35.2) √ √ 46,XX NA18966 dup(Y) √ 46,XY NA18978 del(X) √ 45,X,-X[5]/46,XX[2] NA18987 del(12) √ 46,XX NA19101 del(1)(q44q44) √ 46,XY √ NA19140 dup(9) √ 46,XX NA19193 dup(12) √ √ 47,XX,+12 NA19203 del(2)(q23.3q23.3) √ √ 46,XY √ NA19208 dup(9) √ √ 47,XY,+9[5]/46,XY[1]

Supplementary Table 5A. Summary of chromosomal abnormalities found in the 270 HapMap samples most likely to be cell line artefacts. WGTP, 500K EA, and karyotyping analyses detect chromosomal imbalances at different levels of resolution. A possible artefact was called by WGTP for chromosomes showing a deviation of normalised log2 signal ratios >0.05, and for 500K EA data, a deviation of normalised intensity ratios >0.025 (or >0.05 for the X chromosome). In both cases, whole chromosomes involved (summarized in the column named 'Chromosomal Imbalance') were removed from CNV analysis for both platforms, except in three cases where one whole chromosome anomaly was detected only by WGTP with a deviation of normalised log2 signal ratios <0.1 (in italics). For LTA analysis, tracts of Mendelian inconsistent SNP genotypes were identified as possible deletion artefacts and any associated CNVs were removed from both platforms. FISH analysis confirmed the calls in lines NA07019 and NA18966. For all analyses the IgK (chr.2; nt. 88,825,453 to 90,016,977), IgH (chr. 14; nt. 105,267,348 to 106,339,477), and IgL (chr. 22; nt. 20,745,361 to 21,675,457) were removed before calling CNVs. We note that the other chromosomal changes are known to exist in some HapMap samples. For example, there is an inversion of chromosome 1q21.1 in GM10835 and GM12240 as described in the Supplementary Information (and there are many other such examples in the literature).

Supplementary Table 5B: DNA samples, lot number information, and Karyotype for 270 HapMap individuals

population DNA sample gender family ID relationship Lot # WGTP Lot # 500KEA Karyotyping

Ceph NA10846 Male 1334-1 father 5 5 Karyotype unavailable Ceph NA10847 Female 1334-2 mother 3 3 46,XX Ceph NA12144 Male 1334-10 paternal grandfather 4 4 46,XY Ceph NA12145 Female 1334-11 paternal grandmother 4 4 46,XX Ceph NA12146 Male 1334-12 maternal grandfather 4 4 46,XY Ceph NA12239 Female 1334-13 maternal grandmother 3 3 46,XX,t(2;14)(p11;q32)[4]/46,XX[2] Ceph NA07029 Male 1340-1 father A1 A1 46,XY Ceph NA07019 Female 1340-2 mother 3 3 46,XX Ceph NA06994 Male 1340-9 paternal grandfather 3 3 46,XY Ceph NA07000 Female 1340-10 paternal grandmother 5 5 46,XX Ceph NA07022 Male 1340-11 maternal grandfather 4 4 46,XY Ceph NA07056 Female 1340-12 maternalgrandmother A1 A1 46,XY Ceph NA07048 Male 1341-1 father 4 4 46,XY Ceph NA06991 Female 1341-2 mother 3 3 46,XX Ceph NA07034 Male 1341-11 paternal grandfather B3 B3 46,XY Ceph NA07055 Female 1341-12 paternal grandmother B2 B2 46,XX,t(4;6)(q21;q2?6)[2]/46,XX[4] Ceph NA06993 Male 1341-13 materna lgrandfather 4 4 45,XY,der(13;14)(q10;q10)[3]/46,XY[5] Ceph NA06985 Female 1341-14 maternal grandmother A5 A5 46,XX Ceph NA10851 Male 1344-1 father 3 3 46,XY Ceph NA12056 Male 1344-12 paternal grandfather 3 3 46,XY Ceph NA12057 Female 1344-13 paternal grandmother 3 3 47,XX,+12[10]/46,XX[1] Ceph NA07348 Female 1345-2 mother A2 A2 45,X,-X[4]/46,XX[2] Ceph NA07357 Male 1345-12 maternal grandfather 3 3 46,XY Ceph NA07345 Female 1345-13 maternal grandmother A4 A4 46,XX Ceph NA10857 Male 1346-1 father 2 2 46,XY Ceph NA12043 Male 1346-11 paternal grandfather 3 3 47,XY,+9[3]/46,XY[3] Ceph NA12044 Female 1346-12 paternal grandmother 3 3 46,XX Ceph NA10859 Female 1347-2 mother A6 A6 46,XX Ceph NA11881 Male 1347-14 maternal grandfather 4 4 46,XY Ceph NA11882 Female 1347-15 maternal grandmother A1 A1 46,XX Ceph NA10854 Female 1349-2 mother 2 2 46,X,-X,+9[3]/45,X,-X[3] Ceph NA11839 Male 1349-13 maternal grandfather A2 A2 47,XY,+12[7]/46,XY[3] Ceph NA11840 Female 1349-14 maternal grandmother 2 2 46,XX Ceph NA10856 Male 1350-1 father 3 3 46,XY Ceph NA10855 Female 1350-2 mother 3 3 46,XX Ceph NA11829 Male 1350-10 paternal grandfather 3 3 46,XY Ceph NA11830 Female 1350-11 paternal grandmother 3 3 46,XX Ceph NA11831 Male 1350-12 maternal grandfather 4 4 46,XY Ceph NA11832 Female 1350-13 maternal grandmother 3 3 46,XX Ceph NA12707 Male 1358-1 father 3 3 46,XY Ceph NA12716 Male 1358-11 paternal grandfather 4 4 46,XY Ceph NA12717 Female 1358-12 paternal grandmother B3 B3 46,XX Ceph NA10860 Male 1362-1 father 5 5 46,XY Ceph NA10861 Female 1362-2 mother 5 5 46,XX Ceph NA11992 Male 1362-13 paternal grandfather 4 4 46,XY,add(6)(p2?3)[6]/46,sl,del(16)(q10)[2]/ 46,XY[2] Ceph NA11993 Female 1362-14 paternal grandmother 4 4 46,XX Ceph NA11994 Male 1362-15 maternal grandfather 3 3 46,XY Ceph NA11995 Female 1362-16 maternal grandmother 3 3 46,XX Ceph NA10863 Female 1375-2 mother A2 A2 46,XX Ceph NA12264 Male 1375-11 maternal grandfather 4 4 46,XY Ceph NA12234 Female 1375-12 maternal grandmother 2 2 46,XX Ceph NA10830 Male 1408-1 father 6 6 46,XY Ceph NA10831 Female 1408-2 mother 5 5 46,XX,add(21)(q22)[4]/46,XX[10] Ceph NA12236 Female 1408-11 paternal grandmother A3 A3 not available from Coriell Ceph NA12154 Male 1408-10 paternal grandfather 3 3 46,XY Ceph NA12155 Male 1408-12 maternal grandfather 3 3 46,XY Ceph NA12156 Female 1408-13 maternal grandmother A3 A3 46,XX Ceph NA10835 Male 1416-1 father 4 4 46,XY 50,XY,+9,+12,+14,+22[1]/50,sl,add(8)(q24)[3]/50,sl,der(8)t Ceph NA12248 Male 1416-11 paternal grandfather A3 A3 (8;?11)(q24;q13)[2]/50,sl,add(9)(q34)[2] Ceph NA12249 Female 1416-12 paternal grandmother A1 A1 46,XX Ceph NA10838 Male 1420-1 father 2 2 46,XY Ceph NA10839 Female 1420-2 mother 2 2 46,XX Ceph NA12003 Male 1420-9 paternal grandfather 3 3 46,XY Ceph NA12004 Female 1420-10 paternal grandmother 4 4 46,XX Ceph NA12005 Male 1420-11 maternal grandfather 3 3 46,XY Ceph NA12006 Female 1420-12 maternal grandmother 4 4 46,XX Ceph NA12740 Female 1444-2 mother 3 3 46,XX Ceph NA12750 Male 1444-13 maternal grandfather 2 2 46,XY Ceph NA12751 Female 1444-14 maternal grandmother 2 2 46,XX Ceph NA12752 Male 1447-1 father 2 2 46,XY Ceph NA12753 Female 1447-2 mother 3 3 46,XX Ceph NA12760 Male 1447-9 paternal grandfather 2 2 46,XY Ceph NA12761 Female 1447-10 paternal grandmother 3 3 46,XX Ceph NA12762 Male 1447-11 maternal grandfather 2 2 46,XY Ceph NA12763 Female 1447-12 maternal grandmother 2 2 46,XX Ceph NA12801 Male 1454-1 father 2 2 46,XY Ceph NA12802 Female 1454-2 mother 3 3 46,XX Ceph NA12812 Male 1454-12 paternal grandfather 2 2 46,XX Ceph NA12813 Female 1454-13 paternal grandmother 3 3 46,XX Ceph NA12814 Male 1454-14 maternal grandfather 2 2 46,XY Ceph NA12815 Female 1454-15 maternal grandmother 2 2 46,XX Ceph NA12864 Male 1459-1 father 3 3 46,XY Ceph NA12865 Female 1459-2 mother 4 4 45,X,-X[5]/46,XX[4] Ceph NA12872 Male 1459-9 paternal grandfather 3 3 46,XY Ceph NA12873 Female 1459-10 paternal grandmother 2 2 46,XX Ceph NA12874 Male 1459-11 maternal grandfather 2 2 47,XY,+12[7]/46,XY[3] Ceph NA12875 Female 1459-12 maternal grandmother 2 2 47,XX,+2[6]/46,XX[1] Ceph NA12878 Female 1463-2 mother 4 4 45,XX Ceph NA12891 Male 1463-15 maternal grandfather 2 2 46,XY Ceph NA12892 Female 1463-16 maternal grandmother 2 2 46,XX population DNA sample gender family ID relationship Lot # WGTP Lot # 500KEA Karyotyping

Asian NA18524 Male CHINA 2 2 46,XY Asian NA18526 Female CHINA 1 1 46,XX Asian NA18529 Female CHINA 2 2 46,XX,inv(6)(p11q27)/46,sl,-16,+mar[3] Asian NA18532 Female CHINA 2 2 47,XX,+X[5]/46,XX[9] Asian NA18537 Female CHINA 2 2 46,XX Asian NA18540 Female CHINA 2 2 50,X,-X,+4,+7,+9,+14,+21[5]/46,XX[1] Asian NA18542 Female CHINA 1 1 46,XX Asian NA18545 Female CHINA 2 2 46,XX Asian NA18547 Female CHINA 2 2 46,XX Asian NA18550 Female CHINA 2 2 46,XX Asian NA18552 Female CHINA 2 2 46,XX Asian NA18555 Female CHINA 2 2 46,XX Asian NA18558 Male CHINA 2 2 46,XY Asian NA18561 Male CHINA 2 2 46,XY Asian NA18562 Male CHINA 2 2 46,XY Asian NA18563 Male CHINA 2 2 46,XY Asian NA18564 Female CHINA 2 2 46,XX Asian NA18566 Female CHINA 2 2 46,XX Asian NA18570 Female CHINA 1 1 46,XX Asian NA18571 Female CHINA 2 2 46,XX Asian NA18572 Male CHINA 2 2 46,XY Asian NA18573 Female CHINA 2 2 46,XX Asian NA18576 Female CHINA 2 2 46,XX Asian NA18577 Female CHINA 2 2 46,XX Asian NA18579 Female CHINA 2 2 46,XX Asian NA18582 Female CHINA 2 2 46,XX Asian NA18592 Female CHINA 2 2 46,XX Asian NA18593 Female CHINA 1 1 46,XX Asian NA18594 Female CHINA 2 2 46,XX,t(2;14)(p11;q32) Asian NA18603 Male CHINA 2 2 46,XY Asian NA18605 Male CHINA 1 1 46,XY Asian NA18608 Male CHINA 1 1 46,XY Asian NA18609 Male CHINA 2 2 46,XY Asian NA18611 Male CHINA 1 1 46,XY Asian NA18612 Male CHINA 1 1 46,XY Asian NA18620 Male CHINA 1 1 46,XY Asian NA18621 Male CHINA 1 1 46,XY Asian NA18622 Male CHINA 1 1 46,XY Asian NA18623 Male CHINA 1 1 46,XY Asian NA18624 Male CHINA 2 2 46,XY Asian NA18632 Male CHINA 2 2 46,XY Asian NA18633 Male CHINA 1 1 46,XY Asian NA18635 Male CHINA 1 1 46,XY Asian NA18636 Male CHINA 1 1 46,XY Asian NA18637 Male CHINA 1 1 46,XY Asian NA18940 Male JAPAN 2 2 46,XY Asian NA18942 Female JAPAN 2 2 46,XX Asian NA18943 Male JAPAN 1 1 46,XY Asian NA18944 Male JAPAN 2 2 46,XY Asian NA18945 Male JAPAN 1 1 46,XX Asian NA18947 Female JAPAN 1 1 46,XX Asian NA18948 Male JAPAN 1 1 46,XY Asian NA18949 Female JAPAN 2 2 46,XX Asian NA18951 Female JAPAN 2 2 46,XX Asian NA18952 Male JAPAN 2 2 46,XY Asian NA18953 Male JAPAN 2 2 46,XY Asian NA18956 Female JAPAN 1 1 46,XX Asian NA18959 Male JAPAN 2 2 46,XY Asian NA18960 Male JAPAN 2 2 46,XY Asian NA18961 Male JAPAN 2 2 46,XY Asian NA18964 Female JAPAN 2 2 46,XX Asian NA18965 Male JAPAN 2 2 46,XY Asian NA18966 Male JAPAN 2 2 46,XY Asian NA18967 Male JAPAN 2 2 46,XY Asian NA18968 Female JAPAN 2 2 46,XX Asian NA18969 Female JAPAN 2 2 46,XX Asian NA18970 Male JAPAN 2 2 46,XY Asian NA18971 Male JAPAN 2 2 46,XY Asian NA18972 Female JAPAN 1 1 46,XX Asian NA18973 Female JAPAN 1 1 46,XX Asian NA18974 Male JAPAN 2 2 46,XY Asian NA18975 Female JAPAN 2 2 46,XX Asian NA18976 Female JAPAN 2 2 46,XX Asian NA18978 Female JAPAN 1 1 45,X,-X[5]/46,XX[2] Asian NA18980 Female JAPAN 2 2 46,XX Asian NA18981 Female JAPAN 1 1 46,XX Asian NA18987 Female JAPAN 2 2 46,XX Asian NA18990 Male JAPAN 2 2 46,XY Asian NA18991 Female JAPAN 2 2 46,XX,inv(9)(p12q13) Asian NA18992 Female JAPAN 1 1 46,XX Asian NA18994 Male JAPAN 2 2 46,XY Asian NA18995 Male JAPAN 2 2 46,XY Asian NA18997 Female JAPAN 2 2 46,XX Asian NA18998 Female JAPAN A1 A1 46,XX Asian NA18999 Female JAPAN 2 2 46,XX Asian NA19000 Male JAPAN 2 2 46,XY Asian NA19003 Female JAPAN 2 2 46,XX Asian NA19005 Male JAPAN A1 A1 46,XY Asian NA19007 Male JAPAN 3 3 46,XY Asian NA19012 Male JAPAN 1 1 46,XY population DNA sample gender family ID relationship Lot # WGTP Lot # 500KEA Karyotyping

Yoruba NA18500 Male Y004-1 child 2 1 46,XY Yoruba NA18502 Female Y004-2 mother 2 1 46,XX Yoruba NA18501 Male Y004-3 father 2 1 46,XY Yoruba NA18503 Male Y005-1 child 1 1 46,XY Yoruba NA18505 Female Y005-2 mother 2 1 46,XX Yoruba NA18504 Male Y005-3 father 2 1 46,XY Yoruba NA18506 Male Y009-1 child 1 1 46,XY Yoruba NA18508 Female Y009-2 mother 2 1 46,XX Yoruba NA18507 Male Y009-3 father 2 1 46,XY Yoruba NA18860 Male Y012-1 child 2 1 46,XY Yoruba NA18858 Female Y012-2 mother 1 1 46,XX Yoruba NA18859 Male Y012-3 father 2 1 46,XY Yoruba NA18515 Male Y013-1 child 2 1 46,XY Yoruba NA18517 Female Y013-2 mother 1 1 46,XX Yoruba NA18516 Male Y013-3 father 2 1 46,XY Yoruba NA18521 Male Y016-1 child 1 1 46,XY Yoruba NA18523 Female Y016-2 mother 2 1 46,XX inv(1)(p13q25) Yoruba NA18522 Male Y016-3 father 1 1 46,XY Yoruba NA18872 Male Y017-1 child 2 1 46,XY Yoruba NA18870 Female Y017-2 mother 2 1 46,XX Yoruba NA18871 Male Y017-3 father 2 1 46,XY Yoruba NA18854 Male Y018-1 child 1 1 46,XY Yoruba NA18852 Female Y018-2 mother 2 1 46,XX Yoruba NA18853 Male Y018-3 father 2 1 46,XY Yoruba NA18857 Male Y023-1 child 1 1 47,XY,+12[2]/46,XY[9] Yoruba NA18855 Female Y023-2 mother 1 1 47~51,XX,+X[2],+5[4],+9[1],+11[9],+12[5], +17[3][cp9] Yoruba NA18856 Male Y023-3 father 2 1 46,XY Yoruba NA18863 Male Y024-1 child 1 1 46,XY Yoruba NA18861 Female Y024-2 mother 2 1 46,XX Yoruba NA18862 Male Y024-3 father 2 1 46,XY,add(3)(q29)[6]/46,XY[16] Yoruba NA18914 Male Y028-1 child 1 1 46,XY Yoruba NA18912 Female Y028-2 mother 2 1 46,XX Yoruba NA18913 Male Y028-3 father 2 1 46,XY Yoruba NA19094 Female Y040-1 child 1 1 46,XX Yoruba NA19093 Female Y040-2 mother 1 1 46,XX Yoruba NA19092 Male Y040-3 father 2 1 46,XY Yoruba NA19103 Male Y042-1 child 1 1 46,XY Yoruba NA19102 Female Y042-2 mother 2 1 46,XX Yoruba NA19101 Male Y042-3 father 1 1 46,XY Yoruba NA19139 Male Y043-1 child 1 1 46,XY Yoruba NA19137 Female Y043-2 mother 2 1 46,XX Yoruba NA19138 Male Y043-3 father 1 1 46,XY Yoruba NA19202 Female Y045-1 child 1 1 46,XX Yoruba NA19201 Female Y045-2 mother 2 1 46,XX Yoruba NA19200 Male Y045-3 father 2 1 46,XY Yoruba NA19173 Male Y047-1 child 2 1 46,XY Yoruba NA19172 Female Y047-2 mother 2 1 46,XX Yoruba NA19171 Male Y047-3 father 2 1 46,XY Yoruba NA19205 Male Y048-1 child 2 1 46,XY Yoruba NA19204 Female Y048-2 mother 2 1 46,XX Yoruba NA19203 Male Y048-3 father 1 1 46,XY Yoruba NA19211 Male Y050-1 child 2 1 46,XY Yoruba NA19209 Female Y050-2 mother 2 1 46,XX Yoruba NA19210 Male Y050-3 father 2 1 46,XY Yoruba NA19208 Male Y051-1 child 1 1 47,XY,+9[5]/46,XY[1] Yoruba NA19206 Female Y051-2 mother 2 1 46,XX Yoruba NA19207 Male Y051-3 father 2 1 46,XY Yoruba NA19161 Male Y056-1 child 1 1 46,XY Yoruba NA19159 Female Y056-2 mother 2 1 46,XX Yoruba NA19160 Male Y056-3 father 1 1 46,XY Yoruba NA19221 Female Y058-1 child 2 1 46,XX Yoruba NA19222 Female Y058-2 mother 1 1 46,XX Yoruba NA19223 Male Y058-3 father 2 1 46,XY Yoruba NA19120 Male Y060-1 child 1 1 46,XY Yoruba NA19116 Female Y060-2 mother 1 1 46,XX Yoruba NA19119 Male Y060-3 father 2 1 46,XY Yoruba NA19142 Male Y071-1 child 1 1 46,XY Yoruba NA19140 Female Y071-2 mother 1 1 46,XX Yoruba NA19141 Male Y071-3 father 1 1 46,XY Yoruba NA19154 Male Y072-1 child 1 1 46,XY Yoruba NA19152 Female Y072-2 mother 1 1 46,XX Yoruba NA19153 Male Y072-3 father 2 1 46,XY Yoruba NA19145 Male Y074-1 child 2 1 46,XY Yoruba NA19143 Female Y074-2 mother 1 1 46,XX Yoruba NA19144 Male Y074-3 father 2 1 46,XY Yoruba NA19129 Female Y077-1 child 2 1 46,XX Yoruba NA19127 Female Y077-2 mother 2 1 46,XX Yoruba NA19128 Male Y077-3 father 1 1 46,XY Yoruba NA19132 Female Y101-1 child 2 1 46,XX Yoruba NA19131 Female Y101-2 mother 2 1 46,XX Yoruba NA19130 Male Y101-3 father 1 1 46,XY Yoruba NA19100 Female Y105-1 child 1 1 46,XX Yoruba NA19099 Female Y105-2 mother 1 1 46,XX Yoruba NA19098 Male Y105-3 father 1 1 46,XY,inv(9)(p12q13) Yoruba NA19194 Male Y112-1 child 1 1 46,XY Yoruba NA19193 Female Y112-2 mother 2 1 47,XX,+12 Yoruba NA19192 Male Y112-3 father 2 1 46,XY Yoruba NA19240 Female Y117-1 child 2 1 46,XX Yoruba NA19238 Female Y117-2 mother 2 1 46,XX Yoruba NA19239 Male Y117-3 father 2 1 46,XY

Note: The original NA19012sample is currently being substituted by the HapMap Consortium Supplementary Table 5C: Regions detected as cell line artefacts from the WGTP platform -- List of samples whose chromosome has been excluded from cnv call results average ratio (whole chromosome sample chromosome finding with WGTP array artefacts only) NA07019 7 partial 7q deletion NA07019 5 partial 5q duplication NA07055 2 partial 2q23.1-q24.3 deletion NA10856 13 partial 13q duplication NA11839 10 partial 10p15.3-q21.1 deletion NA11882 19 partial 19q13.41-q13.43 duplication NA12056 17 partial 17p13.3-p13.1 deletion NA12056 16 partial 16q23.2-q24.3 duplication NA12248 22 whole chr22 duplication 0.069 NA12248 9 whole chr12 duplication 0.061 NA12248 14 whole chr9 duplication 0.076 NA12248 12 whole chr14 duplication 0.1055 NA12707 16 partial 16q11.2-q24.3 deletion NA12875 2 whole chr2 duplication 0.139 NA18529 16 partial 16q11.2-q24.3 deletion NA18540 7 whole chr7 duplication 0.2245 NA18540 4 whole chr14 duplication 0.222 NA18540 21 whole chr4 duplication 0.2065 NA18540 14 whole chr9 duplication 0.2335 NA18540 9 whole chr21 duplication 0.235 NA18635 X whole chrX duplication 0.0515 NA18862 12 whole chr12 duplication 0.0535 NA18956 4 partial 4q31.3-q35.2 duplication NA18966 Y whole Y duplication 0.1385 NA18987 12 whole chr12 deletion -0.0535 NA19140 9 whole chr9 duplication 0.052 NA19193 12 whole chr12 duplication 0.357 NA19208 9 whole chr9 duplication 0.265

-- List of Igs regions that have been masked before calling cnv

Igl-K region on chr2 from sanger_genomic_start 88825453 to sanger_genomic_end 90016977 this includes, the following clones chr2 Chr2tp-20E7 chr2 Chr2tp-31D6 chr2 Chr2tp-19B12 chr2 Chr2tp-28B12 chr2 Chr2tp-31F7 chr2 Chr2tp-16F6 chr2 Chr2tp-20D11 chr2 Chr2tp-10B5 chr2 Chr2tp-22D7 chr2 Chr2tp-4C7 chr2 Chr2tp-10D5

IgH region on chr14 from sanger_genomic_start 105267348 to sanger_genomic_end 106339477 this includes, the following clones chr14 Chr14tp-8C9 chr14 Chr14tp-12C3 chr14 Chr14tp-10B2 chr14 Chr14tp-10F5 chr14 Chr14tp-11A3 chr14 Chr14tp-12H5 chr14 Chr14tp-10B5 chr14 Chr14tp-10F11 chr14 Chr14tp-10D11

IgL-L region on chr22 from sanger_genomic_start 20745361 to sanger_genomic_end 21675457 this includes, the following clones chr22 Chr22tp-6E7 chr22 Chr22tp-6C1 chr22 Chr22tp-6B9 chr22 Chr22tp-6F3 chr22 Chr22tp-6F9 chr22 Chr22tp-6A12 chr22 Chr22tp-6E2 chr22 Chr22tp-6F11 chr22 Chr22tp-6B7 chr22 Chr22tp-6C4 chr22 Chr22tp-6D3 chr22 Chr22tp-6D2 chr22 Chr22tp-6B12 chr22 Chr22tp-6C2 chr22 Chr22tp-6C12 chr22 Chr22tp-6E12 chr22 Chr22tp-6C10 chr22 Chr22tp-6D7 chr22 Chr22tp-6B10 chr22 Chr22tp-6E4 chr22 Chr22tp-6E8 chr22 Chr22tp-6B4 chr22 Chr22tp-6B3 chr22 Chr22tp-6D11 chr22 Chr22tp-4G1 chr22 Chr22tp-4D7 Supplementary Table 5D: Regions detected as cell line artefacts from the 500K EA platform average ratio sampleID chr start end length(kb) (0 remarks cytoband in/del normalized) NA7019 7 61076556 158626072 97550 -0.057 partial 7q deletion NA7019 5 49596616 180625439 131029 0.056 partial 5q insertion NA7055 2 149199923 165796119 16596 -0.396 partial 2q23.1-q24.3 deletion NA10831 21 9941889 46902240 36960 -0.030 whole chr21 deletion NA10856 13 17960319 114093419 96133 0.198 partial 13q insertion NA11839 10 101955 55998618 55897 -0.042 partial 10p15.3-q21.1 deletion NA11882 19 57202822 63785051 6582 0.167 partial 19q13.41-q13.43 insertion NA12056 17 6888 7901105 7894 -0.552 partial 17p13.3-p13.1 deletion NA12056 16 79678854 88690776 9012 0.297 partial 16q23.2-q24.3 insertion NA12248 22 14461115 49509150 35048 0.053 whole chr22 insertion NA12248 12 36594 132369744 132333 0.060 whole chr12 insertion NA12248 9 30910 138363203 138332 0.061 whole chr9 insertion NA12248 14 19272965 106334195 87061 0.077 whole chr14 insertion NA12707 16 45262450 88690776 43428 -0.037 partial 16q11.2-q24.3 deletion NA12875 2 18722 242730382 242712 0.132 whole chr2 insertion NA18522 12 36594 132369744 132333 0.068 whole chr12 insertion NA18529 16 45167588 88690776 43523 -0.047 partial 16q11.2-q24.3 deletion NA18540 7 141322 158626072 158485 0.174 whole chr7 insertion NA18540 14 19272965 106334195 87061 0.175 whole chr14 insertion NA18540 4 19099 191351910 191333 0.175 whole chr4 insertion NA18540 9 30910 138363203 138332 0.176 whole chr9 insertion NA18540 21 9941889 46902240 36960 0.176 whole chr21 insertion NA18862 12 36594 132369744 132333 0.052 whole chr12 insertion NA18956 4 155295933 191351910 36056 0.051 partial 4q31.3-q35.2 insertion NA19193 12 36594 132369744 132333 0.201 whole chr12 insertion NA19208 9 30910 138363203 138332 0.212 whole chr9 insertion

X chromosome changes NA18507 X 2696752 154479679 151783 0.052 whole,maleX chrX insertion NA18516 X 2696752 154479679 151783 -0.062 whole,maleX chrX deletion NA18524 X 2696752 154479679 151783 0.055 whole,maleX chrX insertion NA18562 X 2696752 154479679 151783 0.056 whole,maleX chrX insertion NA7348 X 2696752 154479679 151783 -0.227 whole,femaleX chrX deletion NA10854 X 2696752 154479679 151783 -0.379 whole,femaleX chrX deletion NA10859 X 2696752 154479679 151783 -0.137 whole,femaleX chrX deletion NA12145 X 2696752 154479679 151783 -0.146 whole,femaleX chrX deletion NA18540 X 2696752 154479679 151783 -0.312 whole,femaleX chrX deletion NA18978 X 2696752 154479679 151783 -0.126 whole,femaleX chrX deletion

-- List of Igs regions that have been masked before calling cnv 0 2 88961343 89723057 762 IgL-K mmunoglobul 0 14 105170875 106204241 1033 IgH mmunoglobul 0 22 20772047 21576156 804 IgL-L mmunoglobul

Supplementary Table 5E: Regions detected as cell line artefacts by LTA analysis and removed

population DNA sample chrom start stop log(p-value) platform Ceph NA07034 7 37991943 38296695 -148.393122 WGTP Ceph NA07034 7 38084338 38160031 -188.4227 500KEA Ceph NA07345 9 7282836 7771365 -30.8600657 500KEA Ceph NA07345 4 158076756 158236808 -9.10910727 WGTP Ceph NA07345 9 7165387 7825237 -48.893644 WGTP Ceph NA07348 4 190967344 191053255 -13.5726984 500KEA Ceph NA07348 4 190784196 191053457 -23.6563838 WGTP Ceph NA10831 7 83929570 84164663 -7.85221174 500KEA Ceph NA10831 7 83900853 84254267 -8.2421631 WGTP Ceph NA10859 8 2105020 2279641 -20.8901997 WGTP Ceph NA11839 14 21970760 21987473 -6.1668178 500KEA Ceph NA11839 14 21867480 22006855 -7.292536 WGTP Ceph NA12057 1 242399333 242697905 -14.6168775 WGTP Ceph NA12891 15 81149336 81250549 -29.3936681 500KEA Ceph NA12891 19 41815435 42022453 -32.1822338 500KEA Ceph NA12891 19 41730238 42087750 -39.3052952 WGTP Yoruba NA18507 7 56998826 57202820 -12.986322 WGTP Yoruba NA18852 3 147114997 147144469 -5.71543244 500KEA Yoruba NA18852 13 97603066 97845997 -11.0634178 WGTP Yoruba NA18852 13 97712694 97740231 -13.90544 500KEA Yoruba NA18855 18 61788347 61951445 -7.31402484 WGTP Yoruba NA18859 4 19301 54508 -9.88039873 500KEA Yoruba NA19101 1 244273235 244554473 -7.0216648 WGTP Yoruba NA19203 2 151551300 153541902 -434.024446 500KEA Yoruba NA19203 2 151470035 153617318 -436.976823 WGTP -- see Supplementary note for details on LTA analysis

Regions confrimed as cell line artefacts by FISH

population DNA sample Platform FISH Ceph NA07019 WGTP, 500K EA 5q+ in 19%; 7q ok in 89% Ceph NA12057 LTA Confirmed by RP11-91C5 Ceph NA07345 LTA 9p24.1 Confirmed by RP11-79K3 Ceph NA12891 LTA 19q13.2 Confirmed by RP11-55J12 Supplementary table 6. Data reproducibility on WGTP array: analysis of ten technical triplicates

NA12144

replicate A B C average median SDe 0.024 0.028 0.045 0.032 35 8 3 15.3 calls 1x 36.5% 11.9% 8.8% 19.1% 32 30 2 21.3 calls 2x 33.3% 44.8% 5.9% 28.0% 29 29 29 29.0 calls 3x 30.2% 43.3% 85.3% 52.9% total calls 96 67 34 65.7

NA12239

replicate A B C average median SDe 0.032 0.044 0.038 0.038 31 12 8 17.0 calls 1x 35.6% 20.0% 13.8% 23.1% 18 10 12 13.3 calls 2x 20.7% 16.7% 20.7% 19.3% 38 38 38 38.0 calls 3x 43.7% 63.3% 65.5% 57.5% total calls 87 60 58 68.3

NA12892

replicate A B C average median SDe 0.051 0.047 0.058 0.052 12 7 5 8.0 calls 1x 23.5% 14.6% 16.1% 18.1% 15 17 2 11.3 calls 2x 29.4% 35.4% 6.5% 23.8% 24 24 24 24.0 calls 3x 47.1% 50.0% 77.4% 58.2% total calls 51 48 31 43.3

NA18500

replicate A B C average median SDe 0.038 0.042 0.053 0.044 26 26 5 19.0 calls 1x 28.9% 29.2% 10.2% 22.8% 25 24 5 18.0 calls 2x 27.8% 27.0% 10.2% 21.6% 39 39 39 39.0 calls 3x 43.3% 43.8% 79.6% 55.6% total calls 90 89 49 76.0 NA18576

replicate A B C average median SDe 0.039 0.041 0.039 0.040 calls 1x 15 10 13 12.7 22.1% 16.4% 21.7% 20.0% calls 2x 12 10 6 9.3 17.6% 16.4% 10.0% 14.7% calls 3x 41 41 41 41.0 60.3% 67.2% 68.3% 65.3% total calls 68 61 60 63.0

NA18621

replicate A B C average median SDe 0.031 0.042 0.049 0.041 calls 1x 34 13 10 19.0 38.6% 20.0% 20.4% 26.3% calls 2x 21 19 6 15.3 23.9% 29.2% 12.2% 21.8% calls 3x 33 33 33 33.0 37.5% 50.8% 67.3% 51.9% total calls 88 65 49 67.3

NA18980

replicate A B C average median SDe 0.038 0.05 0.041 0.043 17 15 8 13.3 calls 1x 27.0% 25.9% 16.3% 23.1% 14 11 9 11.3 calls 2x 22.2% 19.0% 18.4% 19.9% 32 32 32 32.0 calls 3x 50.8% 55.2% 65.3% 57.1% total calls 63 58 49 56.7

NA18860

replicate A B C average median SDe 0.035 0.042 0.042 0.040 calls 1x 25 19 6 16.7 28.4% 23.5% 9.5% 20.5% calls 2x 23 22 17 20.7 26.1% 27.2% 27.0% 26.8% calls 3x 40 40 40 40.0 45.5% 49.4% 63.5% 52.8% total calls 88 81 63 77.3 NA18971

replicate A B C average median SDe 0.028 0.038 0.039 0.035 calls 1x 34 2 8 14.7 30.6% 2.9% 12.5% 15.4% calls 2x 32 21 11 21.3 28.8% 30.9% 17.2% 25.6% calls 3x 45 45 45 45.0 40.5% 66.2% 70.3% 59.0% total calls 111 68 64 81.0

NA19099

replicate A B C average median SDe 0.031 0.032 0.05 0.038 calls 1x 33 8 1 14.0 27.3% 8.4% 1.8% 12.5% calls 2x 40 39 7 28.7 33.1% 41.1% 12.5% 28.9% calls 3x 48 48 48 48.0 39.7% 50.5% 85.7% 58.6% total calls 121 95 56 90.7

AVERAGE WGTP Reproducibility

replicate A B C average median SDe 0.035 0.041 0.045 0.040 calls 1x 26.2 12.0 6.7 15.0 29.9% 17.3% 13.1% 20.1% calls 2x 23.2 20.3 7.7 17.1 26.3% 28.8% 14.1% 23.0% calls 3x 36.9 36.9 36.9 36.9 43.9% 54.0% 72.8% 56.9% total calls 86.3 69.2 51.3 68.9

Supplementary table 6A: Data reproducibility on WGTP array: analysis of ten technical triplicates. For ten DNA samples from the HapMap collection, triplicate experiments were made on the WGTP array, at different dates and using different batches of slides. Each table corresponds to one DNA sample and reports for each replicate experiment the number and percentage of calls found in only one replicate (1x), two replicates (2x) or 3 replicates (3x). The last table gives the average values derived from the 10 individual tables.

AVERAGE 500K EA Reproducibility

Avg data Rep1 Rep2 Rep3 Avg Called 1x 2 0.9 1.8 1.6 12.8% 6.2% 12.3% 10.4% Called 2x 1.7 1.8 0.9 1.5 10.9% 12.3% 6.2% 9.8% Called 3x 11.9 11.9 11.9 11.9 76.3% 81.5% 81.5% 79.8% total 15.6 14.6 14.6 14.9

Supplementary Table 6B: Summary data of 10 technical replicate DNA samples, (NA18500, NA18860, NA19099, NA12144, NA12239, NA12892, NA18621, NA18576, NA18971, NA18980) each tested with 3 replicates and analyzed by comparing to the 270 HapMap samples. The numbers reported are the average number of CNVs for each replicate called in one experiment (1x), two experiments (2x) or all three experiments (3x). Based on these experiments, the majority of CNVs called by 500K EA are highly reproducible, with an average of 80% of calls found in all three replicates. In a typical experiment, about 10% of CNVs are found only once, and an additional 10% are called twice.

Supplementary Table7A: CNV genotypes from WGTP data Clone Chr1tp-32E9 Chr1tp-13A8 Chr1tp-15A9 Chr3tp-23C12 Chr4tp-6G5 Chr6tp-5C11 Chr6tp-18F9 Chr8tp-17E9 Chr12tp-19A11 Chr20tp-4A10 Chr1tp-4C10 Chr1tp-31C8 Chr 1 1 1 3 4 6 6 8 12 20 1 1 Start 193424505 218684362 245013551 164054860 173771510 32503398 103834514 39364955 31089219 1424781 72463446 149285912 End 193544439 218846708 245191415 164221008 173963412 32593944 103911696 39524881 31253169 1540258 72598834 149400186 NA06985 GG GG AG AG NN AA AA AG AG AA AA AG NA06991 AG GG GG AG AA AG AA AG AG AA AG AA NA06993 AG GG GG AG AG GG AA AG AA AG AG AG NA06994 AG AG GG NN NN AG AA AG NN AG AA GG NA07000 GG AG AG AG AG AA NN GG AA AG AG AG NA07019 GG AG GG AG AA AG AG GG AA AA AA AG NA07022 GG AG GG AG NN GG AG GG AG AA AG GG NA07029 AG AG GG AG AG AG AA GG AA GG AA AG NA07034 GG GG GG NN AA GG AG GG AG AA NN AG NA07048 GG AG GG AG AA AG AG AG AA AA AA AA NA07055 GG NN GG AG AG AA AA AG AA AA AA AA NA07056 AG GG GG AA AG NN GG GG AG AA AA AA NA07345 GG AG GG NN AA AG NN NN GG AG AA AG NA07348 GG AA NN AG NN AG GG GG AG AG AA AA NA07357 GG AA AG NN AG AG AG GG AA AA AA AG NA10830 AG AG GG AG AA AA GG AG AA GG AG AG NA10831 GG AG GG GG AG AG AA AA AA AA AG AG NA10835 AG GG GG AG AA NN AG AA NN NN NN GG NA10838 GG AA NN AG NN AA AG AG NN AA AA AG NA10839 AG GG GG AG AA AA AG AA NN AG AA AA NA10846 AG GG GG GG NN AG AG AG AG AA AA AA NA10847 NN AA GG GG AA AA NN AG NN GG NN AA NA10851 AG AG GG AA AG GG AA AG AA AG AG AG NA10854 NN GG AG GG GG GG AG AG AG AG GG AG NA10855 GG AA GG GG AG AA AG AG AG AG AA AG NA10856 GG GG GG GG AG AG AG AG GG AA NN AA NA10857 AG AG GG GG AA AA AA GG GG AA AA AG NA10859 AA AG AG GG AA AG AG GG AA AG NN AG NA10860 AG GG GG GG AA AA AG AG AG AG AG AA NA10861 GG GG NN NN AG AG NN GG AA AG AA AG NA10863 GG AG AG NN AA AG AG AG AA AA AA AG NA11829 AG GG AG GG GG GG GG AA GG AA AA AA NA11830 GG GG GG GG AG AG AG AG NN AA AG AG NA11831 AG AG GG GG AG AA GG AG GG AG AA AG NA11832 AG AG GG AG AG AA NN GG AA AA NN AG NA11839 AA GG GG GG GG AG AG AG NN GG GG AG NA11840 NN GG AG AG AG GG AG AG AG AA AG AG NA11881 AA GG AG AG AA AA NN GG NN AA AA AG NA11882 AG AG GG NN AA AG AG GG AA AG AG AA NA11992 GG AG GG GG AG AA AG AA AG NN AG AA NA11993 AA AG GG GG AA AA AG GG NN AA AA AA NA11994 GG NN AG AG AG GG GG AG AG AG NN AG NA11995 GG GG AG GG NN NN AG GG GG NN AA GG NA12003 GG AA GG AA AA AG AG GG NN AA AG AG NA12004 GG NN GG GG AG NN AA AG NN AG AA AG NA12005 GG AG GG AA AG AA GG AG GG AG AA AA NA12006 AG AG GG AG AA AG AA AG AG GG NN AA NA12043 GG GG GG NN AG AG NN AG NN AG AG GG NA12044 AG AA GG GG AA AA AA AG AG AA AG AG NA12056 GG NN GG AG AA AG AA AG AA AG GG AG NA12057 AG AG GG AA GG AG AG AG AG AG AA AA NA12144 AG AG GG GG AA AG GG AA AA AA AA AA NA12145 GG GG AG AG AA AA NN AG AA AG AG AG NA12146 NN NN GG GG NN AA AA AG NN AG AG AA NA12154 GG AG GG NN NN AG GG AA AA AG AA GG NA12155 AG NN GG GG AG AG AA AG NN AA NN AA NA12156 AG AG GG GG NN GG NN AA NN AA GG GG NA12234 AG AG AG AG AA AG GG GG AG AA AG AA NA12236 AG GG GG AG NN AG AG GG AG AG AG AA NA12239 GG AA GG AG AA AG GG AA AG AG AA AA NA12248 GG AG GG NN AA AG AG AG GG AG GG AG NA12249 AG AG GG AG AA AG AA AA AG AA AG AG NA12264 GG GG GG NN NN GG AG AA AG AA AG AG NA12707 GG AG GG GG AA AG AA AG NN AG AG AG NA12716 GG AA GG AG AA AG AG AA AA AG AA AG NA12717 GG GG GG GG AG AA AG GG AG AA GG AA NA12740 GG AG GG AA NN AG AA AG GG AG AA GG NA12750 GG AG GG AA AG AG AG AG AG AG NN AG NA12751 GG AG GG NN GG AG AG GG AG AA AG GG NA12752 GG AA GG NN NN AG AG AG AA AG AG AA NA12753 AG AA GG GG AA AA AG GG AG AA AG AG NA12760 GG AA GG NN AA GG AA AG AA AA GG AG NA12761 AG AA AG AG AG NN GG GG AG AG AG AG NA12762 GG AA GG GG NN AG AG GG AA AA AG AG NA12763 AA AG GG GG AG AA NN AG GG AG AG AA NA12801 GG AG AG AA AA AG AG AG NN AG AA AA NA12802 GG AG GG NN AA AG AG AG AG AG AG AA NA12812 GG GG GG AG NN AG AA GG GG AG AA AA NA12813 AG AG AG AG AA GG GG AA AA AA AA AG NA12814 GG AG GG NN AA AA AG AA AA AG AG AA NA12815 GG GG GG GG AA AG AA GG AG AA AG AA NA12864 GG GG GG NN NN AA AA AA AA NN AA GG NA12865 AG AG GG AG NN AA AA AG AA AG NN AG NA12872 GG GG GG NN AA AG AG AG AG AG AA GG NA12873 GG AG GG GG NN AA AA AA AA NN AG GG NA12874 NN AA GG AA AG AA AA AG AA NN AG GG NA12875 AA GG GG AG NN AA AG AA AA AG GG AG NA12878 GG AG AA AG NN AA AG AG AA AG AA AG NA12891 GG NN AG AA AA AA AG AA AG GG AA AA NA12892 GG AG AG AG AA AA AG AG AA AA AA GG NA18500 AG AG NN NN AA AG AG GG GG AA AG AG Clone Chr1tp-32E9 Chr1tp-13A8 Chr1tp-15A9 Chr3tp-23C12 Chr4tp-6G5 Chr6tp-5C11 Chr6tp-18F9 Chr8tp-17E9 Chr12tp-19A11 Chr20tp-4A10 Chr1tp-4C10 Chr1tp-31C8 Chr 1 1 1 3 4 6 6 8 12 20 1 1 Start 193424505 218684362 245013551 164054860 173771510 32503398 103834514 39364955 31089219 1424781 72463446 149285912 End 193544439 218846708 245191415 164221008 173963412 32593944 103911696 39524881 31253169 1540258 72598834 149400186 NA18501 AG GG GG AG NN AA GG GG GG AA AG AG NA18502 AA AG NN NN AG AG NN AG NN AA GG AG NA18503 NN AG GG AG NN AA NN GG AA NN NN AG NA18504 AG AG AG GG NN AA GG GG AG NN AG GG NA18505 NN GG AG NN NN AA GG GG AG AG AG AA NA18506 AA GG NN NN AA AG AG GG AG AA AG GG NA18507 AA GG GG NN AA AA GG GG AG AA AG NN NA18508 AG AG AG AG AG AA AG GG GG AA NN AG NA18515 AG AG AG GG AG AA NN GG GG AA AG AG NA18516 AG AG AG NN NN AA NN GG NN AA AG AG NA18517 AA GG AG AG AG AA NN GG AG AA GG AG NA18521 AA GG GG GG NN NN NN GG AG AA GG GG NA18522 AA AG AG NN AG NN AG GG NN AA NN AG NA18523 AG GG AG AG AA NN AA GG GG AA AG GG NA18524 GG GG GG AA AG AA NN AA NN NN AA GG NA18526 NN AG GG AG NN AA NN AA AA AA AA AG NA18529 GG AG GG NN AA NN AA GG AA NN AA AA NA18532 GG AG GG AA AA GG AG GG AG AA AA AG NA18537 AG NN GG AG AA AG AA GG AG AA AG AG NA18540 NN NN GG AA NN AA AG GG AA NN AA AA NA18542 GG GG GG AA AA AG AG GG AA AG AA GG NA18545 AG GG GG AG AA GG NN GG AG AG AA AG NA18547 GG GG GG AA AA AG AG AG GG AA AA AG NA18550 GG GG AA AA AA AG AA GG AG AG AG AG NA18552 AG GG GG AA AA AG AA AG GG AA AA NN NA18555 AG AG AG AA AA NN AG GG AG AA AA AG NA18558 GG GG AG AG AA AG GG AG AG AG AG AA NA18561 GG AG AG AA NN AG AA GG NN AA AA AA NA18562 GG GG GG AG AA AG NN GG GG AA AG AG NA18563 AA GG GG AA AA AG AA GG GG GG AA AA NA18564 GG AG GG NN AA AG GG GG AA AA AA AA NA18566 NN NN GG AA AA AA AA GG GG AA AA GG NA18570 GG GG AG AA AG AG NN AG GG AA AG AG NA18571 GG AG GG AG AA AG AG GG AG AA AA AA NA18572 GG GG AG AG AA AA AG GG GG AA AA AG NA18573 GG GG AG AA AA GG AA GG GG AA AG AG NA18576 GG AG NN AA AA AA AG GG GG AA AA AG NA18577 GG AG GG AG AA AA NN GG AA AA AA AA NA18579 GG NN GG AA AA NN AG AG NN AA AG AA NA18582 GG GG GG AA AA AG AA GG AG AA NN AA NA18592 GG GG GG AA NN AA AA GG NN AA AG AA NA18593 GG GG GG AA AA AG AA AG NN AA AA AA NA18594 GG AG AG AA AG AA GG GG GG AA AA AA NA18603 NN GG GG AA NN GG AA GG AG AA NN AG NA18605 GG GG AA AA NN AA AG AG NN AG AA AG NA18608 AG GG GG NN AA AA AA GG AG AA AG AG NA18609 NN AG GG AA AA AA GG GG AG AG AA AG NA18611 AG GG AG AG AA AA AA GG AG AA AA AA NA18612 GG GG GG AA AA AA AA GG NN AG AA AA NA18620 GG GG GG AA AA NN AA GG AG AA AA AA NA18621 GG AG GG AA AG AG AG GG AA AA AA AA NA18622 GG GG AG AA AA GG GG GG AA AA AA AG NA18623 AG GG GG AA AG GG AG AG AG AG NN GG NA18624 GG GG GG AA AA AG AG AG GG AG AA AA NA18632 GG GG AG AA NN AG NN GG GG AG AA AA NA18633 GG GG GG AA AA AG NN GG AG AG AG AG NA18635 GG GG AG AA NN GG AA GG AA GG AA AA NA18636 GG GG GG AA AA AG AG GG AA AG AA AA NA18637 GG GG GG NN AA NN NN GG AG AG AG AA NA18852 AG GG AG NN GG GG AG GG NN AA GG GG NA18853 GG GG GG GG AG AG AG AG GG AG GG AG NA18854 AG GG GG GG NN GG AG GG AG AG GG GG NA18855 GG NN AG AA AG AA GG GG GG AA GG GG NA18856 AG AG AG NN NN AA NN GG NN AA AA GG NA18857 AG AG AA NN AA AA GG GG GG AA AA GG NA18858 AG AG GG NN AG AA GG AG AA AA AA AG NA18859 AG GG AG AA GG AA GG GG AA AA AA AG NA18860 GG GG AG AA NN AA GG AG AA AA AA AG NA18861 AA AG GG AA AA AA AG GG AG AG AG AG NA18862 AG GG GG AG GG GG AG GG AG AA AG AG NA18863 AA AG GG AA AG NN NN GG GG AG GG AG NA18870 AG GG GG GG AA AG GG AG AG AA AA GG NA18871 AA AG AG AG AG AA AG GG GG AA GG AG NA18872 AA AG NN AG AA AA GG GG GG AA AG GG NA18912 GG AG GG GG AG AA GG GG GG AA AG GG NA18913 GG GG GG AG GG AA AG GG GG AA AG AG NA18914 GG AG GG AG GG AA AG GG NN AA AA AG NA18940 GG GG GG AA AA AA AA GG AG AG AA AA NA18942 AG GG GG AG AG AG AG AA NN AA AA AA NA18943 GG GG GG AA AA AA GG GG GG GG AA AG NA18944 GG GG GG AA AA AA AG GG AG AA AA AA NA18945 GG GG GG AA AA AG AA GG AG AG AA AG NA18947 GG GG GG AG AA AA NN GG AA AG AA AG NA18948 GG NN AG AA AA AG AG AG AG AG AA AG NA18949 GG GG GG AA AA AG GG GG GG AA AA AA NA18951 GG GG GG AA AA AG AG GG AA AA AA AA NA18952 GG AG GG NN AA AG AG AG AG AG AA AA NA18953 GG AG GG AA AA NN AG GG GG AA AA GG NA18956 NN GG GG AA AG AG GG GG AG AG AA AG NA18959 NN GG GG AA AA AA AG GG AG AG AG AG NA18960 GG GG GG AA NN GG AA AG AG AA AA AA NA18961 AG NN GG AG AA GG AG GG AG AA AA GG Clone Chr1tp-32E9 Chr1tp-13A8 Chr1tp-15A9 Chr3tp-23C12 Chr4tp-6G5 Chr6tp-5C11 Chr6tp-18F9 Chr8tp-17E9 Chr12tp-19A11 Chr20tp-4A10 Chr1tp-4C10 Chr1tp-31C8 Chr 1 1 1 3 4 6 6 8 12 20 1 1 Start 193424505 218684362 245013551 164054860 173771510 32503398 103834514 39364955 31089219 1424781 72463446 149285912 End 193544439 218846708 245191415 164221008 173963412 32593944 103911696 39524881 31253169 1540258 72598834 149400186 NA18964 GG GG GG NN AA AG AA GG AA AG AA AA NA18965 NN NN GG AA AA GG AA AG AG AA AA GG NA18966 GG GG AA AG AA AA AG GG AA AG AA AA NA18967 GG GG AG AA AA AG AA AA GG AG AA AG NA18968 GG GG GG AA AA AA AG GG AG AA AG GG NA18969 GG AG GG AG AA AA NN GG AA AA AA AA NA18970 GG GG GG GG AA AG GG AG NN AA AA AG NA18971 GG GG GG AA AA AG AA AG AA AG AA AG NA18972 GG GG GG AA AA AG AG GG AG AG AA GG NA18973 GG GG NN NN AA AA AA GG GG NN AA AA NA18974 GG GG NN AA NN AG NN GG GG AG AA AA NA18975 GG GG GG AG AA AG AA AG NN GG AG AA NA18976 GG NN AG AA AA AA AA AG NN AG AA NN NA18978 AG AG AG AA AA AG GG GG AG AA AA AA NA18980 GG GG GG AG AA AA AG GG AG AG AA GG NA18981 GG GG GG AA NN AA AG GG GG AA AG AA NA18987 GG GG GG AA NN AA AG AG AG AA AA AG NA18990 GG AG GG NN AA AG AA GG AG AA AA AG NA18991 GG GG GG AA AA AG GG GG AA AA GG AA NA18992 GG AG GG AA NN NN GG GG AG AA AA GG NA18994 AG GG GG NN AA NN NN GG GG AA AA AA NA18995 GG AG GG AA AG NN AA GG GG AA AA AA NA18997 AG AG GG AA AA GG AG AG AA AA AA GG NA18998 GG AG GG AA NN AA NN GG AG AG AA AA NA18999 GG AG GG AG NN GG AG GG AG AA AA AA NA19000 GG GG AG AG AG AG AG GG AG AG AA AG NA19003 NN AG GG AA AA AA AG NN AG AA NN GG NA19005 GG GG GG AA AA NN NN GG AG AA AA AG NA19007 AG GG GG AA AA NN AG GG AG AA AA AG NA19012 GG GG AG AA NN GG AG AG NN AA NN AG NA19092 AG GG GG AG NN AA GG GG GG AA AA GG NA19093 AG GG GG NN GG AA AG GG NN AA AG AG NA19094 AG GG GG AG AG AA NN GG GG AA AA AG NA19098 AA GG NN AA AG AG AG GG NN AA AA GG NA19099 AA GG AG AG GG AG AG GG AG AA AA GG NA19100 AA GG AG AA GG AA NN GG GG AA AA GG NA19101 GG AG AA AA AA AA AG GG GG AA AG GG NA19102 AG GG AG AG GG AA GG GG GG AA AG GG NA19103 AG GG AA NN NN NN GG GG GG AA GG GG NA19116 NN AG AG AA NN AA NN AG GG AA GG AG NA19119 AA GG AA NN GG AG AG GG GG AA AG GG NA19120 AA GG AG NN GG AG NN GG GG AA GG GG NA19127 AG GG NN AG NN AA GG GG AG AA AG AA NA19128 AA AG GG GG NN AA AG GG AG AA AG AG NA19129 AG AG AG GG AG AA GG GG AG AA AA AA NA19130 NN GG AG NN NN AA AG GG NN AA AG GG NA19131 NN GG AG AG AA AA AG GG AG AG AG GG NA19132 AA GG GG GG AA AA AA GG AA AG GG GG NA19137 AG GG AG AG GG AA GG GG GG AA AA GG NA19138 AA GG AG AA AG NN GG GG AG AG GG GG NA19139 AA GG AG NN GG AA GG GG NN AG AG GG NA19140 AG AG GG AG NN AA GG GG AA AA NN GG NA19141 AG AG AA GG AA AA AG GG AG AA AG GG NA19142 AA GG AG NN AG AA GG GG AA AA GG GG NA19143 AA AG GG NN AG NN GG GG GG AA AG AA NA19144 AA GG AG NN NN NN AG GG NN AA NN GG NA19145 AA AG GG AG AG AA GG GG GG AA AG AG NA19152 AG GG AG AA AG AA AG GG AG AA AA GG NA19153 GG GG GG AG AG AA AG GG AA AA AG GG NA19154 AG GG AG AA NN AA AG GG AA AA AG GG NA19159 AG AG AG AG AG AG GG GG AA AG GG AG NA19160 GG GG AG AG AG NN AA GG AG AA AG AA NA19161 AG AG AA AA NN AG AG GG AA NN AG AG NA19171 AA GG AG GG AA AA NN GG GG AA AG GG NA19172 AG GG GG AG AG AG GG GG AG AA AG GG NA19173 AA GG GG GG AA NN AG GG GG AA AA GG NA19192 AG AG GG GG AG AA AG AG GG AA AA AG NA19193 AA AA AG NN AG AG NN GG NN AA GG GG NA19194 AG AG AG GG AG AG AG GG GG AA AG GG NA19200 AG AG AG AA AG AA AG GG AA AA AG AA NA19201 GG NN AG GG GG AG AG GG AG AA AA AG NA19202 AG GG AA AG NN AA GG GG NN AA AA AG NA19203 AG GG GG GG GG AG AG AG GG AA NN GG NA19204 GG AG GG AA GG GG GG GG NN AA AG AG NA19205 GG AG GG NN GG NN AG AG GG AA GG GG NA19206 AG NN AG NN AA AA GG AG AG AA AA GG NA19207 AG AG GG AA GG NN AG AG GG AA AA AA NA19208 AG GG AG AA AA NN GG AG AG AA AA AG NA19209 AG AG GG AA GG AA GG GG NN AA AA GG NA19210 AA GG GG AG AA AA GG GG GG AA AA GG NA19211 AG AG GG AA AG NN GG GG GG AA AA GG NA19221 AA NN AA NN AG NN GG GG AA AA AG AG NA19222 AG GG AA AA AG AG GG GG AA AA GG AG NA19223 AA GG AG AA AG AA GG GG AA AA NN AG NA19238 GG GG GG AG GG AA AA GG AG AA AG AG NA19239 NN GG AG NN AG AA NN GG AG AG GG GG NA19240 GG GG AG AG GG NN AG GG AG AA GG AG Clone Chr1tp-21E1 Chr3tp-10A3 Chr5tp-22E4 Chr9tp-2A1 Chr11tp-5D4 Chr12tp-19H4 Chr4tp-23H10 Chr6tp-5C12 Chr4tp-18E9 Chr4tp-10F11 Chr1tp-7D2 Chr15tp-9C6 Chr 135911124644115 Start 203946290 46770243 150080197 41194015 55073652 9451354 69126468 32610887 70153744 190866051 142391276 28279020 End 204141479 46947493 150239374 41282840 55268838 9630395 69296476 32634805 70322413 191064871 142548088 28402108 NA06985 AG GG GG AA AG AG NN AA AG NN AG GG NA06991 AG GG GG AA AG AG GG AA AG AG AG GG NA06993 AG GG GG AA GG AA GG AA NN GG AG GG NA06994 AG GG GG AA AG NN AG AA NN AG NN GG NA07000 NN GG GG NN GG AA GG GG GG NN GG GG NA07019 AG GG NN AA GG AA AG AG GG AG GG GG NA07022 NN GG GG AA GG NN GG AA NN AA GG GG NA07029 AA GG GG AG GG AA NN AG GG NN GG GG NA07034 AA NN GG AG AG AG AG AA GG NN AG GG NA07048 AG GG GG NN AG AA AG AA GG GG GG GG NA07055 AG GG GG GG GG AA AG NN NN GG AG AG NA07056 GG GG GG AA GG AG AG GG GG GG GG GG NA07345 AA GG GG GG GG NN AG AA NN AG GG GG NA07348 AA GG GG AG AG AG AG AA GG NN GG GG NA07357 AA GG GG AA AG AA GG NN GG AA GG GG NA10830 AA GG GG AA GG AA NN GG GG AG GG AG NA10831 AA GG GG GG GG AA AA AG GG GG GG GG NA10835 GG GG GG AA AG GG GG AG GG AG AG GG NA10838 AA AG GG AG AG AG AG AA GG GG GG GG NA10839 AA GG GG AA AG GG GG AA GG AG GG GG NA10846 AA GG GG AG GG AG AG AG AG GG AG GG NA10847 AG GG GG AA AG NN GG AA GG AG NN GG NA10851 AA GG GG AG GG AA AA AA NN AA AA GG NA10854 AA GG GG AA GG AG NN AA GG GG AG GG NA10855 AG GG GG AA AG AG GG GG GG GG AG GG NA10856 AG GG GG GG GG NN AG AG GG GG GG GG NA10857 GG GG GG AA AG GG AG AG GG GG AG GG NA10859 AA GG GG AG GG AA GG AA AG GG NN GG NA10860 AG GG GG AA GG AG GG AA GG GG GG AG NA10861 AA GG GG AA GG AG AG AG GG AG NN AG NA10863 AG GG GG GG AG AA AG NN GG AG AG GG NA11829 AA GG GG GG AG GG AG AA GG AG GG GG NA11830 GG GG GG AG GG GG AG AG GG NN GG GG NA11831 AA GG GG AA AG NN NN AG GG GG AG AG NA11832 AG GG GG AA AA AA AG AG GG AG AG GG NA11839 NN GG GG NN AG AA AG AA GG AG GG GG NA11840 AA GG GG AA AG AG GG AA GG GG NN GG NA11881 AG GG GG AA AG NN GG AA GG NN AG AG NA11882 AG GG GG AG GG AA AG AA AG AG AG GG NA11992 AG GG GG NN AG AG AG AG GG GG AG AA NA11993 AA GG GG AA GG AG GG AA GG GG GG GG NA11994 AA GG GG AA GG AG GG AA GG NN GG AG NA11995 AG GG AG AA GG GG AG AG AG GG AG GG NA12003 AA AG GG AA AA NN GG AA AG GG AG GG NA12004 AA GG GG GG GG GG AG AA GG NN GG GG NA12005 NN GG GG AG GG GG GG AA GG AG AG GG NA12006 GG GG GG AG AG AG GG AA GG AG GG GG NA12043 GG GG GG AA AG GG AG AA GG AG GG GG NA12044 AG GG GG AA GG AG GG AG GG AG AG GG NA12056 AG GG GG AG GG AA AA AA AG AG AG GG NA12057 AA GG GG AG GG AG AA AG NN AA AA GG NA12144 AA GG GG AG GG AA GG AA GG GG AA GG NA12145 NN GG GG AA NN NN AG AG NN GG AG GG NA12146 AA GG GG AG GG NN GG AA GG AG GG GG NA12154 AA GG GG AG GG AA AG AG GG NN GG AG NA12155 AA GG GG GG GG AA AG NN GG GG GG GG NA12156 AA GG GG AG GG AG AG AA GG GG AG GG NA12234 AG GG GG GG AG AG GG AG GG AG AG GG NA12236 AA GG AG AG GG AG GG AG AG AA GG GG NA12239 AG GG GG AA AG AG GG AA AG AG AG GG NA12248 AG GG GG AA AG GG AG AA AG GG NN GG NA12249 AG GG GG AA GG AG GG AG GG GG GG GG NA12264 AA GG GG AG GG NN AA AA AG NN AG AG NA12707 AG GG GG AG GG AG AG AA GG GG GG GG NA12716 AA GG GG AG GG AA AA AA GG GG GG GG NA12717 AG GG GG AG GG AG AG AG AG GG GG GG NA12740 AG GG GG AG GG GG AG AG GG AG NN GG NA12750 GG GG GG GG AG AG AG AA GG AG AA GG NA12751 AA GG GG AA GG NN AG AG GG GG AA GG NA12752 NN GG GG AG GG NN AG AA GG AG GG GG NA12753 AA GG GG AA AG AG GG AA GG AG GG GG NA12760 AG GG GG AA AG AA GG AA AG AG GG GG NA12761 AA GG GG GG AG AG AG AG GG AG GG GG NA12762 AA GG GG AA AG AA GG AA GG GG AG GG NA12763 AA GG GG AA AA GG GG AA GG AG GG AG NA12801 AG GG GG AA GG AG AG AG GG AG AG AG NA12802 AA GG GG AG AG NN GG AA GG NN AG GG NA12812 AG GG GG AA GG GG GG AG GG AG AA GG NA12813 AA GG GG AG GG AA AA AA GG GG AG AG NA12814 AA GG GG AG AG AA GG AA GG GG GG GG NA12815 AA GG GG AG GG AG AG AG GG AG AG AG NA12864 AA GG GG AG AA AA AG AG GG AA GG GG NA12865 AG GG GG AA GG AA NN AA AG GG GG AG NA12872 AA GG GG AG AG AG GG AG GG NN AG GG NA12873 AA GG GG AA AG AA AG AA GG AG GG GG NA12874 AA GG AG AA AG AA GG AA GG AG GG GG NA12875 AG GG GG NN GG AA GG AA AG GG GG AG NA12878 AA GG GG GG AG AA AA AG AG AG GG AG NA12891 NN GG GG GG AG AG AG AG AG AG AG GG NA12892 AG GG GG GG GG AA AA AA AG AG NN GG NA18500 AA AA AA AG AG GG AG AA AG AG AG GG Clone Chr1tp-21E1 Chr3tp-10A3 Chr5tp-22E4 Chr9tp-2A1 Chr11tp-5D4 Chr12tp-19H4 Chr4tp-23H10 Chr6tp-5C12 Chr4tp-18E9 Chr4tp-10F11 Chr1tp-7D2 Chr15tp-9C6 Chr 135911124644115 Start 203946290 46770243 150080197 41194015 55073652 9451354 69126468 32610887 70153744 190866051 142391276 28279020 End 204141479 46947493 150239374 41282840 55268838 9630395 69296476 32634805 70322413 191064871 142548088 28402108 NA18501 NN AG AG AG GG GG GG AG AG AG AA GG NA18502 NN GG AA NN AG GG AG AG AG AG AG GG NA18503 AA AG AG GG NN AA AG GG AA NN GG GG NA18504 AA GG AG AG GG AA AG AG AA AA AG GG NA18505 AA AG AG GG GG AG GG AG AG AG GG GG NA18506 AA AG GG GG GG AG GG GG AG GG AA GG NA18507 NN AG GG NN GG AG NN AG GG GG AG GG NA18508 AA GG GG AG GG GG GG GG AA AG AG GG NA18515 AG GG AG AG GG GG GG GG AG GG AA AG NA18516 NN GG AA GG GG GG GG AG AA GG AG AG NA18517 AA AG NN NN NN NN AG GG GG NN AG GG NA18521 NN AG GG AA GG AG GG GG NN GG AG GG NA18522 NN AG AG NN GG AG GG NN AG AG GG GG NA18523 GG AG AG AA GG GG GG GG AG AG AG AG NA18524 AA GG GG AA AA GG AG NN GG AG GG GG NA18526 AG GG GG AA AG AA AA GG GG NN GG GG NA18529 AA GG GG AG AG AA AG AA AG AG GG GG NA18532 AA GG GG AA AA AG AA AA GG AG GG GG NA18537 AA GG AA AG AA AG AA AA GG AG AG GG NA18540 AA GG NN NN GG AA NN AG NN NN GG GG NA18542 AA GG NN AG GG AA AG AG AG GG GG AG NA18545 AA GG AA AG AG AG AA AA GG AG GG GG NA18547 AA GG AA AA AG GG AA AG GG AG NN GG NA18550 AA GG AG GG AG AG GG NN GG AG AG GG NA18552 AA GG GG AA AG NN AA AG AG NN AG GG NA18555 AA GG AA AA AG AG AG NN GG GG GG GG NA18558 AA GG GG NN GG AG NN NN GG AA GG GG NA18561 AA GG NN AG NN AG AA AA GG NN GG GG NA18562 AA GG AG AG AG NN AA AG GG GG GG GG NA18563 AA GG AG AA AG GG AA AG GG AG GG GG NA18564 NN GG AG AG AG AA AG AG GG AA GG GG NA18566 AA GG AG AA AG NN AA GG NN GG GG GG NA18570 AA GG AA GG AG GG AA AG GG GG GG GG NA18571 AA GG NN AG AG AG AA AA GG GG NN GG NA18572 NN GG AA AA GG GG AA GG GG AA GG GG NA18573 AA GG AG AA AG NN AG AA NN GG GG GG NA18576 AA GG AA AA GG GG AA AG GG NN GG AG NA18577 AA GG GG AA AA AA AG AG GG GG GG AG NA18579 AA GG NN AA GG AG AA AG GG GG GG GG NA18582 AA GG GG AG NN AG AA AA GG GG GG AG NA18592 AA GG GG AG AG NN AA AA AG GG GG AG NA18593 AA GG AG AA GG AG AA AA AG GG GG AG NA18594 NN GG AG AA GG GG AA GG GG GG GG GG NA18603 AA GG GG AA GG AG AA AA GG AG GG AA NA18605 AA GG AA AA GG AG AA AA GG GG GG GG NA18608 AA GG GG AA GG AG AA GG AG GG GG GG NA18609 NN GG AG GG AA AG AG AG GG AG GG GG NA18611 AA GG AG AG AG AG AA AG GG GG NN AG NA18612 AA GG AG GG GG AG AG AG AG AG GG GG NA18620 AA GG GG AA GG AG AA GG GG GG NN GG NA18621 AA GG GG AG AG AA GG NN GG GG GG GG NA18622 AA GG AG AA GG AA AA AA GG GG GG GG NA18623 AA GG NN AG AG NN AA AA GG GG GG AG NA18624 AA GG AG AA AG GG AA AA AG GG AG GG NA18632 NN GG AG AA AG GG AA GG GG GG GG GG NA18633 AA GG GG NN AG NN AA NN GG AG GG GG NA18635 AA GG AG AG AG AA AA NN GG GG GG GG NA18636 AA GG NN AA GG AA AA AA GG AG GG GG NA18637 AA GG AG AA GG AG NN AG NN AG GG GG NA18852 NN AA GG AG NN AG GG AA GG AG AA AG NA18853 AG AG AG AG GG GG GG AG GG GG AG GG NA18854 AA AG AG AG NN AG GG AA GG AG AG GG NA18855 AG AG AG AG GG GG AG GG AG NN AG GG NA18856 AG GG AA GG AG AG AG AA GG GG AG GG NA18857 GG AG AA GG AG GG AG GG GG GG GG GG NA18858 AG GG AG NN GG AG AG NN AG GG AA GG NA18859 AG NN GG AG AA AA GG AA AG AG AA GG NA18860 GG NN AG AA AG AA AG AA NN AG AA GG NA18861 AA AG AG AG AG AG GG AG GG GG NN GG NA18862 AA AG AA GG GG AG AG AA GG GG AA GG NA18863 AA AG AG GG GG GG AG AA GG GG AA GG NA18870 AA GG GG GG GG AG AG AG GG AG AA AG NA18871 AG AG NN GG GG GG AG AA AG AG AG AG NA18872 AG AG GG GG GG GG AG AG GG GG AA AG NA18912 AG AG AG AA GG GG GG GG AA GG GG GG NA18913 AA AG GG AA AG GG GG GG GG GG AG GG NA18914 AA AG GG AG GG GG GG GG AG GG GG GG NA18940 AG GG AG AA AG AG AA AA GG GG AG GG NA18942 AA GG AG AA AG AG AA AG GG GG GG GG NA18943 AA GG AA GG AG NN AG AA GG AG GG GG NA18944 AA GG GG AG GG AG AG AG AG GG GG GG NA18945 AA GG AA GG GG AG AG AG GG NN GG GG NA18947 AA GG NN AA AG AA AA AA AA GG AG GG NA18948 AA GG GG AA GG AG AG AA AG GG AG GG NA18949 AA GG AA GG AG GG AG AA AG AG NN GG NA18951 AA GG GG AA GG AA AG AG GG GG GG GG NA18952 AA GG GG AA AA AG AA AG AG GG GG GG NA18953 AA GG AA AA GG GG AA AA NN AG GG GG NA18956 AA GG AG AG AA AG GG AA GG GG GG GG NA18959 AA GG AG AG GG AG AA AA AG GG GG AG NA18960 AA GG GG AA AG AG AG AA GG AG GG AG NA18961 AA GG NN AG GG AG AA NN GG GG GG GG Clone Chr1tp-21E1 Chr3tp-10A3 Chr5tp-22E4 Chr9tp-2A1 Chr11tp-5D4 Chr12tp-19H4 Chr4tp-23H10 Chr6tp-5C12 Chr4tp-18E9 Chr4tp-10F11 Chr1tp-7D2 Chr15tp-9C6 Chr 135911124644115 Start 203946290 46770243 150080197 41194015 55073652 9451354 69126468 32610887 70153744 190866051 142391276 28279020 End 204141479 46947493 150239374 41282840 55268838 9630395 69296476 32634805 70322413 191064871 142548088 28402108 NA18964 AA GG AG AA AG AA AA AA AG GG GG GG NA18965 AA GG GG AG AG AG AG NN AA GG GG GG NA18966 AA NN GG AA AG AA AA AA GG GG GG GG NA18967 AA GG AG AA GG GG AA AG GG GG GG GG NA18968 AA GG GG GG AA AG AA AG AG GG GG GG NA18969 NN GG GG AA GG AA AA AG GG GG GG GG NA18970 AA GG AG AA GG AG AA AG GG GG GG GG NA18971 AA GG GG AA AG AA AA AG GG AG GG GG NA18972 AA GG GG AG GG AA AA AA AG GG GG GG NA18973 AA GG NN AA GG NN AA AG GG NN GG AA NA18974 AG GG GG AG GG GG NN AA AG GG GG GG NA18975 AA GG GG NN GG AG AA AA GG GG AG GG NA18976 AA GG AG GG GG AG AA GG AG GG GG GG NA18978 AA GG AG GG AG AG AG AG GG GG AG GG NA18980 AA GG AA AA AG AG AA NN GG GG GG GG NA18981 AA GG GG AA GG GG AA AA AG AG GG GG NA18987 AA GG AG AG GG AG AA GG GG GG GG GG NA18990 AA GG AA AG GG AG AA AG GG GG AG AG NA18991 AA GG GG AG NN AA AA AA GG GG GG GG NA18992 AA GG GG AG AA NN AA AA GG GG GG GG NA18994 AA GG AG AA NN GG AA AA GG AA AG GG NA18995 AA GG AA AG GG GG NN GG GG AG NN GG NA18997 AA GG AG AG AA AA AA AA GG GG GG GG NA18998 AA GG AG AA AA AG AA AA AG GG GG GG NA18999 AA GG AG AA AG NN AA NN NN GG GG GG NA19000 AA GG AA NN NN AG AG AA AG GG AG AG NA19003 AA GG GG AA NN NN AG AG GG NN GG GG NA19005 AA GG AG GG NN NN AA NN GG NN AG AG NA19007 AA GG GG AG AG AG AA AA GG AG GG AG NA19012 AA GG AG GG GG AG AA AA GG AG NN GG NA19092 AG AA AG GG GG GG GG GG AG AG AG GG NA19093 AA AG AA AG NN GG GG NN AA AG AA GG NA19094 AA AA AG AG NN GG GG GG AA AG AA GG NA19098 AA AA AA AG GG GG AA AA AG GG AG GG NA19099 AG AA AG AG GG AG GG NN GG AG AG AG NA19100 AA AA AG AG GG GG AG AA GG AG AA GG NA19101 AG AA GG AA AG GG GG GG AG GG AA GG NA19102 AG GG AG AA GG GG AG AA AG GG AA AG NA19103 AG AG NN AA AG GG GG AG AG GG AA GG NA19116 NN GG AG AG NN GG GG GG GG GG GG AG NA19119 AA GG AA AA GG GG AG AG AA GG AG AG NA19120 NN GG AG AG GG NN GG AG AG GG AG GG NA19127 NN AG AA AA GG AG GG AG AG AG AG AG NA19128 AA AA GG GG AG AG GG GG AG GG AA GG NA19129 AA AA AG AG AG AG GG AG AA GG AA GG NA19130 AA AG AA NN AG AG AG AG AG AG AG GG NA19131 AG GG AG AA GG AG GG AG AG GG AA AG NA19132 AA GG AG GG GG AA GG AG AG AG AG AG NA19137 AA AG AA AG AG GG AG AG GG GG GG GG NA19138 AG AG GG AG NN AG GG AG GG GG AA AG NA19139 AA AG AG AG AG AG GG AG GG GG NN GG NA19140 AA AA AA AG AG AA AG AG AG AG NN AG NA19141 GG GG AG AA GG AG GG GG GG AG AG GG NA19142 AG AG AA AG AG NN AG GG GG AG AG AG NA19143 AG AG GG AG AG GG AG GG AG GG GG GG NA19144 AG AA AG AG GG AG GG GG GG GG AA GG NA19145 AG AA GG GG GG GG AG GG AG GG AG GG NA19152 AA AG AG AG AG AG GG GG AG GG NN AG NA19153 AA AG GG AG GG AA GG GG AA AG AG AG NA19154 AG AG GG AG AG AA GG GG AG GG GG AA NA19159 AA AG AA GG GG NN AG AG GG GG AA GG NA19160 AG NN AG NN GG AG AA GG AA AA AA GG NA19161 AG GG AA AA GG AA AA AG AG AG AA GG NA19171 AA AG AA AG GG GG GG GG GG AG AA GG NA19172 AG AG AA GG GG AG AA AA GG AG AA GG NA19173 AG AG AA AG GG GG AG NN NN AG AA GG NA19192 AA AA AA GG GG GG GG AA AG AA AA GG NA19193 GG AA AG AA AG NN GG NN AA GG AA GG NA19194 AG AA AG AG GG GG GG AA GG AG AA GG NA19200 AA AG AA AG GG AA AG AG GG AG GG GG NA19201 AA AG AG NN GG AG GG NN AA AG NN AG NA19202 AA GG AA GG GG AG AG AG AG AG GG AG NA19203 AA AG AG GG NN GG GG AG GG AG AA GG NA19204 NN AA GG AG GG GG NN AA GG AG GG GG NA19205 AA AA AG AG GG GG GG AG GG GG AG GG NA19206 AG AA AA GG GG AG GG GG GG AA AA GG NA19207 AA AA AG AG GG GG GG GG AG AG AG AA NA19208 AA AA AG NN GG AG GG GG AG AA AA AG NA19209 AA AG AA AA AG AG AG GG AG GG GG GG NA19210 NN AG AG AA GG NN GG GG NN AG GG GG NA19211 NN GG AG AA NN GG GG GG AG GG NN GG NA19221 AA AG GG GG AG NN GG GG AG AA AA AG NA19222 AA AA AG GG GG AA GG AG AG AA AA GG NA19223 AG AG GG AA AG AA GG GG AG AG AA AA NA19238 AA AA AG AA GG NN GG AG GG GG AA GG NA19239 NN AG GG GG NN AG AG GG GG AG NN GG NA19240 AA AA AG GG GG AG AG AG GG GG AG GG Clone Chr6tp-2C12 Chr3tp-15F5 Chr4tp-1H7 Chr6tp-11A11 Chr10tp-1H10 Chr16tp-3C5 Chr1tp-23H1 Chr11tp-13E10 Chr17tp-2G12 Chr22tp-8C6 Chr15tp-11F12 Chr1tp-7H5 Chr 6 3 4 6 10 16 1 11 17 22 15 1 Start 143357 192349713 34608481 78947195 20782567 70533845 108504425 58482504 41559185 41225348 32385893 145888591 End 346084 192500458 34779109 79116378 20938614 70708777 108699273 58635415 41734030 41326639 32599374 146093292 NA06985 GG GG NN AG AG AA GG AA NN AG GG AA NA06991 GG GG GG AG AA AA GG AA NN AG GG AG NA06993 GG AG AG AG AG AA GG AA AG AA GG GG NA06994 GG AG AG AA GG AA GG AA AG AA GG AG NA07000 NN GG AG GG NN AA GG AA AA AG GG GG NA07019 AG GG AG AA AG AA GG AA AG AA GG AG NA07022 AG AG AG AG GG AA GG AA GG AA AG AG NA07029 GG GG GG AG AG AA GG AA AA AA GG GG NA07034 GG AA AA GG GG AA GG AA AA AG GG NN NA07048 GG GG AG GG GG AA AG AA AG AA AG GG NA07055 GG GG GG GG GG AA AG AA AG AA AG AG NA07056 GG GG GG AA AG AA GG AA AA AA GG AG NA07345 GG GG GG AG GG AA GG NN AG AA GG GG NA07348 GG AG GG AG GG AA GG AA AG AA GG AG NA07357 AG AG GG AG AG AA GG AA AA AA GG AG NA10830 GG AA AG AG AG AA GG AA AG AG GG AG NA10831 NN AG AG GG GG AA AG AA AG AA GG GG NA10835 AG AG GG AG AG AA GG AA AG NN AG GG NA10838 GG AG AG AG NN AA GG AA AA AA GG GG NA10839 AG NN AG GG GG AA GG AA AG AA GG GG NA10846 GG AG AG AA GG AA AG AA AG AG GG GG NA10847 GG GG NN AG NN AA GG AA GG GG GG GG NA10851 AG AG AG AG GG AA AG AA AA AA AG AG NA10854 GG AA GG GG GG AA AG AA AG AA GG AA NA10855 GG AG AG AG AG AA GG AA NN AA AG NN NA10856 GG GG GG GG GG AA GG AA AA AA GG GG NA10857 GG AA AG GG GG AA GG AA AA GG GG AG NA10859 GG AG AA GG AG AA GG AA GG AA GG GG NA10860 GG AG AA GG GG AA GG AG AG AA GG AG NA10861 GG AG NN GG NN NN AG AA AA AA GG GG NA10863 GG GG AG NN AG AA GG AA AG AG GG GG NA11829 GG AG AG GG GG AA GG AA AA AA AG GG NA11830 GG GG GG AG NN AA GG AA AA AG GG GG NA11831 GG AA AG GG GG AA GG AA AA AA AG GG NA11832 GG GG NN AG AG AA GG AA AG AA NN GG NA11839 GG AG GG GG AG AA GG AA AG AA GG AA NA11840 AG AG GG GG GG AA AA AA AA AA NN AA NA11881 GG AA AG AG AA AA GG AA GG AA GG AG NA11882 AG NN AG AG GG AA GG AA AG AG GG GG NA11992 AG NN AA GG GG AA AG AG AG AA GG GG NA11993 GG AG AG GG GG AA GG AA GG AA GG AG NA11994 AG AG GG GG GG AA GG AA AG AG GG GG NA11995 GG GG GG GG AG AA NN AA NN AA GG AG NA12003 GG AG GG AG GG AA AG AA AA AA GG GG NA12004 GG AG AG GG AG AA GG AA AA AA GG AG NA12005 AA GG AG GG AG AA GG AA GG AA GG GG NA12006 GG GG NN GG NN AA NN AA AG AA NN GG NA12043 AG AG GG GG GG AA AG AA AG AG GG GG NA12044 GG AG AG GG GG AA GG AA AG AG GG AG NA12056 GG AG AG AG AG NN GG AA NN AA AG GG NA12057 AG GG GG GG NN AA AG AA AG AG GG AG NA12144 GG AG AG AG AG AA GG AA GG AG GG NN NA12145 NN GG AG AG GG AA NN AA AA AA GG NN NA12146 GG AG AG NN AG AA AG AA GG NN GG GG NA12154 NN AG NN GG NN AA GG AA AA AG GG AG NA12155 GG GG GG GG AG AA AG AA AG AA GG GG NA12156 GG AG AA GG GG AA AG AA AG AA GG GG NA12234 GG GG GG GG AG AA GG AA GG AA GG GG NA12236 GG AA GG AG GG AA GG AA GG AA GG GG NA12239 GG GG NN GG NN AA GG AA AG AA GG AG NA12248 AG GG GG GG AG AA GG AA AG AA AG GG NA12249 GG AG GG AG GG AA GG AA AA AA NN GG NA12264 GG GG AG AG GG AA GG AA AG NN GG GG NA12707 AA AG AG NN GG AA AG AA GG AG GG GG NA12716 AG NN AG GG GG AA AG AA AA AA AG AG NA12717 AG AA AG GG GG AA AG AA GG AG GG AG NA12740 AG AA GG GG AG AA GG AA AG AA GG GG NA12750 AG AG AG AG AG AA AG AA AA AA GG GG NA12751 GG AG AG GG GG AA NN AA GG AA GG GG NA12752 GG GG AG NN GG AA GG AA AG AA GG GG NA12753 GG GG GG AG NN AA GG AA AG AA GG GG NA12760 GG AG AG GG AG AA GG AA AA AA GG GG NA12761 GG NN GG GG GG AA GG AA GG AA GG GG NA12762 GG GG AG NN GG AA GG AA AG AA GG GG NA12763 AG GG AG GG GG AA GG AA AG AA GG NN NA12801 GG AG GG GG AG AA GG AA AA AA GG GG NA12802 GG GG AG AG GG AA GG AA NN AA GG NN NA12812 AG GG GG GG AG AA GG AA GG AA GG NN NA12813 GG AG GG AG GG AA GG AA AG AA GG GG NA12814 GG GG AG AG GG AA GG AA AA AG GG GG NA12815 GG AG AG GG GG AA NN AA AG AA AG GG NA12864 GG GG GG GG GG AA GG AA AG AA GG GG NA12865 NN NN NN AG NN AA GG AA AG AA GG GG NA12872 GG AG GG GG GG AA GG AA AG AA GG GG NA12873 GG AG AG AG AG AA GG AA AG AA GG GG NA12874 GG GG GG AG AA AA GG AA GG AA GG GG NA12875 GG NN GG AG GG AA GG AA AA AA GG GG NA12878 GG NN AA AG GG AA GG AA GG AA GG GG NA12891 AG NN AG AG AG AA GG AA GG NN GG GG NA12892 GG AG AG GG GG AA GG AA AG AA AG GG NA18500 GG AG NN GG GG AA GG AA AA AA AA GG Clone Chr6tp-2C12 Chr3tp-15F5 Chr4tp-1H7 Chr6tp-11A11 Chr10tp-1H10 Chr16tp-3C5 Chr1tp-23H1 Chr11tp-13E10 Chr17tp-2G12 Chr22tp-8C6 Chr15tp-11F12 Chr1tp-7H5 Chr 6 3 4 6 10 16 1 11 17 22 15 1 Start 143357 192349713 34608481 78947195 20782567 70533845 108504425 58482504 41559185 41225348 32385893 145888591 End 346084 192500458 34779109 79116378 20938614 70708777 108699273 58635415 41734030 41326639 32599374 146093292 NA18501 GG AG GG GG GG AA GG AA AA AG AG GG NA18502 GG GG GG GG GG AA GG AA AA AG AG GG NA18503 NN GG GG AG NN GG GG AA AA AG GG GG NA18504 GG GG GG AG GG AG GG AA AA AA GG GG NA18505 AG GG GG GG GG AG GG AA AA AG GG GG NA18506 AG GG AG GG GG AA GG AA AA AA GG AG NA18507 AG GG GG GG NN AA AG AG AA AA GG GG NA18508 GG GG AG GG GG AG GG AA AA AA GG AG NA18515 GG GG GG GG GG AG AG AG AA AG GG GG NA18516 GG GG GG GG GG AA GG AG AA AA GG GG NA18517 GG GG AG GG GG AG GG AA AA AG GG GG NA18521 GG GG GG GG GG NN GG AA AA GG AA GG NA18522 GG AG AG GG GG AG GG AA AA GG AG GG NA18523 GG GG GG GG GG AA GG AA AA AA AG GG NA18524 AG GG GG GG AA AA GG AA AA AA GG GG NA18526 AG GG GG GG NN AA NN AA AA AA GG AG NA18529 GG GG AA GG GG NN GG AA AA AA GG GG NA18532 AG GG GG GG AA AA AG AA AA AA GG GG NA18537 AA GG GG GG GG AA GG AG AA AA GG GG NA18540 GG GG NN GG AG AA GG AA AA AA GG GG NA18542 GG GG GG GG GG AA GG AA AA AA GG GG NA18545 GG GG GG GG AG AA GG AA AA AA GG AG NA18547 GG NN GG GG AG AA GG AG AA AA GG GG NA18550 GG GG GG GG NN AA GG AA AA AA GG GG NA18552 GG NN GG NN GG AA AG AG AA AG GG GG NA18555 NN GG NN GG GG AA GG AA NN AA GG AG NA18558 GG GG GG GG AG AA GG AA AA NN GG AG NA18561 GG GG GG GG AA AA NN AG AA AG GG GG NA18562 GG GG NN GG NN AA AG AA AA AA NN GG NA18563 AG GG NN GG AG AA NN GG AA AG GG GG NA18564 GG GG GG GG AG AA GG AG AA AG GG GG NA18566 AA GG NN NN AG AA NN AG AA AA NN GG NA18570 GG GG GG GG AA AA GG AA AA AA GG GG NA18571 AG GG GG NN GG AA GG AA AA NN GG GG NA18572 NN GG GG GG AG AA AG AG AA AA GG GG NA18573 AG GG GG GG AG AA GG AA AA AA GG GG NA18576 AG GG NN GG GG AA GG AA AA AA GG AG NA18577 AG GG GG GG GG AA AG AA AA AA GG GG NA18579 AG GG GG GG GG AA AG AA NN AA GG GG NA18582 GG GG NN GG GG AA GG AG AA AG AA GG NA18592 GG NN GG GG GG AA AG AA AA AA GG AG NA18593 AA GG GG GG GG AA GG AA AA AA GG AG NA18594 AG GG GG GG AG AA GG AA AA AA GG AG NA18603 AG GG AG GG GG AA AA AA AA AA GG GG NA18605 GG GG GG GG AA AA GG AG AA AA GG GG NA18608 NN GG GG GG GG AA GG AA AA AA GG AG NA18609 GG GG GG GG GG AA GG AG AA AG GG GG NA18611 GG NN GG GG AG AA GG AA AA AA GG GG NA18612 AG GG GG GG AG AA GG AA AA AA GG GG NA18620 AA NN GG GG GG AA AG AA AA AA AG GG NA18621 GG GG GG GG GG AA GG AG AA AA GG AG NA18622 AG GG GG GG GG AA GG AA AA AA GG GG NA18623 GG GG AG GG GG AA NN AA AA NN GG GG NA18624 AG GG GG GG GG AA AG AA AA AA GG GG NA18632 GG GG GG AG GG AA GG AA AA AA GG GG NA18633 AG GG NN GG AA AA GG AA AA AA GG NN NA18635 GG GG GG GG GG AA GG GG AA AA AG AG NA18636 AG GG GG GG AG AA GG AA AA AA GG GG NA18637 GG GG GG GG GG AA GG AA AA AA AG AG NA18852 GG GG GG AG GG AA GG AA AA AA GG GG NA18853 GG GG GG GG NN AA GG AA AA AG GG GG NA18854 GG GG NN GG GG AA GG AA AA AG GG GG NA18855 GG AG GG GG GG AA GG AA AA AA GG GG NA18856 GG AG GG GG GG AG GG AA AA AA AG AG NA18857 GG AG GG GG GG AA GG AA NN AA GG AG NA18858 GG GG AG GG NN AA GG AA AA NN AG GG NA18859 GG AG GG AG GG AG AG AA AA AG GG GG NA18860 GG GG NN GG GG AG AG AA AA GG AG GG NA18861 GG GG GG GG GG AA GG AA AA AA AG GG NA18862 GG GG GG AG GG AA AG AA AA GG GG GG NA18863 GG GG GG AG GG AA GG AA AA AG AG GG NA18870 GG GG NN GG GG AG GG AA AA NN GG GG NA18871 GG GG NN GG GG AA AG AA AA AA GG GG NA18872 GG GG GG GG GG AA AG AA AA AA GG GG NA18912 GG GG AG GG GG AG GG AA AA AA AG GG NA18913 GG GG GG NN GG AG GG AA AA AG AG AG NA18914 GG GG GG AG GG AA GG AA AA AA AG AG NA18940 GG GG GG GG GG AA GG AA AA GG AG AG NA18942 AG GG GG GG GG AA GG AA AA AA GG GG NA18943 GG GG GG GG GG AA AG AA AA AG GG GG NA18944 GG GG GG AG GG AA GG AA AA AA GG GG NA18945 AG GG GG GG GG AA AG AA NN AG AG GG NA18947 GG GG GG AG GG AA GG AA AA AA GG GG NA18948 AG GG GG GG AG AA AA AA AA AG GG GG NA18949 AA GG NN GG GG AA GG GG AA AA GG AG NA18951 GG GG GG GG GG AA GG AG AA AG AG GG NA18952 GG GG GG GG GG AA GG AA AA AA GG GG NA18953 AA GG GG GG GG AA AG AA AA AA AG GG NA18956 AA GG NN GG GG AA AA AA AA AA GG GG NA18959 GG GG GG GG AG AA GG AG AA AA GG GG NA18960 AG GG AG GG GG AA GG AA AA AA AG GG NA18961 GG GG NN NN GG AA AG AA AA NN GG GG Clone Chr6tp-2C12 Chr3tp-15F5 Chr4tp-1H7 Chr6tp-11A11 Chr10tp-1H10 Chr16tp-3C5 Chr1tp-23H1 Chr11tp-13E10 Chr17tp-2G12 Chr22tp-8C6 Chr15tp-11F12 Chr1tp-7H5 Chr 6 3 4 6 10 16 1 11 17 22 15 1 Start 143357 192349713 34608481 78947195 20782567 70533845 108504425 58482504 41559185 41225348 32385893 145888591 End 346084 192500458 34779109 79116378 20938614 70708777 108699273 58635415 41734030 41326639 32599374 146093292 NA18964 AG GG GG AG GG AA GG AA AA AA GG GG NA18965 GG GG GG AG GG AA NN AA NN AA GG GG NA18966 AG GG GG AG AG AA GG AA AA AG GG GG NA18967 AG GG GG GG GG AA GG AA AA AG GG GG NA18968 GG GG NN GG GG NN GG AG NN AA AG AG NA18969 GG GG NN GG GG AA GG AA AA AG GG GG NA18970 AG GG GG GG GG AA AG AA AA AA GG GG NA18971 AG GG GG GG GG AA GG AA AA AA NN GG NA18972 GG GG GG GG GG AA GG AA AA AG GG NN NA18973 GG GG GG GG GG NN GG AA AA AG GG GG NA18974 NN GG GG GG GG AA GG AA AA AA GG GG NA18975 GG GG AG GG GG AA GG AA AA AA AG GG NA18976 GG GG GG GG GG AA GG AA AA GG GG GG NA18978 GG GG GG GG GG AA GG AA AA AG GG AA NA18980 GG GG GG GG AG AA AG AA AA AG GG AG NA18981 GG GG GG GG AG AA GG AA AA AG GG GG NA18987 AG GG GG AG GG AA GG AA AA NN GG GG NA18990 AG GG NN GG GG AA AG AA AA AA GG GG NA18991 NN GG GG GG GG AA GG AG AA AG AG GG NA18992 AG GG GG GG GG AA AG AG AA AG GG GG NA18994 GG GG GG GG GG AA GG AA AA AA GG GG NA18995 GG GG GG AG AG AA GG AA AA AG GG GG NA18997 GG GG NN GG NN AA GG AG AA AG GG AG NA18998 AG GG GG AA GG AA AG AA AA AA GG GG NA18999 AA GG GG GG GG AA GG AA AA NN GG GG NA19000 AG GG GG AG NN AA GG AA AA AA GG AG NA19003 AA GG GG GG NN AA AG AG AA GG GG NN NA19005 GG NN GG GG GG AA AG AA AA AA AG AG NA19007 GG GG GG GG GG AA GG AA AA AG GG AG NA19012 AG NN GG GG GG AA AG AA AA AA NN GG NA19092 GG GG NN GG GG AA GG AA AA AA GG GG NA19093 GG GG AG GG GG AA GG AA AA AA AG GG NA19094 GG GG GG GG GG AA GG AA AA AA AG GG NA19098 GG GG NN GG GG AA GG AG AA AG GG GG NA19099 GG GG GG GG GG AG GG AA AA AG GG AA NA19100 GG GG AG GG GG AA GG AG AA AG GG AG NA19101 GG AA GG GG GG AA GG AA AA AA GG AG NA19102 GG GG GG GG GG AG GG AA AA AG GG AG NA19103 GG AG GG GG GG AG GG AA AA AA GG AG NA19116 GG GG GG NN GG AA GG AA AA AG GG GG NA19119 GG GG GG NN GG AA GG AG AA AA GG GG NA19120 GG GG GG GG GG AA GG AA AA AA GG GG NA19127 GG GG GG GG GG AA GG AA AA AA GG GG NA19128 GG AG GG GG GG AA GG AG AA AA GG GG NA19129 GG GG GG GG GG AA GG AA AA AA GG GG NA19130 GG GG GG GG GG AA GG AA AA NN GG GG NA19131 GG GG AG GG GG AA AG AG AA AA GG GG NA19132 GG GG AG GG GG AA AG AA AA AG GG GG NA19137 GG GG GG GG GG AA GG AG AA AA GG GG NA19138 GG GG GG GG GG AA GG AA AA AA GG GG NA19139 GG GG GG GG GG AA GG AA AA AA GG GG NA19140 GG GG GG GG AG AA AG AA AA AA GG GG NA19141 NN AG GG GG GG AG GG AA AA AG GG GG NA19142 AG AG GG GG AG AG GG AA AA NN GG AG NA19143 GG GG GG GG GG AA GG AA AA AA GG GG NA19144 GG GG AG GG GG AA GG AG AA AA AA GG NA19145 GG GG GG GG GG AA GG AG AA AA AG GG NA19152 AG GG GG GG GG AA GG AA AA AG GG GG NA19153 GG GG NN GG GG AA GG AA AA AA GG GG NA19154 AG GG GG GG GG AA GG AA AA AG GG GG NA19159 GG AG GG GG GG AG GG AA AA AA GG GG NA19160 GG GG NN GG GG AA GG AA AA AA GG GG NA19161 GG AG GG GG GG AG GG AA AA AA GG GG NA19171 AG GG GG AG GG AA GG AA AA AG NN GG NA19172 GG AG GG GG GG NN GG AA AA AG GG GG NA19173 AG AG GG GG GG AG GG AA AA AG AG GG NA19192 GG GG GG GG GG AG GG AA AA NN GG GG NA19193 GG AG AG GG GG AA GG AG AA AA NN GG NA19194 GG AG GG GG GG AG GG AG AA AA GG GG NA19200 GG GG AA GG GG AA GG AA AA AG GG AG NA19201 GG GG GG GG GG AA NN AA AA AA GG GG NA19202 GG GG AG GG GG AA GG AA AA AG NN GG NA19203 GG GG AG GG GG AA GG AA AA AA AG GG NA19204 GG GG GG GG GG AA NN AG AA AA AG GG NA19205 GG GG GG GG GG AA NN AA AA AA AG GG NA19206 AG GG AG GG GG AA GG AG AA AA GG GG NA19207 GG GG GG GG NN AA GG AA AA AA GG GG NA19208 GG GG AG GG GG AA GG AG AA AA GG GG NA19209 GG GG GG NN GG AG AG AA AA AA AG AG NA19210 GG GG GG AG GG AA GG AA AA AG GG GG NA19211 GG GG GG AG GG AA NN AA AA AA GG GG NA19221 GG GG GG GG GG GG GG AA AA AA GG GG NA19222 GG GG AG GG GG AG GG AA AA AA GG GG NA19223 GG GG GG GG GG AG GG AA AA AG GG GG NA19238 GG GG GG GG GG NN NN AA AA AA AG GG NA19239 NN AG GG GG GG AA GG AA AA AA AG GG NA19240 GG GG GG GG NN AG GG AA AA AA GG GG Supplementary Table7B: CNV genotypes from 500K EA data CNPID 37 70 133 214 228 268 293 302 391 418 421 chr11233444666 start 112407136 192669983 89740700 131233075 163700474 34588263 116506964 153149138 29967224 77496587 81332831 end 112421327 192672977 91212000 131291453 163709523 34663930 116533117 153152305 29982554 77529522 81357777 NA06985 AG GG GG AG NN AG GG GG GG GG GG NA06991 AG AG AG AG GG GG GG GG GG GG AG NA06993 GG NN AG AG NN AG GG GG GG GG AG NA06994 GG GG GG GG GG AG GG GG GG AG AG NA07000 GG GG GG AG GG AG GG AG GG GG GG NA07019 AG AG GG AG GG AG GG GG GG AG AG NA07022 AG GG GG AG GG AG GG GG GG GG AG NA07029 GG GG GG GG NN GG GG GG GG GG AG NA07034 GG GG GG AG GG AA GG GG AG AG AG NA07048 GG GG GG GG GG AG GG GG GG AG AG NA07055 GG AG GG GG NN GG GG GG GG GG GG NA07056 GG AA GG AG GG GG GG GG GG AA GG NA07345 AG GG AG AG GG GG GG GG GG AA GG NA07348 AG GG GG AA GG GG GG GG AG AG GG NA07357 GG GG GG AG GG GG GG GG AG GG GG NA10830 GG AG GG GG GG AG GG GG GG GG GG NA10831 AG GG AG AG GG AG GG GG GG GG GG NA10835 AA AG AG GG GG GG GG GG AG GG GG NA10838 GG GG GG AA GG AG GG GG NN GG AG NA10839 AG GG AG AG GG AG AG GG GG AG GG NA10846 GG AG GG AG NN AG GG GG GG AG GG NA10847 AG NN GG AG GG AG GG GG GG GG GG NA10851 AG GG GG AG GG AG GG GG AG AG GG NA10854 AA AG GG AA GG GG GG GG GG AG GG NA10855 GG AG GG GG GG AG AG GG GG GG GG NA10856 GG AG GG AG GG GG GG GG GG AG GG NA10857 AG AG GG AG GG NN GG GG GG AG GG NA10859 GG GG GG AG GG AA GG GG GG AA GG NA10860 AG AA GG AG GG AA GG GG GG GG GG NA10861 GG GG GG NN GG GG GG GG GG GG GG NA10863 GG AG GG GG GG GG GG GG GG AG AA NA11829 AG AA GG GG GG AG GG GG GG GG GG NA11830 GG GG GG AG GG GG GG AG GG AA GG NA11831 GG AG GG AG NN AG GG GG GG GG GG NA11832 GG GG GG GG GG AA AG GG GG GG GG NA11839 AG GG GG AG GG GG GG GG GG AA GG NA11840 AG AA GG AA GG GG GG GG GG AG GG NA11881 GG GG GG AG GG AG GG GG GG AG GG NA11882 GG GG GG AG GG AG GG GG GG AG GG NA11992 AG AG GG AA GG AA GG GG GG GG GG NA11993 AG AG GG GG GG AG GG GG GG GG GG NA11994 AG GG GG AG GG GG GG GG GG GG GG NA11995 NN GG GG GG GG GG GG GG GG AG GG NA12003 GG AG GG AA GG GG GG GG GG GG AG NA12004 GG NN GG AA NN AG AG GG AG AG GG NA12005 AG AG GG AG GG AG AG GG GG GG GG NA12006 AG GG GG AG GG AG GG GG GG AG GG NA12043 AG AG GG AG GG GG GG GG GG GG GG NA12044 AG AG AG AG GG AG GG GG GG AA GG NA12056 AG GG GG AG GG AG GG GG AG AG GG NA12057 AG GG GG GG GG GG GG GG GG GG GG NA12144 GG AG GG GG GG AG GG GG GG AG GG NA12145 GG GG GG AG GG AG AG GG GG GG GG NA12146 NN NN GG GG GG AG GG GG GG AG GG NA12154 GG GG GG GG GG AG AG GG GG GG GG NA12155 AG GG GG AG GG GG AG GG GG AG GG NA12156 AG GG GG AG GG AA GG GG GG GG GG NA12234 GG AA GG GG GG GG AG GG GG AG AG NA12236 GG NN GG GG GG GG GG GG GG GG GG NA12239 GG GG GG AG GG GG GG GG GG AG GG NA12248 AA AA NN GG GG GG GG GG AA GG GG NA12249 AG AG GG GG GG GG GG GG GG GG GG NA12264 GG GG GG GG NN AG GG GG GG GG AG NA12707 GG GG GG AG GG GG GG GG GG GG GG NA12716 AG GG GG AG GG AG GG GG GG AG GG NA12717 GG GG AG AG GG AG GG GG GG AG GG NA12740 GG GG GG GG GG GG GG GG GG GG GG NA12750 AG GG GG AG GG AG GG AG GG GG AG NA12751 GG GG AG AG GG AG GG GG GG GG NN NA12752 NN AA GG AA GG AG GG GG AA GG GG NA12753 GG AG GG AG GG GG GG GG GG GG GG NA12760 NN GG GG AG GG GG GG GG AA GG GG NA12761 AA NN GG AA GG GG GG GG AG GG GG NA12762 GG GG GG AG GG AG GG GG GG AG AG NA12763 AG AG GG GG NN AG GG GG GG GG GG NA12801 AA GG GG GG GG GG GG AG GG GG GG NA12802 AG GG AG GG GG AG GG AG AG AA GG NA12812 NN AG GG GG GG GG GG AG GG GG GG NA12813 AG GG GG GG GG GG GG GG AG GG GG NA12814 GG AG AG AG GG AG GG GG GG AG GG NA12815 AA GG GG GG GG AG GG AG AG AA GG NA12864 AG AG GG AA GG GG GG GG AG GG GG NA12865 AG GG AG GG GG GG GG GG AA AG GG NA12872 GG GG GG AG GG GG GG GG GG GG GG NA12873 NN AG GG AA GG AG AG GG AG GG GG NA12874 AG NN GG GG GG GG GG GG AG AG GG NA12875 GG AG NN AG GG GG GG GG AG GG GG NA12878 GG GG GG AA GG AA NN GG GG GG GG NA12891 GG AG GG AG GG NN GG GG AG GG GG NA12892 GG GG GG AA GG AG AG AG GG GG GG NA18500 GG GG AA GG NN GG GG GG GG GG GG CNPID 37 70 133 214 228 268 293 302 391 418 421 chr11233444666 start 112407136 192669983 89740700 131233075 163700474 34588263 116506964 153149138 29967224 77496587 81332831 end 112421327 192672977 91212000 131291453 163709523 34663930 116533117 153152305 29982554 77529522 81357777 NA18501 GG GG AG AG GG GG GG GG GG GG GG NA18502 GG GG AG GG GG GG GG GG AG GG GG NA18503 GG GG AG AG NN GG GG GG GG GG GG NA18504 GG GG GG AA NN GG GG GG GG GG GG NA18505 GG GG AA GG GG GG GG GG GG GG 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AG GG GG GG GG GG GG AA NA19210 GG GG GG GG GG AG GG GG GG GG AA NA19211 GG GG GG AG GG GG GG GG GG GG AA NA19221 GG GG GG GG GG AG GG AG GG GG AG NA19222 GG GG GG GG GG AG GG GG GG GG AA NA19223 GG GG GG GG GG GG GG AG GG GG AG NA19238 GG GG GG GG GG GG GG GG GG GG AG NA19239 GG GG GG AG GG GG GG GG GG GG GG NA19240 NN GG GG NN GG GG GG GG GG GG GG CNPID 901 1015 1034 1082 1084 1100 1104 1122 1153 chr 14 16 16 18 18 19 19 19 21 start 40684005 22466298 79536934 63111650 64888576 40350568 48362435 59944016 22577771 end 40706033 22612021 79544102 63119574 64903434 40364911 48481823 60040503 22586139 NA06985 GG GG GG GG GG NN GG GG GG NA06991 AG GG GG GG GG GG GG GG GG NA06993 AG GG GG GG GG GG NN GG GG NA06994 GG GG GG GG AG GG GG GG GG NA07000 GG GG AG GG GG GG GG GG GG NA07019 GG GG GG GG GG AG GG GG GG NA07022 GG GG GG GG GG GG GG GG GG NA07029 GG GG AG GG AG GG GG GG GG NA07034 GG GG GG GG GG GG GG GG GG NA07048 AG GG GG GG GG GG GG GG GG NA07055 AG GG GG GG GG GG AG GG AG NA07056 GG NN GG GG GG NN GG GG GG NA07345 GG GG GG GG GG GG AG GG GG NA07348 GG GG GG GG GG GG AG GG GG NA07357 GG GG GG GG GG GG GG GG GG NA10830 GG GG AG GG GG GG GG GG GG NA10831 GG GG GG GG GG GG NN GG GG NA10835 AA NN AG GG GG GG GG GG GG NA10838 AG AG GG GG GG NN GG GG GG NA10839 AG GG GG GG GG GG GG GG GG NA10846 AG GG GG GG GG GG GG GG AG NA10847 GG GG GG GG GG GG GG GG GG NA10851 GG AG GG GG GG GG AG GG GG NA10854 GG AG GG GG GG GG GG GG GG NA10855 GG AG GG GG GG GG GG GG GG NA10856 GG AG GG GG GG GG GG GG GG NA10857 AG AG GG GG GG GG GG GG GG NA10859 AG GG GG GG GG GG GG NN GG NA10860 AA GG GG GG GG GG GG GG GG NA10861 NN GG GG NN GG GG AG GG GG NA10863 GG AG GG GG GG NN GG GG GG NA11829 AG GG GG GG GG GG GG GG GG NA11830 GG AG GG GG GG GG GG GG GG NA11831 GG GG GG GG GG GG AG GG GG NA11832 AG AA GG GG GG GG GG GG GG NA11839 GG AG GG GG GG GG GG GG GG NA11840 GG AA GG GG GG GG NN GG GG NA11881 GG GG GG GG GG AG GG GG GG NA11882 AG GG GG GG GG GG GG GG GG NA11992 AG GG GG GG GG GG AG GG GG NA11993 AA GG GG GG GG GG GG GG GG NA11994 AG GG GG GG GG NN GG GG GG NA11995 AG GG GG GG GG GG GG GG GG NA12003 GG NN GG GG GG NN AG GG AG NA12004 AG AG GG GG GG AG GG GG GG NA12005 GG GG GG GG GG GG GG GG GG NA12006 AG GG GG GG GG GG NN GG GG NA12043 AG AG GG GG GG GG NN GG GG NA12044 GG GG GG GG GG GG GG GG GG NA12056 AG AG GG GG GG GG AG GG GG NA12057 GG GG GG GG GG GG NN GG GG NA12144 AG GG GG GG GG GG NN GG GG NA12145 GG GG GG GG GG NN GG GG AA NA12146 GG GG GG GG GG GG GG GG GG NA12154 AG AG AG GG GG GG GG GG GG NA12155 GG GG GG AG GG GG AG GG GG NA12156 GG GG GG GG GG GG GG GG GG NA12234 GG AG GG GG GG AG GG GG GG NA12236 GG GG AG GG GG GG GG GG GG NA12239 GG GG GG GG GG GG GG GG GG NA12248 AG AA AA GG GG GG GG GG GG NA12249 AG GG GG GG GG GG GG GG GG NA12264 GG AG GG GG GG GG GG GG GG NA12707 GG GG GG GG GG GG AG GG GG NA12716 GG AA AG GG GG GG GG GG GG NA12717 GG GG GG GG GG GG GG GG GG NA12740 AG AG GG GG GG GG GG GG GG NA12750 GG AG GG GG GG GG GG GG GG NA12751 AG GG GG GG GG GG GG GG GG NA12752 AA GG GG GG GG AG GG GG GG NA12753 GG GG GG GG GG AA GG GG GG NA12760 AA NN GG GG GG GG AG GG GG NA12761 AA GG GG GG GG GG GG GG GG NA12762 GG AG GG GG GG NN GG GG GG NA12763 AG GG GG GG GG AG GG GG GG NA12801 AG AG AG GG GG AG GG GG GG NA12802 GG GG GG GG GG GG GG GG GG NA12812 GG NN GG GG GG AG GG GG GG NA12813 AG GG AG GG GG AG AG GG AG NA12814 GG GG GG GG AG GG GG GG GG NA12815 GG GG AG GG GG GG GG GG GG NA12864 AG GG GG GG GG GG AG GG GG NA12865 AG GG GG GG GG GG GG GG GG NA12872 AG GG GG GG GG GG AG GG GG NA12873 GG GG GG GG GG GG AG GG GG NA12874 GG GG GG GG GG GG GG GG GG NA12875 AG GG GG GG GG GG AG GG GG NA12878 GG GG GG GG GG AG GG GG GG NA12891 GG GG GG GG GG NN AG GG GG NA12892 GG GG GG GG GG GG GG GG GG NA18500 GG GG GG GG GG GG AG GG GG CNPID 901 1015 1034 1082 1084 1100 1104 1122 1153 chr 14 16 16 18 18 19 19 19 21 start 40684005 22466298 79536934 63111650 64888576 40350568 48362435 59944016 22577771 end 40706033 22612021 79544102 63119574 64903434 40364911 48481823 60040503 22586139 NA18501 GG GG GG GG GG GG AG GG GG NA18502 GG AG GG GG GG GG GG GG GG NA18503 GG GG GG GG GG GG AG GG GG NA18504 GG GG GG GG GG GG GG GG GG NA18505 GG GG GG NN GG GG AG GG GG NA18506 GG NN GG GG GG GG GG GG GG NA18507 GG NN GG GG GG GG AG GG GG NA18508 GG GG GG AG GG NN AG GG GG NA18515 GG GG AG GG GG GG GG GG GG NA18516 GG GG AG GG GG GG GG GG GG NA18517 GG GG GG GG GG GG GG GG GG NA18521 GG GG GG GG GG GG AG AG GG NA18522 GG GG GG GG GG GG AG AG GG NA18523 GG GG GG GG GG GG GG GG GG NA18524 GG GG GG AG GG GG AG GG AA NA18526 GG GG GG AG GG AG AG GG AA NA18529 GG AG GG AG GG GG AG GG AG NA18532 GG GG GG GG GG GG AG GG NN NA18537 GG AG AG GG GG GG AG AG GG NA18540 AG GG GG AG GG GG AG GG GG NA18542 GG NN GG AG GG GG AG GG AA NA18545 GG GG GG AG GG AG AG GG GG NA18547 GG AG GG GG GG GG AG GG GG NA18550 GG AG GG AG GG GG AG GG AG NA18552 GG GG GG GG GG NN AG GG AA NA18555 GG AA GG AG AG GG GG GG AG NA18558 GG GG GG GG GG GG GG GG AA NA18561 GG AG AG AG AG GG AA GG AG NA18562 GG GG GG NN GG GG AG GG GG NA18563 GG GG GG GG AG GG AA GG AA NA18564 AG AA GG GG GG GG AG GG GG NA18566 GG AG GG AG GG GG AA GG AG NA18570 GG GG GG GG GG GG AG GG GG NA18571 GG GG GG AG GG GG AG GG GG NA18572 GG AG GG AG GG GG GG GG AA NA18573 GG GG GG AG GG GG AG AG AG NA18576 GG AG GG AG GG GG GG GG GG NA18577 AG AA GG NN AG AG GG GG AA NA18579 GG AG GG GG AG GG AG GG GG NA18582 GG AG GG GG GG GG AG GG GG NA18592 AG GG GG GG GG GG AG AG AG NA18593 GG GG GG AG GG GG AG GG GG NA18594 GG GG GG AG GG AG GG GG AG NA18603 GG AG AG GG GG NN AG GG AA NA18605 AG AG AG GG GG GG AG GG GG NA18608 GG GG GG GG GG GG AG GG GG NA18609 GG GG GG NN GG GG AA AG AG NA18611 GG AG GG AG GG NN AG GG GG NA18612 GG GG GG GG GG GG GG GG GG NA18620 GG AG AG GG GG GG AG GG GG NA18621 GG AG GG GG GG GG AA GG AA NA18622 GG AG GG GG GG AG AA GG AG NA18623 GG GG GG GG GG NN AG GG AA NA18624 GG GG AG GG GG GG AG GG AG NA18632 GG AG GG AG GG NN AG GG AA NA18633 AG GG GG GG GG GG AA GG GG NA18635 GG GG AG AG GG GG GG GG GG NA18636 AG GG GG GG AG GG GG GG AA NA18637 GG GG GG GG GG GG AG GG GG NA18852 GG GG GG AG GG GG AG GG GG NA18853 GG AG GG AG GG GG AG GG GG NA18854 GG NN GG NN GG GG AG GG GG NA18855 GG GG AG AG GG GG GG GG GG NA18856 GG NN GG GG GG GG AG AG GG NA18857 GG GG GG GG GG GG AG AG GG NA18858 GG GG GG GG GG GG AG GG GG NA18859 GG NN GG GG GG GG AG GG GG NA18860 GG GG AG GG GG GG GG NN GG NA18861 GG NN GG GG GG GG GG GG GG NA18862 GG GG GG GG GG GG AG GG GG NA18863 GG NN GG GG GG GG NN GG GG NA18870 GG GG GG GG GG GG GG GG GG NA18871 GG GG GG NN GG GG AG GG GG NA18872 GG GG GG AG GG GG AG GG GG NA18912 GG GG GG AG GG GG GG AG GG NA18913 GG GG GG GG GG GG GG GG GG NA18914 GG GG GG AG GG GG NN AG GG NA18940 AG GG AG GG GG AG AG GG AG NA18942 GG AG GG GG AG GG AG GG GG NA18943 GG GG GG GG AG GG AG GG GG NA18944 GG AG GG GG GG GG AA GG AG NA18945 GG GG GG AG GG GG AG GG AG NA18947 GG AG GG AG GG GG GG GG AA NA18948 GG GG GG GG AG AG AG GG AG NA18949 AG AA GG GG GG GG GG GG AG NA18951 AG AG GG GG AG GG AG GG AG NA18952 GG AA GG GG GG AG AG GG GG NA18953 GG GG GG GG AG GG GG GG AA NA18956 GG AG GG GG GG GG GG GG GG NA18959 AG GG GG GG GG GG AA GG GG NA18960 AG AG AG AG GG GG AG GG GG NA18961 AG GG GG AG AG GG GG GG AG CNPID 901 1015 1034 1082 1084 1100 1104 1122 1153 chr 14 16 16 18 18 19 19 19 21 start 40684005 22466298 79536934 63111650 64888576 40350568 48362435 59944016 22577771 end 40706033 22612021 79544102 63119574 64903434 40364911 48481823 60040503 22586139 NA18964 GG GG AG AG AA GG AA GG GG NA18965 AA AG GG GG GG GG AG GG AA NA18966 GG AA AG GG AG AG AA GG AG NA18967 GG GG AG GG AG AG AG GG GG NA18968 GG AG GG AG AG GG AA GG AG NA18969 GG GG GG AG GG AG AG GG AG NA18970 GG GG GG GG GG GG AG GG AA NA18971 AG AA GG NN GG GG AG GG AG NA18972 GG GG GG AG AG GG GG GG AA NA18973 GG GG GG GG GG GG AA GG AA NA18974 GG NN AG GG GG GG AG GG AG NA18975 GG AG GG AG GG GG GG GG AG NA18976 GG GG GG AG AA GG AA GG AA NA18978 GG GG AG GG AG AG GG GG AG NA18980 GG GG GG AG AG GG AA GG GG NA18981 GG NN AG GG AG GG GG GG AG NA18987 GG AG GG GG AG AG AG GG AG NA18990 GG AG AG AG GG GG GG GG AG NA18991 GG GG GG GG GG AG GG GG AG NA18992 GG AG GG GG GG GG AG GG GG NA18994 GG AG AG GG AG GG GG GG AG NA18995 GG AG GG AG GG GG AG GG AG NA18997 GG GG GG GG AG GG AG GG GG NA18998 AG AG GG AG AG GG GG GG GG NA18999 GG GG GG AG GG AG AG GG AG NA19000 GG AA GG AG GG GG AG GG AA NA19003 AG GG GG GG GG AG GG GG AG NA19005 GG GG GG AG AG GG AG GG GG NA19007 AG AG GG AG AG GG AA GG AG NA19012 GG GG GG GG AG GG GG GG AG NA19092 GG GG GG GG GG GG AG GG GG NA19093 GG GG AG AG GG GG GG GG GG NA19094 GG NN AG GG GG GG AG GG GG NA19098 GG GG GG GG GG GG AG GG GG NA19099 GG GG GG GG GG AG GG GG GG NA19100 GG GG GG GG GG GG AG GG GG NA19101 GG GG GG GG GG GG GG GG GG NA19102 GG NN GG GG GG GG GG GG GG NA19103 GG GG GG GG GG GG AG GG GG NA19116 GG GG GG AG GG GG GG GG GG NA19119 GG GG GG GG GG GG NN AG GG NA19120 GG GG GG GG GG GG AG GG GG NA19127 GG GG GG GG GG NN GG GG GG NA19128 GG GG GG GG GG GG GG AG GG NA19129 GG GG GG GG GG NN GG GG GG NA19130 GG GG GG AG GG GG GG GG GG NA19131 GG AG GG GG GG GG AG GG GG NA19132 GG GG GG GG GG GG AG GG GG NA19137 GG GG GG AG GG GG GG AA GG NA19138 GG NN GG GG GG GG GG GG GG NA19139 GG GG GG AG GG GG GG AG GG NA19140 GG NN GG GG GG GG AG GG GG NA19141 GG NN NN GG GG GG GG AG GG NA19142 GG NN GG GG GG GG GG AG GG NA19143 GG GG AG GG GG GG GG AG GG NA19144 GG GG GG GG GG GG NN GG GG NA19145 GG GG AG GG GG GG NN GG GG NA19152 GG GG GG AG GG GG GG GG GG NA19153 GG GG GG GG GG GG GG GG GG NA19154 GG GG GG GG GG GG NN GG GG NA19159 GG GG GG GG GG GG GG GG GG NA19160 GG GG GG AG GG GG GG GG GG NA19161 GG GG GG AG GG GG GG GG GG NA19171 GG GG GG GG GG GG GG GG GG NA19172 GG NN GG GG GG GG AG GG GG NA19173 GG GG GG GG GG GG GG GG GG NA19192 GG GG GG GG GG GG NN GG GG NA19193 GG GG GG GG GG GG AG AG GG NA19194 GG GG GG GG GG GG AG AG GG NA19200 GG GG GG GG GG GG AG GG GG NA19201 GG GG GG AG GG NN AG GG GG NA19202 GG GG GG AG GG GG AG GG GG NA19203 GG GG GG GG GG GG GG GG GG NA19204 GG GG GG GG GG GG AG AG GG NA19205 GG GG GG GG GG GG AG AG GG NA19206 GG GG GG AG GG GG AG GG GG NA19207 GG GG GG GG GG GG GG GG GG NA19208 GG GG GG GG GG GG NN GG GG NA19209 GG NN GG GG GG GG GG GG GG NA19210 GG NN GG GG GG GG GG GG GG NA19211 GG NN GG GG GG GG NN GG GG NA19221 GG GG GG AG GG GG AG GG GG NA19222 GG GG GG AG GG GG AG GG GG NA19223 GG GG GG GG GG GG AG GG GG NA19238 GG GG GG NN GG GG AG AG GG NA19239 GG GG GG GG GG GG NN GG GG NA19240 GG GG GG NN GG GG AG AG GG

Supplementary Table 7: CNV genotypes for 67 nonedundant, biallelic CNVs with a MAF >5%. In each case, the group with the lowest log2 ratio is classified as AA, and the group with the highest log2 ratio is classified as GG. NN indicates no genotype was determined. For CNVs genotyped using WGTP data, genotypes were generated for the reference individual (NA10851) by adding a log2 ratio of zero for this individual into each clustering.

Supplementary Table 8. Summary statistics for CNVRs called from the WGTP and 500K EA platforms.

WGTP 500K EA Total # of unique CNVs 913 980

# of Singletons 440 506 Genome coverage of unique 319Mb 163Mb CNVs Average size 350kb 166kb

Median size 228kb 63kb

Total number of CNVs in 18,735 6,458 HapMap CNVs per person 70 24

Total size of CNVs in HapMap 6,391Mb 1,329Mb

Size per person 23.7Mb 4.9Mb

Supplemental Table 11A: CNV regions from WGTP

overlap with chr start end freq 500K EA WGTP 1 377 1038212 175 yes WGTP 1 1239243 1359795 1 WGTP 1 1409796 2056500 20 yes WGTP 1 2408416 2412411 1 WGTP 1 3312095 3572010 1 WGTP 1 5200140 5470944 1 WGTP 1 8822507 8850906 1 WGTP 1 10172336 10516820 3 WGTP 1 10676768 10989413 12 WGTP 1 12533434 13622361 40 yes WGTP 1 16509639 17229287 102 yes WGTP 1 21481490 21687720 2 WGTP 1 21967827 22158163 1 WGTP 1 31391233 32025943 1 yes WGTP 1 36289232 36556181 1 WGTP 1 39894236 40329525 1 WGTP 1 52838036 53001202 1 WGTP 1 53630573 53741257 20 WGTP 1 64389169 64488417 1 WGTP 1 72454417 72598834 17 WGTP 1 72893633 73019191 1 WGTP 1 73325120 73487705 1 WGTP 1 75698925 75899769 1 yes WGTP 1 83040583 83720332 19 yes WGTP 1 89124089 89272744 27 WGTP 1 90532013 90695320 98 WGTP 1 96127772 96258135 1 WGTP 1 100071676 100210363 1 WGTP 1 103702380 104164023 175 WGTP 1 106472604 106593624 1 yes WGTP 1 107195670 107552925 1 yes WGTP 1 108330916 108808720 113 WGTP 1 112869177 116453414 3 yes WGTP 1 116876957 116986717 56 WGTP 1 119728738 119926619 3 yes WGTP 1 119979355 120958392 99 WGTP 1 141387477 142972397 166 yes WGTP 1 143117214 143257561 1 yes WGTP 1 143352668 143922358 6 yes WGTP 1 144800023 146803586 211 yes WGTP 1 149285912 149711226 138 yes WGTP 1 151908051 152127880 5 WGTP 1 158219386 158356094 55 yes WGTP 1 158807806 159235014 1 yes WGTP 1 163223537 163382643 1 yes WGTP 1 166513664 166616844 116 WGTP 1 170542299 170687600 1 WGTP 1 171200938 171301433 1 WGTP 1 185978190 186380985 5 yes WGTP 1 191987584 192311869 1 WGTP 1 192535421 192851111 1 yes WGTP 1 193322494 193693459 59 yes WGTP 1 193709456 193901429 1 yes WGTP 1 199299046 199455863 1 WGTP 1 203946290 204313462 6 WGTP 1 209036538 209231498 1 WGTP 1 218684362 218846708 5 overlap with chr start end freq 500K EA WGTP 1 220241955 220669898 6 WGTP 1 221394659 221560009 1 WGTP 1 221711686 221833513 69 WGTP 1 227931495 228222731 2 yes WGTP 1 231180061 231434698 13 WGTP 1 234267835 235094143 1 yes WGTP 1 236092135 236715545 1 yes WGTP 1 242733187 243066985 3 WGTP 1 244040626 244603187 6 yes WGTP 1 244826150 245191415 59 yes WGTP 2 157949 915588 2 yes WGTP 2 1866728 2035145 2 WGTP 2 5448267 5618952 3 WGTP 2 13234898 13698420 5 WGTP 2 15152787 15308457 1 WGTP 2 22725791 23031671 190 WGTP 2 27972987 28136281 1 WGTP 2 29265918 30451080 1 yes WGTP 2 35149394 35316635 1 WGTP 2 35775617 36031232 11 WGTP 2 36155103 36502309 1 yes WGTP 2 37708305 38050590 4 yes WGTP 2 40459598 40645427 1 WGTP 2 46444463 46785802 1 yes WGTP 2 51193365 51277533 1 WGTP 2 52639031 52726188 1 WGTP 2 55658890 55892725 3 WGTP 2 56090090 56384045 1 WGTP 2 56571336 56762849 1 yes WGTP 2 57196182 57400047 1 yes WGTP 2 58309948 61194391 1 yes WGTP 2 64164656 64451207 2 yes WGTP 2 66240707 66411516 1 WGTP 2 67198930 67377313 1 yes WGTP 2 73628687 73990247 6 WGTP 2 74391579 74674080 29 WGTP 2 75601060 75924478 3 yes WGTP 2 76453575 76617009 3 WGTP 2 77766753 78013206 2 yes WGTP 2 78038044 78622687 2 yes WGTP 2 80312976 80754119 8 WGTP 2 83160508 83876420 1 yes WGTP 2 84643112 84795200 1 WGTP 2 87067570 87881342 28 yes WGTP 2 91016978 91677266 20 yes WGTP 2 94840283 95041982 1 yes WGTP 2 95392012 95574433 1 WGTP 2 96992983 97795025 10 yes WGTP 2 99839409 100005193 7 WGTP 2 104052123 104218620 1 WGTP 2 107056558 107220149 1 WGTP 2 107908395 108437172 2 yes WGTP 2 110050731 110558272 2 yes WGTP 2 111616014 112463168 26 WGTP 2 113791179 113970010 2 WGTP 2 113970010 114144908 1 WGTP 2 116238026 116516523 1 yes WGTP 2 117260763 117467663 2 yes WGTP 2 122037995 122198553 1 WGTP 2 126749247 126877324 10 overlap with chr start end freq 500K EA WGTP 2 127547173 127722744 3 WGTP 2 129581854 129866275 51 WGTP 2 130063068 133031735 121 yes WGTP 2 141905123 142051301 1 yes WGTP 2 151282785 151669718 1 yes WGTP 2 153450427 153688865 2 yes WGTP 2 154188586 154346292 44 WGTP 2 156262297 156424935 1 WGTP 2 168314876 168465817 1 WGTP 2 179234579 179433748 1 WGTP 2 183263206 183660590 1 yes WGTP 2 184193979 184384414 1 WGTP 2 187158286 187406053 1 yes WGTP 2 188205548 188328691 1 WGTP 2 205365338 205666680 1 WGTP 2 216116776 216276027 1 yes WGTP 2 222187660 222323689 2 yes WGTP 2 232362330 232831363 138 WGTP 2 241085111 241308861 1 yes WGTP 2 242139945 242221648 1 WGTP 2 242619209 242787722 5 yes WGTP 3 46156 773503 19 yes WGTP 3 1244095 1400003 1 yes WGTP 3 1400003 1563295 1 yes WGTP 3 2181272 2470417 1 yes WGTP 3 4158926 4395357 1 yes WGTP 3 12945170 13265554 1 WGTP 3 14886274 15137707 1 yes WGTP 3 20240591 20515632 7 WGTP 3 22052897 22231873 7 WGTP 3 24627517 24917930 1 yes WGTP 3 26040173 26194166 1 yes WGTP 3 29158899 29670492 2 WGTP 3 33270111 33446477 1 WGTP 3 37806487 38079228 8 WGTP 3 38908752 39071102 2 WGTP 3 41314156 41748757 1 yes WGTP 3 46655456 46947493 30 WGTP 3 50173482 50346381 3 WGTP 3 55465669 55640833 1 WGTP 3 60756983 60994043 2 yes WGTP 3 60994043 61160598 1 yes WGTP 3 75428849 75700285 1 yes WGTP 3 75700285 76159980 15 yes WGTP 3 76159980 76249985 1 WGTP 3 76249985 76935064 1 WGTP 3 77481544 77639025 6 WGTP 3 96766457 96876444 1 WGTP 3 98699482 98904950 10 WGTP 3 102096077 102259187 1 WGTP 3 104738943 104903852 1 WGTP 3 105522067 106297806 1 yes WGTP 3 107633520 107818033 1 WGTP 3 111495856 111578020 1 WGTP 3 117624820 117790232 1 WGTP 3 127024031 127185454 1 WGTP 3 129540391 129920515 7 WGTP 3 131142165 131422680 2 yes WGTP 3 139094487 139416533 15 WGTP 3 141408462 142007428 1 yes overlap with chr start end freq 500K EA WGTP 3 143211568 143612534 2 yes WGTP 3 144202928 144445630 1 yes WGTP 3 144475395 144768677 1 WGTP 3 145718900 145874085 1 WGTP 3 149598961 149784837 1 WGTP 3 152274323 152440183 1 WGTP 3 152957978 153145873 1 yes WGTP 3 155740971 156041425 2 WGTP 3 158572868 158737386 1 WGTP 3 162932695 163076472 2 WGTP 3 163953751 164225496 37 WGTP 3 165085151 165392762 1 WGTP 3 169771716 169985812 1 WGTP 3 174622697 174928079 1 yes WGTP 3 177275752 177516301 2 WGTP 3 182334298 182489344 4 WGTP 3 187819836 188050028 2 yes WGTP 3 188092436 188266986 1 WGTP 3 192349713 192761809 35 WGTP 3 194279079 194450436 1 WGTP 3 194716602 194886348 1 WGTP 3 196868577 197559903 184 yes WGTP 3 198343363 198986178 79 yes WGTP 3 199260725 199450740 18 WGTP 4 593208 921184 1 WGTP 4 1592784 1782006 1 WGTP 4 3431313 4469058 2 yes WGTP 4 7106220 7387973 9 WGTP 4 8640244 9950048 222 yes WGTP 4 10019968 10222069 1 WGTP 4 12173444 12335659 1 WGTP 4 15120886 15425789 133 WGTP 4 21549473 21656828 1 WGTP 4 21687850 21906987 13 yes WGTP 4 28220227 28515706 1 yes WGTP 4 29199911 29367346 1 WGTP 4 29805053 29963713 1 WGTP 4 31291394 31478210 1 WGTP 4 32190399 32361018 1 WGTP 4 34040560 34297097 1 yes WGTP 4 34459337 34779109 27 yes WGTP 4 40375955 40580395 1 WGTP 4 48898338 49501045 3 yes WGTP 4 52501046 52679030 65 WGTP 4 57894345 58495951 1 yes WGTP 4 60959924 61146015 1 WGTP 4 61623611 61796922 7 WGTP 4 68605772 68842130 1 yes WGTP 4 68998845 70594932 239 yes WGTP 4 77621775 77774636 1 yes WGTP 4 89275730 89570298 2 yes WGTP 4 92303842 92503292 1 WGTP 4 97866744 98166270 1 WGTP 4 103019877 103366118 2 yes WGTP 4 104137960 104414925 6 WGTP 4 104537529 104699999 6 WGTP 4 115364724 115532828 11 WGTP 4 115699683 115947929 2 yes WGTP 4 116621852 116809401 1 WGTP 4 117879914 117978482 95 overlap with chr start end freq 500K EA WGTP 4 118836451 120032345 2 yes WGTP 4 124568831 125736952 1 yes WGTP 4 132219682 133363089 141 yes WGTP 4 133511465 133655754 1 WGTP 4 138482863 138654737 1 WGTP 4 138897853 139070702 1 WGTP 4 139502133 139670493 1 WGTP 4 142423266 142725556 1 WGTP 4 144705898 145489197 48 yes WGTP 4 158509492 158739893 1 yes WGTP 4 161727569 161909769 1 WGTP 4 162735374 162917315 1 WGTP 4 163092222 163265570 1 WGTP 4 166159421 166333955 1 WGTP 4 168266226 168565721 1 WGTP 4 169109321 169426423 264 yes WGTP 4 172641989 172669987 1 WGTP 4 178540618 178780523 1 yes WGTP 4 183933465 184117496 1 WGTP 4 186688274 186849845 1 WGTP 4 187636479 187797491 8 WGTP 4 189459436 189638677 2 yes WGTP 4 189753545 189837970 1 WGTP 4 190398953 190641305 1 WGTP 4 190658160 191070245 245 yes WGTP 5 70263 648955 12 WGTP 5 673163 1214476 132 yes WGTP 5 3629619 3840514 4 WGTP 5 5033876 5237615 1 WGTP 5 5500098 5817620 1 WGTP 5 9850992 10044066 1 yes WGTP 5 12087304 12261440 1 WGTP 5 12839321 13039901 1 WGTP 5 13218142 13456575 2 yes WGTP 5 17417700 17972161 101 yes WGTP 5 19066044 19245996 1 WGTP 5 21184910 21748947 71 WGTP 5 21814498 22199675 78 WGTP 5 26791054 26970598 1 WGTP 5 31332034 31505885 1 WGTP 5 32047775 32239257 1 yes WGTP 5 32281118 32774401 1 WGTP 5 34134806 34405626 75 WGTP 5 49784109 50093939 2 WGTP 5 61438895 61723574 6 yes WGTP 5 66393681 66586635 1 WGTP 5 69109876 70831640 183 WGTP 5 71935078 72108737 1 WGTP 5 74469516 74647470 1 WGTP 5 81245981 81550493 4 WGTP 5 93790961 94067957 139 WGTP 5 95257462 95566189 1 yes WGTP 5 97421264 97575845 2 yes WGTP 5 98633225 98917493 1 WGTP 5 99235573 99874154 160 yes WGTP 5 100535625 100788621 2 yes WGTP 5 103511683 103661467 2 WGTP 5 104334472 104660077 3 yes WGTP 5 104685688 104853617 2 WGTP 5 106519625 106579710 2 overlap with chr start end freq 500K EA WGTP 5 109669759 110056060 1 yes WGTP 5 117692624 117970146 1 yes WGTP 5 125078762 125315808 1 WGTP 5 128623637 128862751 2 yes WGTP 5 130098933 130316104 1 WGTP 5 130466896 130619811 102 WGTP 5 135193500 135502898 1 yes WGTP 5 140137124 140808866 45 WGTP 5 144153983 144340436 1 WGTP 5 149804786 150265935 112 WGTP 5 153062206 153273106 1 WGTP 5 155313275 155548476 1 yes WGTP 5 156930186 157165622 1 WGTP 5 160477321 160626797 33 yes WGTP 5 165155278 165334527 4 WGTP 5 171473028 171667877 15 WGTP 5 171913937 172117968 5 yes WGTP 5 175337984 175685508 4 yes WGTP 5 176550923 176735050 54 WGTP 5 178593872 178970135 2 yes WGTP 5 179467083 179662550 1 WGTP 5 180019804 180214082 1 yes WGTP 6 5001 720274 167 yes WGTP 6 10551783 10751118 1 yes WGTP 6 11787739 11930337 1 WGTP 6 16981250 17020517 1 WGTP 6 26801198 27203693 2 yes WGTP 6 29577080 29780644 2 WGTP 6 29900413 30083123 21 yes WGTP 6 30752672 30924298 2 yes WGTP 6 31136269 31605085 20 yes WGTP 6 31979491 32317091 35 WGTP 6 32479731 32813412 231 WGTP 6 32973767 33072074 2 WGTP 6 34490470 34822655 1 WGTP 6 35276094 35398980 1 WGTP 6 35571719 35914482 4 WGTP 6 38696947 38819063 6 WGTP 6 41696767 41807431 1 yes WGTP 6 44987769 45164736 1 yes WGTP 6 46808141 47036030 9 WGTP 6 50627298 50775800 1 WGTP 6 51472475 51548810 1 WGTP 6 53947332 54104052 1 yes WGTP 6 57292500 57670563 1 WGTP 6 58442668 58587658 1 WGTP 6 63764581 64043848 1 yes WGTP 6 68213162 68355095 1 yes WGTP 6 69652213 69655072 1 WGTP 6 75018716 75184885 1 yes WGTP 6 78156739 78339761 3 WGTP 6 78393674 78637549 1 WGTP 6 78852599 79250187 112 yes WGTP 6 81870395 81891996 1 WGTP 6 87513222 87701933 31 WGTP 6 87874602 88049676 1 WGTP 6 88415707 88498192 3 WGTP 6 89147456 89318637 5 WGTP 6 95264814 95451409 1 WGTP 6 103255429 103412632 1 overlap with chr start end freq 500K EA WGTP 6 103834514 104012090 130 WGTP 6 105302783 105767502 2 yes WGTP 6 114773001 115633650 1 yes WGTP 6 115895071 116068349 1 WGTP 6 117537917 117733968 2 yes WGTP 6 122765634 122925836 1 WGTP 6 128883885 128886524 1 WGTP 6 129315361 129484648 3 WGTP 6 133486412 133669057 1 WGTP 6 134665824 134752836 1 WGTP 6 137501221 137615031 1 WGTP 6 137914018 137962674 1 WGTP 6 143958314 144121669 1 WGTP 6 151380322 151546953 1 WGTP 6 153155406 153326844 1 WGTP 6 154229897 154386563 8 yes WGTP 6 159974242 160185562 12 WGTP 6 160342655 161205076 204 yes WGTP 6 162161167 162381661 1 WGTP 6 162828733 163110786 1 yes WGTP 6 163962475 164132314 1 WGTP 6 166112052 166269346 1 WGTP 6 167471615 167816346 1 yes WGTP 6 168055424 168533940 4 yes WGTP 6 168701943 168857249 72 WGTP 6 169563923 169651825 2 WGTP 6 170499383 170750395 12 WGTP 6 170750395 170927551 2 WGTP 7 106471 298664 14 yes WGTP 7 972336 1463188 1 WGTP 7 3059866 3333470 2 yes WGTP 7 4365856 4519892 2 WGTP 7 6983151 7267141 3 yes WGTP 7 8846889 9005429 2 yes WGTP 7 11700479 11882659 1 WGTP 7 14670117 15073026 1 yes WGTP 7 16046062 16300630 4 yes WGTP 7 16783293 17304719 1 yes WGTP 7 19209283 19394202 2 yes WGTP 7 22528824 22694150 1 WGTP 7 23493296 23653562 1 WGTP 7 27566856 27746109 1 WGTP 7 29431177 29708612 1 yes WGTP 7 35597466 35893678 1 WGTP 7 37371953 37631800 1 yes WGTP 7 37991943 38296695 1 yes WGTP 7 43725779 43830031 52 WGTP 7 53107233 53259225 1 WGTP 7 53749523 53910569 1 WGTP 7 57396706 57770231 2 yes WGTP 7 60893982 62553525 124 yes WGTP 7 63995424 64730827 15 yes WGTP 7 65845580 66303403 4 WGTP 7 68857155 69038812 1 WGTP 7 71356121 72320549 16 yes WGTP 7 73439084 76494030 47 yes WGTP 7 78906115 79072297 1 WGTP 7 82945157 83104763 1 WGTP 7 84797973 84962693 1 WGTP 7 87731680 87974020 1 yes overlap with chr start end freq 500K EA WGTP 7 97120935 97292680 1 WGTP 7 100000141 100342681 85 WGTP 7 101494175 101666167 2 WGTP 7 104360658 104704532 2 yes WGTP 7 109003931 109201570 4 WGTP 7 109357547 109506183 1 WGTP 7 110117249 110381800 1 WGTP 7 110394862 110898776 4 yes WGTP 7 112086078 112362579 1 WGTP 7 125254760 125488816 2 WGTP 7 126088740 126271794 1 WGTP 7 130179011 130328113 2 WGTP 7 131778945 132001738 2 WGTP 7 133094440 133281052 43 WGTP 7 138190952 138384594 1 WGTP 7 141163595 141382145 19 WGTP 7 141610138 142240984 28 yes WGTP 7 142664612 143806286 206 WGTP 7 148879238 149394063 5 yes WGTP 7 149689597 149901452 1 WGTP 7 149976469 150101345 1 WGTP 7 152438821 152736427 3 yes WGTP 7 152831155 153195879 6 yes WGTP 7 155658864 155925343 4 yes WGTP 7 156849831 157112954 2 WGTP 8 59932 484890 21 yes WGTP 8 2105020 2411266 12 yes WGTP 8 3586932 5909600 6 yes WGTP 8 6719130 8344153 124 yes WGTP 8 11778967 12611672 39 yes WGTP 8 13581607 13896999 1 yes WGTP 8 14721071 15809077 2 yes WGTP 8 16231929 17010633 2 yes WGTP 8 17335551 17685810 1 yes WGTP 8 20273229 20559087 1 WGTP 8 20577324 23167554 2 yes WGTP 8 25324942 25478051 1 WGTP 8 39364955 39716796 191 yes WGTP 8 48343375 48554996 1 WGTP 8 48950846 49170567 2 WGTP 8 50578416 50819905 3 yes WGTP 8 51049146 51300548 2 yes WGTP 8 53823346 54105603 1 yes WGTP 8 54637142 54900026 2 WGTP 8 54995543 55179518 1 WGTP 8 58092946 58637003 170 WGTP 8 79784789 79950902 1 WGTP 8 86592730 87124169 224 WGTP 8 89032945 89202820 1 WGTP 8 91069962 91398845 1 yes WGTP 8 92043675 92342900 1 yes WGTP 8 93612869 93782102 1 WGTP 8 100098024 100265857 9 WGTP 8 100473327 100907800 17 WGTP 8 114644879 115391133 2 yes WGTP 8 116967502 117250765 1 yes WGTP 8 120012490 120344931 2 WGTP 8 129633607 129784954 1 WGTP 8 133470532 133754071 154 WGTP 8 137585971 138040412 6 yes overlap with chr start end freq 500K EA WGTP 8 145203172 145357632 1 WGTP 8 145494501 145668486 2 WGTP 9 21994 373816 9 yes WGTP 9 514413 843033 2 yes WGTP 9 1045347 1519128 1 yes WGTP 9 5287921 5444512 1 yes WGTP 9 6566991 6828660 1 yes WGTP 9 7165387 7472982 1 yes WGTP 9 10178450 10360398 1 WGTP 9 11783343 12164755 4 yes WGTP 9 12225048 12611991 1 yes WGTP 9 12611991 12774092 1 yes WGTP 9 16631966 16799203 1 WGTP 9 28462018 28840774 1 yes WGTP 9 29125948 29299828 1 WGTP 9 29784954 30063518 2 yes WGTP 9 30199650 30421507 2 yes WGTP 9 30854032 31028881 1 WGTP 9 38557168 45935928 216 yes WGTP 9 64135929 68383081 178 yes WGTP 9 76595419 76903461 2 WGTP 9 80822890 80931674 1 WGTP 9 83643578 83833156 1 WGTP 9 85353708 85507991 1 WGTP 9 87248281 87654534 1 WGTP 9 101719787 101905114 1 yes WGTP 9 106230185 106435633 1 yes WGTP 9 109264965 109454331 1 WGTP 9 112320009 113082505 8 yes WGTP 9 120727751 120922549 1 WGTP 9 125955511 126116512 1 WGTP 9 130767120 131058115 1 WGTP 9 131300676 131448167 1 yes WGTP 9 133461155 133485243 3 WGTP 9 136526666 137102322 9 WGTP 9 137473621 137617588 2 WGTP 9 138161400 138429268 27 WGTP 10 50001 214405 2 WGTP 10 2650802 3188773 1 yes WGTP 10 5677111 5844786 2 yes WGTP 10 7463502 7777745 1 yes WGTP 10 19754643 20065000 1 yes WGTP 10 20726725 20938614 54 yes WGTP 10 37325769 37665705 2 WGTP 10 38908842 39194941 8 yes WGTP 10 42004899 42199692 1 yes WGTP 10 42285137 42830197 5 yes WGTP 10 45341719 48101925 260 yes WGTP 10 48213402 49121538 174 WGTP 10 50641980 51595172 23 WGTP 10 55030618 55256936 2 yes WGTP 10 56078033 56236143 2 yes WGTP 10 56503549 56781399 1 WGTP 10 58160636 58359959 1 yes WGTP 10 59214388 59489499 1 yes WGTP 10 60388039 60641367 2 yes WGTP 10 68016700 68162396 1 yes WGTP 10 70127725 70301318 3 WGTP 10 74105644 74277126 1 WGTP 10 76904943 77106586 4 overlap with chr start end freq 500K EA WGTP 10 77106586 77440455 1 yes WGTP 10 78781397 78992207 1 WGTP 10 78992207 79248885 1 yes WGTP 10 80945468 81810835 32 yes WGTP 10 88505038 89299742 176 yes WGTP 10 90825044 91007466 1 WGTP 10 98779953 98952462 1 WGTP 10 102141840 102369625 1 yes WGTP 10 102369625 102555726 1 WGTP 10 107519652 107743529 31 yes WGTP 10 110448977 110633486 1 WGTP 10 122625702 122891863 3 WGTP 10 124253065 124444805 23 WGTP 10 125047207 125259149 6 WGTP 10 127443890 127776692 2 WGTP 10 128798515 129129012 1 yes WGTP 10 134076220 134277057 3 WGTP 10 134515692 134683302 1 yes WGTP 10 134733303 135111183 39 yes WGTP 10 135111207 135279389 13 yes WGTP 11 399846 1313968 166 WGTP 11 2745620 2920188 2 WGTP 11 3193088 3758005 89 yes WGTP 11 4012521 4466764 69 yes WGTP 11 4864469 5091907 2 yes WGTP 11 5686953 5927293 5 yes WGTP 11 8741389 8966149 1 WGTP 11 18775305 19038644 11 yes WGTP 11 25148529 25322096 3 yes WGTP 11 25590379 25799242 5 yes WGTP 11 28881069 29029074 1 WGTP 11 30936338 31020588 1 WGTP 11 32671219 33006516 1 yes WGTP 11 34986509 35183360 1 yes WGTP 11 35275896 35437098 1 WGTP 11 40879434 41039419 1 WGTP 11 41077222 41290487 1 yes WGTP 11 48260247 48813553 1 yes WGTP 11 48813553 49141766 2 yes WGTP 11 49168813 49425542 2 yes WGTP 11 50013000 50404139 4 yes WGTP 11 54978996 55378460 45 yes WGTP 11 58456668 58765249 23 yes WGTP 11 60671936 60837233 182 WGTP 11 65316469 65478939 2 WGTP 11 67281513 67616066 3 yes WGTP 11 71041287 71335224 3 WGTP 11 73565215 74235245 1 yes WGTP 11 81088432 81508270 2 yes WGTP 11 84858128 85281636 2 yes WGTP 11 88083993 88339832 39 WGTP 11 89082686 89569836 2 yes WGTP 11 90247849 90559703 180 WGTP 11 96408179 96553513 1 yes WGTP 11 96553513 96698006 1 WGTP 11 98575697 98717492 1 yes WGTP 11 113877495 114024335 1 WGTP 11 122784405 123050005 1 WGTP 11 129474432 129847927 2 yes WGTP 11 130938011 131254195 16 overlap with chr start end freq 500K EA WGTP 12 327694 860805 1 yes WGTP 12 6324145 6534096 1 yes WGTP 12 7748086 8515254 30 yes WGTP 12 9262862 9814796 93 yes WGTP 12 10860887 11606188 37 yes WGTP 12 12511921 12674391 2 WGTP 12 16156359 16337645 1 WGTP 12 20833482 21009087 14 WGTP 12 22032101 22230566 1 WGTP 12 22230566 22628174 2 WGTP 12 25883598 26052383 1 WGTP 12 29002049 29181116 1 WGTP 12 29914434 30066499 3 WGTP 12 31016734 31382371 71 yes WGTP 12 33333291 34462575 2 yes WGTP 12 36142962 37321303 6 yes WGTP 12 44435605 44636158 1 WGTP 12 46715969 47111766 2 yes WGTP 12 50849531 51055601 1 yes WGTP 12 52633336 52820913 3 WGTP 12 56116000 56288135 37 WGTP 12 57308996 57609312 1 yes WGTP 12 62196683 62538439 2 yes WGTP 12 70388731 70594440 1 yes WGTP 12 71276974 71537376 1 yes WGTP 12 81603513 81860089 1 yes WGTP 12 90649382 90813144 1 WGTP 12 96672954 96848094 1 WGTP 12 119878565 120047533 1 WGTP 12 127597185 127906190 2 WGTP 12 128471344 129640456 2 yes WGTP 12 130371694 130935124 3 yes WGTP 12 132095571 132307316 1 yes WGTP 13 17918001 18354948 5 yes WGTP 13 19918915 20122478 1 yes WGTP 13 25898592 26065378 1 WGTP 13 33768946 33934202 8 WGTP 13 48181984 48370518 1 WGTP 13 56523625 56729961 170 yes WGTP 13 62097238 62520980 2 yes WGTP 13 65062295 65292451 2 yes WGTP 13 71226326 71383406 2 WGTP 13 74102052 74275589 1 WGTP 13 75219611 75440004 2 WGTP 13 76523033 76666465 1 WGTP 13 82035430 82280653 1 WGTP 13 82592802 82779067 1 WGTP 13 82956558 83175698 1 yes WGTP 13 86954602 87112550 1 WGTP 13 88209082 88673975 2 yes WGTP 13 92972655 93146180 1 WGTP 13 104418323 104585016 1 yes WGTP 13 107090320 107274703 3 yes WGTP 13 108719614 109007551 3 WGTP 13 110460034 110604912 1 yes WGTP 13 110872855 111151995 1 WGTP 13 112424858 112739202 20 WGTP 13 113086430 113259065 1 WGTP 14 18732531 19626027 205 yes WGTP 14 20285948 20541454 14 yes overlap with chr start end freq 500K EA WGTP 14 25297720 25474958 15 WGTP 14 27134939 27513082 7 WGTP 14 31928231 32086193 4 WGTP 14 41115623 41329261 1 WGTP 14 41933545 42078579 1 yes WGTP 14 43468955 43714231 8 yes WGTP 14 44127583 44383416 1 yes WGTP 14 44775832 45052160 3 yes WGTP 14 45863402 46018276 1 WGTP 14 47329907 47516073 1 WGTP 14 59477247 59652794 1 yes WGTP 14 73030050 73196823 52 WGTP 14 77143933 77332325 1 yes WGTP 14 77973363 78243281 1 yes WGTP 14 82105460 82216550 1 WGTP 14 83206211 83363593 1 WGTP 14 85228067 85495155 1 yes WGTP 14 86259051 86411966 2 WGTP 14 103217278 103482566 1 WGTP 14 104584391 105020471 1 WGTP 15 18263733 21365850 225 yes WGTP 15 21805431 22452007 12 yes WGTP 15 25060215 25335769 1 WGTP 15 26086062 26763830 37 WGTP 15 28080236 28939783 66 yes WGTP 15 29553592 30773871 64 yes WGTP 15 32330313 32775539 213 yes WGTP 15 35618861 35759779 1 WGTP 15 38619837 38782403 1 WGTP 15 41610450 41935933 6 yes WGTP 15 42756160 43210134 1 yes WGTP 15 46296330 46451070 1 WGTP 15 49069549 49617631 1 yes WGTP 15 63967839 64137439 1 WGTP 15 66325126 66601717 1 WGTP 15 67421806 67579253 31 WGTP 15 70606839 70907613 3 WGTP 15 72002167 72251969 6 WGTP 15 74957605 75160503 1 WGTP 15 77142292 77305824 1 WGTP 15 79728575 80011124 1 yes WGTP 15 80676701 81107580 41 WGTP 15 82506626 82870925 30 yes WGTP 15 83063933 83217534 1 WGTP 15 83451942 83685716 11 WGTP 15 88366960 88590229 4 yes WGTP 15 89632854 89841316 1 WGTP 15 93267980 93447142 1 WGTP 15 94219335 94439704 1 WGTP 15 95508704 95833748 1 yes WGTP 15 98091816 98574562 1 yes WGTP 15 99298613 99478425 1 WGTP 15 99550339 99720607 15 yes WGTP 15 99720607 99872978 1 yes WGTP 15 100089153 100248597 1 WGTP 16 21052 133600 20 WGTP 16 266993 1111069 64 WGTP 16 2476826 2810537 6 WGTP 16 4912851 5364830 3 yes WGTP 16 6588011 6878909 1 yes overlap with chr start end freq 500K EA WGTP 16 9968477 10165051 2 WGTP 16 14529556 15274051 37 WGTP 16 16092718 16831289 27 yes WGTP 16 17480600 19066807 23 yes WGTP 16 21241957 21833734 75 yes WGTP 16 22201625 22679810 162 yes WGTP 16 24850896 25094479 2 yes WGTP 16 25532212 25718755 1 WGTP 16 28082639 29058054 9 WGTP 16 29181449 29609853 13 WGTP 16 29981456 30290781 13 WGTP 16 31658070 34219714 213 yes WGTP 16 34219714 34627143 234 yes WGTP 16 45874367 46163788 1 yes WGTP 16 46886938 47037255 1 WGTP 16 53121783 53309710 1 WGTP 16 54226897 54541091 4 WGTP 16 57136506 57433538 4 WGTP 16 68412623 68870723 19 yes WGTP 16 69364623 69874484 3 yes WGTP 16 70533845 70831848 20 WGTP 16 72892281 73144686 16 WGTP 16 73977115 74134472 2 WGTP 16 76811430 76929139 2 yes WGTP 16 85399263 85564336 1 yes WGTP 16 86476851 86671233 1 WGTP 16 86986673 87137417 2 WGTP 16 87970408 88179649 58 WGTP 16 88398233 88495450 3 WGTP 17 343377 440727 1 WGTP 17 568336 1008155 2 yes WGTP 17 13821966 14069281 1 yes WGTP 17 16467781 16758162 4 yes WGTP 17 18175250 18387109 68 WGTP 17 18771341 19132640 96 WGTP 17 20227887 20640432 6 WGTP 17 21191534 22014559 120 yes WGTP 17 22045526 22465691 4 WGTP 17 22902614 23201246 6 WGTP 17 27245834 27562095 1 WGTP 17 31309398 31981395 201 yes WGTP 17 32036161 32221507 1 yes WGTP 17 32642843 32848430 1 WGTP 17 33140728 34010545 193 WGTP 17 36001826 36103630 1 WGTP 17 36554901 37123136 2 yes WGTP 17 40977732 41171794 2 yes WGTP 17 41439751 42632332 207 yes WGTP 17 42875373 43119955 95 WGTP 17 43957672 44191836 2 yes WGTP 17 48369345 48627779 2 yes WGTP 17 53997375 54149948 4 WGTP 17 54437361 54780416 1 WGTP 17 55350429 55513944 31 WGTP 17 57650339 57826573 60 WGTP 17 65403530 65490775 1 WGTP 17 72638503 72807003 1 WGTP 17 76741026 76933757 8 WGTP 18 3667422 4160252 2 yes WGTP 18 6752909 6933645 1 overlap with chr start end freq 500K EA WGTP 18 11887023 12066102 4 WGTP 18 12230681 12489525 1 WGTP 18 13988748 15367893 9 yes WGTP 18 19024430 19181612 1 WGTP 18 28637325 28828735 1 WGTP 18 32304033 32733948 1 yes WGTP 18 35736115 35903305 1 WGTP 18 61863327 62021348 17 WGTP 18 62157007 62341492 11 WGTP 18 64138015 64399757 1 yes WGTP 18 64399757 64543942 3 WGTP 18 67703807 68125877 1 yes WGTP 18 73047414 73306926 13 WGTP 18 74125373 74378820 4 WGTP 19 183069 327646 1 WGTP 19 902641 1495933 4 WGTP 19 8758670 8832847 128 WGTP 19 14957950 15120179 1 WGTP 19 20028401 20290544 1 yes WGTP 19 20321226 20637787 3 yes WGTP 19 21777328 22863139 1 yes WGTP 19 22863139 23732307 2 yes WGTP 19 24142405 24349203 1 yes WGTP 19 32658593 32953337 4 WGTP 19 34038496 34356975 1 WGTP 19 38468914 39273401 2 yes WGTP 19 39817858 39984175 1 WGTP 19 40402918 40578953 3 WGTP 19 44919744 45212970 5 WGTP 19 45304260 45531360 1 WGTP 19 45983467 46237908 3 yes WGTP 19 47734587 48590893 12 yes WGTP 19 52549596 52717317 3 WGTP 19 55228822 55344796 136 WGTP 19 56683708 56958512 15 yes WGTP 19 57037904 57225638 2 yes WGTP 19 58102271 58344387 6 yes WGTP 19 59359391 60158136 35 yes WGTP 20 8001 11943 1 WGTP 20 1424781 1627256 78 WGTP 20 2078560 2423469 1 yes WGTP 20 8002182 8595665 1 yes WGTP 20 8898291 9227700 1 WGTP 20 10840138 11064725 6 WGTP 20 11638021 12381393 2 yes WGTP 20 14679344 14803457 1 yes WGTP 20 22977404 23121240 1 yes WGTP 20 25649992 26267569 15 WGTP 20 28033231 28267569 21 yes WGTP 20 30959468 31211827 47 WGTP 20 36392696 36498327 1 yes WGTP 20 44126322 44398283 118 WGTP 20 45701817 45957486 3 WGTP 20 55604184 56121677 36 WGTP 20 59894657 60016638 10 WGTP 20 60464834 60897084 32 WGTP 20 61572793 61846811 116 WGTP 20 62108666 62435964 12 WGTP 21 10023842 10197104 5 yes WGTP 21 13556403 14261623 28 yes overlap with chr start end freq 500K EA WGTP 21 15834517 16018549 1 WGTP 21 20637992 20877335 3 yes WGTP 21 27302101 27462314 1 WGTP 21 32151463 32438711 2 WGTP 22 14509865 15652016 157 yes WGTP 22 16926349 17436267 109 yes WGTP 22 18401047 18684001 2 WGTP 22 20619657 20733158 7 WGTP 22 23382276 23422245 1 WGTP 22 23691355 24281461 27 yes WGTP 22 25223053 25354450 1 WGTP 22 32193499 32234100 11 WGTP 22 32494349 32528033 1 WGTP 22 33068219 33107464 1 WGTP 22 33762965 33957507 1 yes WGTP 22 35231063 35366534 1 WGTP 22 35499654 35685405 33 WGTP 22 36328377 36590378 6 WGTP 22 41091699 41407804 25 yes WGTP 22 42968722 43026202 6 WGTP 22 43347341 43531066 6 WGTP 22 43894761 44221622 1 yes WGTP 22 44975462 45018495 80 WGTP 22 45709833 45931039 7 WGTP 22 46845829 46850201 48 WGTP 22 47095130 47136752 7 WGTP 22 47465793 47475686 14 WGTP 22 48248831 48252981 1 WGTP 22 49219663 49307552 1 WGTP 22 49392382 49495206 10 WGTP 23 313529 532251 3 WGTP 23 1865728 3187726 1 yes WGTP 23 7061134 7483618 1 yes WGTP 23 9138826 9310156 28 WGTP 23 9860872 10041747 1 WGTP 23 27962843 28108827 1 yes WGTP 23 28108827 28359884 1 yes WGTP 23 31123273 31278805 1 yes WGTP 23 47523164 47902964 4 yes WGTP 23 56622090 56770769 74 WGTP 23 57515394 57773429 18 WGTP 23 61984759 62329082 2 WGTP 23 63321820 63666298 1 yes WGTP 23 66282690 66582954 1 yes WGTP 23 70654274 71083437 3 WGTP 23 77031055 77115217 1 WGTP 23 89260661 89673776 1 WGTP 23 89957981 90252381 1 yes WGTP 23 96741719 96861762 2 WGTP 23 102888546 103261206 2 yes WGTP 23 104109151 104221182 1 WGTP 23 105343681 105487922 1 WGTP 23 108585146 108787037 2 WGTP 23 109387916 109517626 1 WGTP 23 114768844 114795257 1 WGTP 23 115711880 115883234 1 yes WGTP 23 118739321 119110866 3 WGTP 23 119183307 119364831 1 WGTP 23 122690351 122888100 1 WGTP 23 125340415 125399344 1 overlap with chr start end freq 500K EA WGTP 23 126868603 127019222 1 WGTP 23 128423110 128689620 37 WGTP 23 133926407 134223835 1 WGTP 23 134328057 134880261 40 yes WGTP 23 139711783 140559532 46 yes WGTP 23 141595220 141794235 38 WGTP 23 148422218 148687904 5 yes WGTP 23 151881624 151947652 1 yes WGTP 24 5999160 6369813 7 WGTP 24 7738992 7981359 1 WGTP 24 9174325 10072259 44 WGTP 24 10432535 10697914 16 WGTP 24 19062951 19393189 1 WGTP 24 21771803 22936103 63 WGTP 24 22936103 26838610 41 WGTP 24 26838610 27123476 1 Supplemental Table 11B: CNV events from WGTP WGTP event CNV_id chromosome start end call Chr1_1 chr1 2408416 2412411 del Chr1_2 chr1 8822507 8850906 dup Chr1_3 chr1 142820056 142972397 dup Chr1_4 chr1 144800023 145140950 complex Chr1_5 chr1 64389169 64488417 del Chr1_6 chr1 171200938 171301433 dup Chr1_7 chr1 166513664 166616844 complex Chr1_8 chr1 119979355 120409198 del Chr1_9 chr1 116876957 116986717 complex Chr1_10 chr1 1651818 1762425 del/dup Chr1_11 chr1 53630573 53741257 del Chr1_12 chr1 231180061 231434698 complex Chr1_13 chr1 149285912 149711226 dup Chr1_14 chr1 10676768 10989413 del Chr1_15 chr1 16509639 17229287 del/dup Chr1_16 chr1 103702380 104164023 multiallelic Chr1_17 chr1 193322494 193693459 del Chr1_18 chr1 1239243 1359795 del Chr1_19 chr1 106472604 106593624 del Chr1_20 chr1 561232 682895 multiallelic Chr1_21 chr1 221711686 221833513 complex Chr1_22 chr1 72893633 73019191 dup Chr1_23 chr1 141851837 141979099 dup Chr1_24 chr1 158219386 158356094 del/dup Chr1_25 chr1 96127772 96258135 dup Chr1_26 chr1 10383709 10516820 dup Chr1_27 chr1 72454417 72598834 dup Chr1_28 chr1 100071676 100210363 del Chr1_29 chr1 143117214 143257561 del Chr1_30 chr1 170542299 170687600 del Chr1_31 chr1 89124089 89272744 complex Chr1_32 chr1 377 852347 complex Chr1_33 chr1 141387477 142972397 del Chr1_34 chr1 199299046 199455863 del Chr1_35 chr1 185978190 186380985 del Chr1_36 chr1 145513740 145671828 dup Chr1_37 chr1 163223537 163382643 del Chr1_38 chr1 218684362 218846708 del Chr1_39 chr1 73325120 73487705 dup Chr1_40 chr1 52838036 53001202 del Chr1_41 chr1 90532013 90695320 complex Chr1_42 chr1 141387477 141551836 del Chr1_43 chr1 221394659 221560009 dup Chr1_44 chr1 377 167280 dup Chr1_45 chr1 244826150 245191415 del Chr1_46 chr1 672781 1038212 dup Chr1_47 chr1 220488331 220669898 dup Chr1_48 chr1 12533434 12954117 del/dup Chr1_49 chr1 146522914 146711869 dup Chr1_50 chr1 220241955 220576430 del Chr1_51 chr1 21967827 22158163 del Chr1_52 chr1 193709456 193901429 del Chr1_53 chr1 1409796 1601817 dup Chr1_54 chr1 209036538 209231498 del Chr1_55 chr1 203946290 204313462 del/dup Chr1_56 chr1 119728738 119926619 del/dup Chr1_57 chr1 75698925 75899769 del Chr1_58 chr1 21481490 21687720 complex Chr1_59 chr1 151908051 152127880 dup Chr1_60 chr1 3312095 3572010 dup Chr1_61 chr1 10172336 10436014 del WGTP event CNV_id chromosome start end call Chr1_62 chr1 36289232 36556181 del Chr1_63 chr1 5200140 5470944 dup Chr1_64 chr1 244040626 244603187 dup Chr1_65 chr1 83040583 83720332 del/dup Chr1_66 chr1 108330916 108808720 del/dup Chr1_67 chr1 227931495 228222731 dup Chr1_68 chr1 144800023 146803586 del/dup Chr1_69 chr1 192535421 192851111 dup Chr1_70 chr1 191987584 192311869 dup Chr1_71 chr1 242733187 243066985 dup Chr1_72 chr1 143352668 143922358 dup Chr1_73 chr1 107195670 107552925 del Chr1_74 chr1 112869177 113231408 dup Chr1_75 chr1 158807806 159235014 dup Chr1_76 chr1 39894236 40329525 del Chr1_77 chr1 144920632 145671828 complex Chr1_78 chr1 141387477 141979099 complex Chr1_79 chr1 120181092 120958392 complex Chr1_80 chr1 236092135 236715545 dup Chr1_81 chr1 31391233 32025943 del Chr1_82 chr1 115353371 115992862 dup Chr1_83 chr1 1409796 2056500 dup Chr1_84 chr1 12608657 13622361 del/dup Chr1_85 chr1 234267835 235094143 dup Chr1_86 chr1 112869177 116453414 del Chr2_1 chr2 242139945 242221648 del Chr2_2 chr2 51193365 51277533 dup Chr2_3 chr2 91159351 91243749 del Chr2_4 chr2 52639031 52726188 del Chr2_5 chr2 74391579 74482924 del Chr2_6 chr2 188205548 188328691 dup Chr2_7 chr2 126749247 126877324 dup Chr2_8 chr2 222187660 222323689 del Chr2_9 chr2 141905123 142051301 dup Chr2_10 chr2 80312976 80754119 del Chr2_11 chr2 168314876 168465817 dup Chr2_12 chr2 84643112 84795200 del Chr2_13 chr2 130291879 133031735 complex Chr2_14 chr2 87428555 87583439 dup Chr2_15 chr2 15152787 15308457 del Chr2_16 chr2 154188586 154346292 del/dup Chr2_17 chr2 91016978 91677266 complex Chr2_18 chr2 242619209 242787722 del/dup Chr2_19 chr2 216116776 216276027 del Chr2_20 chr2 122037995 122198553 dup Chr2_21 chr2 156262297 156424935 dup Chr2_22 chr2 27972987 28136281 dup Chr2_23 chr2 76453575 76617009 dup Chr2_24 chr2 107056558 107220149 dup Chr2_25 chr2 130063068 130745921 complex Chr2_26 chr2 99839409 100005193 del/dup Chr2_27 chr2 104052123 104218620 dup Chr2_28 chr2 111616014 112463168 del/dup Chr2_29 chr2 35149394 35316635 del Chr2_30 chr2 35775617 36031232 del Chr2_31 chr2 1866728 2035145 del Chr2_32 chr2 5448267 5618952 del Chr2_33 chr2 66240707 66411516 del Chr2_34 chr2 77766753 78013206 del/dup Chr2_35 chr2 232362330 232831363 complex Chr2_36 chr2 127547173 127722744 dup Chr2_37 chr2 157949 334228 dup WGTP event CNV_id chromosome start end call Chr2_38 chr2 113968175 114144908 dup Chr2_39 chr2 22725791 23031671 complex Chr2_40 chr2 132013599 132548178 complex Chr2_41 chr2 67198930 67377313 dup Chr2_42 chr2 113791179 113971846 complex Chr2_43 chr2 95392012 95574433 del Chr2_44 chr2 132364625 132548178 dup Chr2_45 chr2 40459598 40645427 del Chr2_46 chr2 97305870 97492237 dup Chr2_47 chr2 13234898 13698420 complex Chr2_48 chr2 96992983 97492237 del Chr2_49 chr2 184193979 184384414 dup Chr2_50 chr2 132786146 132976848 dup Chr2_51 chr2 56571336 56762849 del Chr2_52 chr2 91016978 91211972 complex Chr2_53 chr2 87157420 87446513 del Chr2_54 chr2 179234579 179433748 del Chr2_55 chr2 94840283 95041982 dup Chr2_56 chr2 57196182 57400047 dup Chr2_57 chr2 117260763 117467663 del Chr2_58 chr2 87659623 87881342 del Chr2_59 chr2 241085111 241308861 dup Chr2_60 chr2 55658890 55892725 dup Chr2_61 chr2 153450427 153688865 del Chr2_62 chr2 187158286 187406053 dup Chr2_63 chr2 73628687 73990247 dup Chr2_64 chr2 116238026 116516523 dup Chr2_65 chr2 74391579 74674080 del Chr2_66 chr2 129581854 129866275 complex Chr2_67 chr2 64164656 64451207 dup Chr2_68 chr2 56090090 56384045 dup Chr2_69 chr2 205365338 205666680 dup Chr2_70 chr2 75601060 75924478 del/dup Chr2_71 chr2 37708305 38050590 del Chr2_72 chr2 131439785 131953801 complex Chr2_73 chr2 46444463 46785802 del Chr2_74 chr2 36155103 36502309 del Chr2_75 chr2 78038044 78622687 del Chr2_76 chr2 151282785 151669718 dup Chr2_77 chr2 183263206 183660590 dup Chr2_78 chr2 130935780 131391022 del Chr2_79 chr2 97305870 97795025 dup Chr2_80 chr2 110050731 110558272 del/dup Chr2_81 chr2 107908395 108437172 dup Chr2_82 chr2 87067570 87881342 del/dup Chr2_83 chr2 83160508 83876420 del Chr2_84 chr2 178829 915588 dup Chr2_85 chr2 29265918 30451080 dup Chr2_86 chr2 58309948 61194391 dup Chr3_1 chr3 198772060 198823587 del Chr3_2 chr3 111495856 111578020 dup Chr3_3 chr3 76158979 76250987 dup Chr3_4 chr3 96766457 96876444 dup Chr3_5 chr3 162932695 163076472 del/dup Chr3_6 chr3 192349713 192761809 del Chr3_7 chr3 37806487 38079228 del Chr3_8 chr3 26040173 26194166 del Chr3_9 chr3 182334298 182489344 dup Chr3_10 chr3 145718900 145874085 del Chr3_11 chr3 77481544 77639025 dup Chr3_12 chr3 198343363 198986178 complex Chr3_13 chr3 127024031 127185454 del WGTP event CNV_id chromosome start end call Chr3_14 chr3 38908752 39071102 del Chr3_15 chr3 102096077 102259187 del Chr3_16 chr3 20240591 20515632 complex Chr3_17 chr3 158572868 158737386 dup Chr3_18 chr3 104738943 104903852 dup Chr3_19 chr3 75698633 76160982 complex Chr3_20 chr3 117624820 117790232 del Chr3_21 chr3 152274323 152440183 dup Chr3_22 chr3 163953751 164225496 complex Chr3_23 chr3 194716602 194886348 dup Chr3_24 chr3 194279079 194450436 dup Chr3_25 chr3 46156 773503 complex Chr3_26 chr3 50173482 50346381 del Chr3_27 chr3 196868577 197559903 multiallelic Chr3_28 chr3 188092436 188266986 del Chr3_29 chr3 55465669 55640833 del Chr3_30 chr3 1244095 1420317 dup Chr3_31 chr3 33270111 33446477 dup Chr3_32 chr3 46655456 46947493 del Chr3_33 chr3 22052897 22231873 del Chr3_34 chr3 29158899 29340599 del Chr3_35 chr3 1379689 1563295 dup Chr3_36 chr3 107633520 107818033 dup Chr3_37 chr3 149598961 149784837 dup Chr3_38 chr3 139094487 139416533 del Chr3_39 chr3 152957978 153145873 del Chr3_40 chr3 60971918 61160598 del Chr3_41 chr3 198343363 198532077 complex Chr3_42 chr3 199260725 199450740 dup Chr3_43 chr3 129540391 129920515 del Chr3_44 chr3 98699482 98904950 del/dup Chr3_45 chr3 169771716 169985812 dup Chr3_46 chr3 187819836 188050028 del Chr3_47 chr3 4158926 4395357 del Chr3_48 chr3 177275752 177516301 dup Chr3_49 chr3 144202928 144445630 dup Chr3_50 chr3 14886274 15137707 dup Chr3_51 chr3 60756983 61016168 del Chr3_52 chr3 75428849 75701937 del Chr3_53 chr3 131142165 131422680 del Chr3_54 chr3 2181272 2470417 dup Chr3_55 chr3 24627517 24917930 del Chr3_56 chr3 144475395 144768677 del Chr3_57 chr3 155740971 156041425 del Chr3_58 chr3 174622697 174928079 dup Chr3_59 chr3 165085151 165392762 dup Chr3_60 chr3 12945170 13265554 del Chr3_61 chr3 143211568 143612534 dup Chr3_62 chr3 41314156 41748757 del Chr3_63 chr3 29158899 29670492 del Chr3_64 chr3 141408462 142007428 dup Chr3_65 chr3 76248984 76935064 dup Chr3_66 chr3 105522067 106297806 del Chr4_1 chr4 172641989 172669987 dup Chr4_2 chr4 189753545 189837970 del Chr4_3 chr4 117879914 117978482 complex Chr4_4 chr4 21549473 21656828 dup Chr4_5 chr4 8640244 9950048 complex Chr4_6 chr4 132955042 133085203 complex Chr4_7 chr4 133511465 133655754 del Chr4_8 chr4 77621775 77774636 del Chr4_9 chr4 68998845 69296476 dup WGTP event CNV_id chromosome start end call Chr4_10 chr4 21687850 21906987 del Chr4_11 chr4 29805053 29963713 dup Chr4_12 chr4 187636479 187797491 dup Chr4_13 chr4 186688274 186849845 del Chr4_14 chr4 15120886 15425789 complex Chr4_15 chr4 104137960 104414925 dup Chr4_16 chr4 12173444 12335659 del Chr4_17 chr4 104537529 104699999 del Chr4_18 chr4 144705898 145489197 del/dup Chr4_19 chr4 29199911 29367346 del Chr4_20 chr4 115364724 115532828 dup Chr4_21 chr4 139502133 139670493 del Chr4_22 chr4 32190399 32361018 del Chr4_23 chr4 34459337 34779109 del Chr4_24 chr4 49329870 49501045 del Chr4_25 chr4 138482863 138654737 del Chr4_26 chr4 138897853 139070702 dup Chr4_27 chr4 61623611 61796922 dup Chr4_28 chr4 163092222 163265570 del Chr4_29 chr4 132581414 133363089 complex Chr4_30 chr4 166159421 166333955 dup Chr4_31 chr4 145223093 145489197 del/dup Chr4_32 chr4 52501046 52679030 dup Chr4_33 chr4 189459436 189638677 del Chr4_34 chr4 3431313 3610714 dup Chr4_35 chr4 119851522 120032345 dup Chr4_36 chr4 162735374 162917315 del Chr4_37 chr4 161727569 161909769 dup Chr4_38 chr4 183933465 184117496 del Chr4_39 chr4 60959924 61146015 del Chr4_40 chr4 31291394 31478210 del Chr4_41 chr4 116621852 116809401 del Chr4_42 chr4 115699683 115947929 del Chr4_43 chr4 1592784 1782006 dup Chr4_44 chr4 169109321 169426423 del Chr4_45 chr4 92303842 92503292 dup Chr4_46 chr4 10019968 10222069 del Chr4_47 chr4 190658160 191070245 del/dup Chr4_48 chr4 40375955 40580395 del Chr4_49 chr4 9734495 9950048 dup Chr4_50 chr4 158509492 158739893 dup Chr4_51 chr4 68605772 68842130 dup Chr4_52 chr4 178540618 178780523 dup Chr4_53 chr4 190398953 190641305 del Chr4_54 chr4 34040560 34297097 dup Chr4_55 chr4 7106220 7387973 dup Chr4_56 chr4 89275730 89570298 dup Chr4_57 chr4 68998845 70594932 del Chr4_58 chr4 28220227 28515706 del Chr4_59 chr4 168266226 168565721 dup Chr4_60 chr4 97866744 98166270 del Chr4_61 chr4 142423266 142725556 del Chr4_62 chr4 593208 921184 del Chr4_63 chr4 103019877 103366118 dup Chr4_64 chr4 132219682 132762927 dup Chr4_65 chr4 57894345 58495951 dup Chr4_66 chr4 48898338 49501045 del Chr4_67 chr4 3431313 4469058 dup Chr4_68 chr4 118836451 119926714 dup Chr4_69 chr4 124568831 125736952 dup Chr5_1 chr5 106519625 106579710 del Chr5_2 chr5 34134806 34405626 complex WGTP event CNV_id chromosome start end call Chr5_3 chr5 99235573 99537338 complex Chr5_4 chr5 21184910 21748947 complex Chr5_5 chr5 160477321 160626797 multiallelic Chr5_6 chr5 103511683 103661467 del Chr5_7 chr5 21814498 22199675 complex Chr5_8 chr5 130466896 130619811 complex Chr5_9 chr5 97421264 97575845 dup Chr5_10 chr5 69109876 69264678 dup Chr5_11 chr5 149804786 150265935 del Chr5_12 chr5 104685688 104853617 dup Chr5_13 chr5 140137124 140307304 del Chr5_14 chr5 13218142 13456575 del Chr5_15 chr5 71935078 72108737 del Chr5_16 chr5 31332034 31505885 dup Chr5_17 chr5 12087304 12261440 dup Chr5_18 chr5 74469516 74647470 del Chr5_19 chr5 93790961 94067957 complex Chr5_20 chr5 165155278 165334527 complex Chr5_21 chr5 26791054 26970598 del Chr5_22 chr5 19066044 19245996 del Chr5_23 chr5 17417700 17972161 complex Chr5_24 chr5 81245981 81550493 del Chr5_25 chr5 176550923 176735050 dup Chr5_26 chr5 144153983 144340436 dup Chr5_27 chr5 70263 648955 del Chr5_28 chr5 140488471 140678806 dup Chr5_29 chr5 70072978 70425468 multiallelic Chr5_30 chr5 32047775 32239257 dup Chr5_31 chr5 66393681 66586635 dup Chr5_32 chr5 9850992 10044066 del Chr5_33 chr5 180019804 180214082 dup Chr5_34 chr5 171473028 171667877 del/dup Chr5_35 chr5 179467083 179662550 dup Chr5_36 chr5 12839321 13039901 dup Chr5_37 chr5 5033876 5237615 del Chr5_38 chr5 171913937 172117968 dup Chr5_39 chr5 3629619 3840514 del Chr5_40 chr5 153062206 153273106 del Chr5_41 chr5 130098933 130316104 del Chr5_42 chr5 673163 1214476 multiallelic Chr5_43 chr5 99413870 99874154 complex Chr5_44 chr5 155313275 155548476 del Chr5_45 chr5 156930186 157165622 del Chr5_46 chr5 125078762 125315808 del Chr5_47 chr5 128623637 128862751 del Chr5_48 chr5 100535625 100788621 dup Chr5_49 chr5 104334472 104660077 del Chr5_50 chr5 175337984 175685508 dup Chr5_51 chr5 117692624 117970146 del Chr5_52 chr5 178593872 178970135 dup Chr5_53 chr5 98633225 98917493 dup Chr5_54 chr5 61438895 61723574 complex Chr5_55 chr5 95257462 95566189 dup Chr5_56 chr5 135193500 135502898 del Chr5_57 chr5 49784109 50093939 dup Chr5_58 chr5 5500098 5817620 del Chr5_59 chr5 109669759 110056060 del Chr5_60 chr5 32281118 32774401 del Chr5_61 chr5 69109876 70831640 complex Chr5_62 chr5 140137124 140808866 dup Chr5_63 chr5 70234598 70831640 dup Chr6_1 chr6 128883885 128886524 dup WGTP event CNV_id chromosome start end call Chr6_2 chr6 69652213 69655072 dup Chr6_3 chr6 31338567 31342560 dup Chr6_4 chr6 32634806 32650604 complex Chr6_5 chr6 81870395 81891996 dup Chr6_6 chr6 32610887 32650604 dup Chr6_7 chr6 31568086 31605085 del Chr6_8 chr6 16981250 17020517 dup Chr6_9 chr6 79116279 79156482 dup Chr6_10 chr6 168811525 168857249 del Chr6_11 chr6 137914018 137962674 dup Chr6_12 chr6 51472475 51548810 del Chr6_13 chr6 78156739 78233520 del Chr6_14 chr6 103834514 104012090 dup Chr6_15 chr6 88415707 88498192 del Chr6_16 chr6 5001 91701 complex Chr6_17 chr6 134665824 134752836 del Chr6_18 chr6 169563923 169651825 del Chr6_19 chr6 32479731 32813412 dup Chr6_20 chr6 29577080 29780644 del/dup Chr6_21 chr6 32973767 33072074 dup Chr6_22 chr6 29900413 30083123 complex Chr6_23 chr6 168701943 168857249 complex Chr6_24 chr6 41696767 41807431 del Chr6_25 chr6 137501221 137615031 del Chr6_26 chr6 38696947 38819063 complex Chr6_27 chr6 31338567 31605085 del/dup Chr6_28 chr6 35276094 35398980 del Chr6_29 chr6 78198715 78339761 del Chr6_30 chr6 68213162 68355095 del Chr6_31 chr6 160743309 161050209 complex Chr6_32 chr6 11787739 11930337 del Chr6_33 chr6 58442668 58587658 dup Chr6_34 chr6 50627298 50775800 del Chr6_35 chr6 154229897 154386563 del Chr6_36 chr6 53947332 54104052 dup Chr6_37 chr6 103255429 103412632 del Chr6_38 chr6 166112052 166269346 del Chr6_39 chr6 122765634 122925836 del Chr6_40 chr6 143958314 144121669 del Chr6_41 chr6 159974242 160185562 dup Chr6_42 chr6 75018716 75184885 del Chr6_43 chr6 151380322 151546953 dup Chr6_44 chr6 31979491 32317091 del/dup Chr6_45 chr6 78852599 79250187 del Chr6_46 chr6 129315361 129484648 dup Chr6_47 chr6 35571719 35914482 dup Chr6_48 chr6 163962475 164132314 del Chr6_49 chr6 26801198 27203693 dup Chr6_50 chr6 89147456 89318637 del Chr6_51 chr6 153155406 153326844 del Chr6_52 chr6 30752672 30924298 del Chr6_53 chr6 117537917 117733968 del Chr6_54 chr6 115895071 116068349 dup Chr6_55 chr6 87874602 88049676 del Chr6_56 chr6 44987769 45164736 dup Chr6_57 chr6 133486412 133669057 del Chr6_58 chr6 95264814 95451409 dup Chr6_59 chr6 170738849 170927551 complex Chr6_60 chr6 87513222 87701933 del/dup Chr6_61 chr6 46808141 47036030 complex Chr6_62 chr6 10551783 10751118 del Chr6_63 chr6 5001 598718 del WGTP event CNV_id chromosome start end call Chr6_64 chr6 31136269 31460757 dup Chr6_65 chr6 513061 720274 del Chr6_66 chr6 162161167 162381661 dup Chr6_67 chr6 78393674 78637549 dup Chr6_68 chr6 170499383 170761941 dup Chr6_69 chr6 63764581 64043848 dup Chr6_70 chr6 162828733 163110786 dup Chr6_71 chr6 34490470 34822655 dup Chr6_72 chr6 167471615 167816346 dup Chr6_73 chr6 57292500 57670563 dup Chr6_74 chr6 105302783 105767502 dup Chr6_75 chr6 168055424 168533940 dup Chr6_76 chr6 114773001 115633650 dup Chr6_77 chr6 160342655 161205076 dup Chr7_1 chr7 64424689 64515187 del Chr7_2 chr7 43725779 43830031 dup Chr7_3 chr7 156849831 157112954 dup Chr7_4 chr7 149976469 150101345 del Chr7_5 chr7 75208500 75447331 dup Chr7_6 chr7 100000141 100342681 complex Chr7_7 chr7 109357547 109506183 dup Chr7_8 chr7 130179011 130328113 del Chr7_9 chr7 53107233 53259225 del Chr7_10 chr7 4365856 4519892 dup Chr7_11 chr7 8846889 9005429 del Chr7_12 chr7 82945157 83104763 dup Chr7_13 chr7 66143652 66303403 dup Chr7_14 chr7 23493296 23653562 del Chr7_15 chr7 109003931 109201570 complex Chr7_16 chr7 53749523 53910569 dup Chr7_17 chr7 125254760 125488816 dup Chr7_18 chr7 110394862 110559484 del Chr7_19 chr7 84797973 84962693 dup Chr7_20 chr7 22528824 22694150 del Chr7_21 chr7 78906115 79072297 dup Chr7_22 chr7 152438821 152736427 del/dup Chr7_23 chr7 97120935 97292680 del Chr7_24 chr7 101494175 101666167 dup Chr7_25 chr7 27566856 27746109 del Chr7_26 chr7 106471 298664 complex Chr7_27 chr7 68857155 69038812 dup Chr7_28 chr7 11700479 11882659 del Chr7_29 chr7 142664612 143806286 multiallelic Chr7_30 chr7 71640441 71823049 dup Chr7_31 chr7 126088740 126271794 del Chr7_32 chr7 19209283 19394202 dup Chr7_33 chr7 133094440 133281052 complex Chr7_34 chr7 6983151 7267141 del Chr7_35 chr7 60893982 61087258 complex Chr7_36 chr7 138190952 138384594 dup Chr7_37 chr7 143176789 143479566 multiallelic Chr7_38 chr7 74410376 74608092 complex Chr7_39 chr7 149106042 149304235 dup Chr7_40 chr7 149689597 149901452 del Chr7_41 chr7 141163595 141382145 del/dup Chr7_42 chr7 110462178 110898776 del Chr7_43 chr7 131778945 132001738 dup Chr7_44 chr7 63995424 64730827 complex Chr7_45 chr7 74410376 76494030 del/dup Chr7_46 chr7 87731680 87974020 del Chr7_47 chr7 16046062 16300630 del Chr7_48 chr7 37371953 37631800 del WGTP event CNV_id chromosome start end call Chr7_49 chr7 152831155 153195879 dup Chr7_50 chr7 110117249 110381800 del Chr7_51 chr7 155658864 155925343 del Chr7_52 chr7 3059866 3333470 del Chr7_53 chr7 112086078 112362579 dup Chr7_54 chr7 29431177 29708612 dup Chr7_55 chr7 35597466 35893678 dup Chr7_56 chr7 37991943 38296695 del Chr7_57 chr7 141610138 142240984 del Chr7_58 chr7 65845580 66303403 dup Chr7_59 chr7 104360658 104704532 dup Chr7_60 chr7 71640441 72320549 complex Chr7_61 chr7 57396706 57770231 dup Chr7_62 chr7 14670117 15073026 del Chr7_63 chr7 62132321 62553525 dup Chr7_64 chr7 71356121 71823049 dup Chr7_65 chr7 73439084 74608092 del/dup Chr7_66 chr7 972336 1463188 del Chr7_67 chr7 148879238 149394063 dup Chr7_68 chr7 16783293 17304719 dup Chr7_69 chr7 74410376 74952654 dup Chr7_70 chr7 60893982 62499664 dup Chr8_1 chr8 2303623 2411266 del Chr8_2 chr8 100473327 100907800 del Chr8_3 chr8 129633607 129784954 del Chr8_4 chr8 7873151 8024993 del Chr8_5 chr8 58092946 58525998 complex Chr8_6 chr8 25324942 25478051 del Chr8_7 chr8 59932 223973 complex Chr8_8 chr8 145203172 145357632 dup Chr8_9 chr8 6719130 8212456 multiallelic Chr8_10 chr8 4596112 4890346 del Chr8_11 chr8 39364955 39716796 del Chr8_12 chr8 115165252 115326300 del Chr8_13 chr8 79784789 79950902 del Chr8_14 chr8 100098024 100265857 dup Chr8_15 chr8 58468949 58637003 del Chr8_16 chr8 93612869 93782102 del Chr8_17 chr8 89032945 89202820 del Chr8_18 chr8 86592730 87124169 complex Chr8_19 chr8 7156826 7328299 multiallelic Chr8_20 chr8 22241469 22414061 del Chr8_21 chr8 145494501 145668486 del/dup Chr8_22 chr8 11778967 12611672 del/dup Chr8_23 chr8 51049146 51300548 del Chr8_24 chr8 2105020 2411266 del/dup Chr8_25 chr8 50578416 50819905 dup Chr8_26 chr8 133470532 133754071 complex Chr8_27 chr8 59932 484890 dup Chr8_28 chr8 120012490 120344931 dup Chr8_29 chr8 54995543 55179518 dup Chr8_30 chr8 48343375 48554996 dup Chr8_31 chr8 48950846 49170567 del Chr8_32 chr8 11819907 12078007 dup Chr8_33 chr8 54637142 54900026 del Chr8_34 chr8 137585971 138040412 del Chr8_35 chr8 53823346 54105603 dup Chr8_36 chr8 116967502 117250765 dup Chr8_37 chr8 20273229 20559087 del Chr8_38 chr8 92043675 92342900 del Chr8_39 chr8 13581607 13896999 del Chr8_40 chr8 91069962 91398845 del WGTP event CNV_id chromosome start end call Chr8_41 chr8 17335551 17685810 del Chr8_42 chr8 7942417 8344153 dup Chr8_43 chr8 4230863 4755808 del Chr8_44 chr8 16231929 17010633 dup Chr8_45 chr8 114644879 115391133 dup Chr8_46 chr8 14721071 15809077 del Chr8_47 chr8 3586932 5909600 dup Chr8_48 chr8 20577324 23167554 del Chr9_1 chr9 133461155 133485243 del/dup Chr9_2 chr9 44502980 44567187 dup Chr9_3 chr9 38557168 44769175 complex Chr9_4 chr9 66093288 66188415 del Chr9_5 chr9 40004730 40155117 del/dup Chr9_6 chr9 80822890 80931674 dup Chr9_7 chr9 64724577 64835350 del Chr9_8 chr9 39175643 39294206 multiallelic Chr9_9 chr9 42650537 45935928 del/dup Chr9_10 chr9 137473621 137617588 del Chr9_11 chr9 40012313 40513847 multiallelic Chr9_12 chr9 131300676 131448167 dup Chr9_13 chr9 85353708 85507991 del Chr9_14 chr9 138161400 138429268 dup Chr9_15 chr9 5287921 5444512 del Chr9_16 chr9 64135929 68383081 del/dup Chr9_17 chr9 125955511 126116512 dup Chr9_18 chr9 12611942 12774092 del Chr9_19 chr9 66093288 67978103 complex Chr9_20 chr9 44037059 44769175 complex Chr9_21 chr9 16631966 16799203 del Chr9_22 chr9 76595419 76903461 del Chr9_23 chr9 29125948 29299828 del Chr9_24 chr9 30854032 31028881 dup Chr9_25 chr9 11783343 12164755 del Chr9_26 chr9 21994 373816 del/dup Chr9_27 chr9 39258647 39435726 del Chr9_28 chr9 112905346 113082505 dup Chr9_29 chr9 38704188 40155117 complex Chr9_30 chr9 38557168 38736668 del Chr9_31 chr9 67346070 68383081 del Chr9_32 chr9 10178450 10360398 del Chr9_33 chr9 101719787 101905114 del Chr9_34 chr9 64724577 65072855 dup Chr9_35 chr9 29784954 30063518 del Chr9_36 chr9 109264965 109454331 del Chr9_37 chr9 83643578 83833156 dup Chr9_38 chr9 66093288 66380661 del Chr9_39 chr9 44819176 45013784 del Chr9_40 chr9 120727751 120922549 del Chr9_41 chr9 68065023 68383081 del/dup Chr9_42 chr9 44037059 44239139 del Chr9_43 chr9 106230185 106435633 del Chr9_44 chr9 67037466 67533672 dup Chr9_45 chr9 41415897 41784440 dup Chr9_46 chr9 30199650 30421507 dup Chr9_47 chr9 6566991 6828660 del Chr9_48 chr9 130767120 131058115 del Chr9_49 chr9 43456697 43755411 del Chr9_50 chr9 7165387 7472982 del Chr9_51 chr9 41194015 41507122 del Chr9_52 chr9 42650537 43065826 del/dup Chr9_53 chr9 514413 843033 del Chr9_54 chr9 136526666 137102322 del WGTP event CNV_id chromosome start end call Chr9_55 chr9 28462018 28840774 del Chr9_56 chr9 12225048 12612041 del Chr9_57 chr9 65483586 65886538 del Chr9_58 chr9 87248281 87654534 del Chr9_59 chr9 112320009 113082505 dup Chr9_60 chr9 45063785 45935928 del/dup Chr9_61 chr9 1045347 1519128 del Chr9_62 chr9 41573887 42118524 del/dup Chr9_63 chr9 40205118 41016432 del Chr9_64 chr9 40719624 43755411 del/dup Chr10_1 chr10 81418250 81553432 del Chr10_2 chr10 55030618 55256936 del Chr10_3 chr10 68016700 68162396 del Chr10_4 chr10 80945468 81810835 del/dup Chr10_5 chr10 107519652 107743529 complex Chr10_6 chr10 20726725 20938614 del Chr10_7 chr10 56078033 56236143 del Chr10_8 chr10 60388039 60641367 dup Chr10_9 chr10 51118852 51278775 del/dup Chr10_10 chr10 46999176 47262482 del/dup Chr10_11 chr10 135111207 135279389 dup Chr10_12 chr10 88505038 89299742 del/dup Chr10_13 chr10 38908842 39194941 complex Chr10_14 chr10 134733303 135111183 complex Chr10_15 chr10 50001 214405 dup Chr10_16 chr10 50641980 50807416 del Chr10_17 chr10 134515692 134683302 dup Chr10_18 chr10 5677111 5844786 dup Chr10_19 chr10 74105644 74277126 dup Chr10_20 chr10 98779953 98952462 del Chr10_21 chr10 47796101 47972148 del/dup Chr10_22 chr10 70127725 70301318 del Chr10_23 chr10 122625702 122891863 del Chr10_24 chr10 90825044 91007466 del Chr10_25 chr10 88715605 88898563 del Chr10_26 chr10 110448977 110633486 dup Chr10_27 chr10 102368626 102555726 del Chr10_28 chr10 124253065 124444805 complex Chr10_29 chr10 42004899 42199692 dup Chr10_30 chr10 45341719 47972148 del/dup Chr10_31 chr10 58160636 58359959 del Chr10_32 chr10 134076220 134277057 del Chr10_33 chr10 51392922 51595172 del Chr10_34 chr10 45341719 46063691 del/dup Chr10_35 chr10 47897414 48101925 dup Chr10_36 chr10 48213402 49121538 del/dup Chr10_37 chr10 125047207 125259149 del Chr10_38 chr10 78781397 78996345 del Chr10_39 chr10 76904943 77122607 del Chr10_40 chr10 102141840 102370625 dup Chr10_41 chr10 42285137 42830197 del Chr10_42 chr10 78988070 79248885 dup Chr10_43 chr10 59214388 59489499 del Chr10_44 chr10 45896971 46174280 dup Chr10_45 chr10 56503549 56781399 del Chr10_46 chr10 19754643 20065000 del Chr10_47 chr10 7463502 7777745 del Chr10_48 chr10 128798515 129129012 dup Chr10_49 chr10 127443890 127776692 dup Chr10_50 chr10 37325769 37665705 complex Chr10_51 chr10 77090565 77440455 dup Chr10_52 chr10 50641980 51595172 del/dup WGTP event CNV_id chromosome start end call Chr10_53 chr10 2650802 3188773 dup Chr11_1 chr11 30936338 31020588 del Chr11_2 chr11 67367400 67459594 dup Chr11_3 chr11 4012521 4466764 multiallelic Chr11_4 chr11 3193088 3376156 dup Chr11_5 chr11 49168813 49425542 del/dup Chr11_6 chr11 90247849 90559703 complex Chr11_7 chr11 88083993 88339832 complex Chr11_8 chr11 98575697 98717492 del Chr11_9 chr11 48806924 49141766 dup Chr11_10 chr11 113877495 114024335 dup Chr11_11 chr11 28881069 29029074 dup Chr11_12 chr11 40879434 41039419 del Chr11_13 chr11 129474432 129635215 del Chr11_14 chr11 35275896 35437098 dup Chr11_15 chr11 55216263 55378460 del Chr11_16 chr11 65316469 65478939 dup Chr11_17 chr11 89207823 89372535 dup Chr11_18 chr11 60671936 60837233 multiallelic Chr11_19 chr11 96530728 96698006 del Chr11_20 chr11 96408179 96576298 del Chr11_21 chr11 3483885 3758005 complex Chr11_22 chr11 25148529 25322096 del Chr11_23 chr11 50013000 50404139 dup Chr11_24 chr11 2745620 2920188 dup Chr11_25 chr11 58456668 58765249 dup Chr11_26 chr11 399846 1313968 complex Chr11_27 chr11 54978996 55268838 del Chr11_28 chr11 34986509 35183360 del Chr11_29 chr11 25590379 25799242 del Chr11_30 chr11 41077222 41290487 del Chr11_31 chr11 8741389 8966149 dup Chr11_32 chr11 4864469 5091907 del Chr11_33 chr11 5686953 5927293 del/dup Chr11_34 chr11 130938011 131254195 dup Chr11_35 chr11 84858128 85107139 dup Chr11_36 chr11 85020345 85281636 del Chr11_37 chr11 18775305 19038644 dup Chr11_38 chr11 122784405 123050005 del Chr11_39 chr11 71041287 71335224 complex Chr11_40 chr11 129537862 129847927 del Chr11_41 chr11 67281513 67616066 del Chr11_42 chr11 32671219 33006516 dup Chr11_43 chr11 81088432 81508270 del Chr11_44 chr11 3193088 3656689 dup Chr11_45 chr11 89082686 89569836 dup Chr11_46 chr11 48260247 48820182 del Chr11_47 chr11 73565215 74235245 dup Chr12_1 chr12 7918138 7989956 dup Chr12_2 chr12 130371694 130509579 del Chr12_3 chr12 22333762 22472221 dup Chr12_4 chr12 7748086 8515254 complex Chr12_5 chr12 29914434 30066499 dup Chr12_6 chr12 10961112 11122296 del Chr12_7 chr12 12511921 12674391 dup Chr12_8 chr12 90649382 90813144 dup Chr12_9 chr12 25883598 26052383 del Chr12_10 chr12 119878565 120047533 del Chr12_11 chr12 56116000 56288135 dup Chr12_12 chr12 96672954 96848094 dup Chr12_13 chr12 20833482 21009087 del Chr12_14 chr12 9262862 9814796 del WGTP event CNV_id chromosome start end call Chr12_15 chr12 29002049 29181116 del Chr12_16 chr12 31016734 31382371 del/dup Chr12_17 chr12 16156359 16337645 dup Chr12_18 chr12 128471344 128658697 del Chr12_19 chr12 52633336 52820913 dup Chr12_20 chr12 10860887 11606188 del/dup Chr12_21 chr12 33884264 34084037 dup Chr12_22 chr12 44435605 44636158 del Chr12_23 chr12 70388731 70594440 dup Chr12_24 chr12 50849531 51055601 dup Chr12_25 chr12 6324145 6534096 dup Chr12_26 chr12 132095571 132307316 del Chr12_27 chr12 22032101 22250748 del Chr12_28 chr12 36142962 36470532 dup Chr12_29 chr12 127597185 127906190 del Chr12_30 chr12 36860465 37089322 dup Chr12_31 chr12 46715969 47111766 del/dup Chr12_32 chr12 7748086 7989956 dup Chr12_33 chr12 81603513 81860089 del Chr12_34 chr12 71276974 71537376 del Chr12_35 chr12 57308996 57609312 dup Chr12_36 chr12 62196683 62538439 dup Chr12_37 chr12 22210384 22628174 dup Chr12_38 chr12 327694 860805 dup Chr12_39 chr12 130371694 130935124 dup Chr12_40 chr12 33333291 34462575 dup Chr12_41 chr12 128471344 129640456 dup Chr12_42 chr12 36142962 37321303 dup Chr13_1 chr13 56523625 56729961 complex Chr13_2 chr13 76523033 76666465 del Chr13_3 chr13 110460034 110604912 dup Chr13_4 chr13 71226326 71383406 del Chr13_5 chr13 86954602 87112550 del Chr13_6 chr13 65062295 65292451 del/dup Chr13_7 chr13 33768946 33934202 del/dup Chr13_8 chr13 88476233 88642741 del Chr13_9 chr13 104418323 104585016 dup Chr13_10 chr13 25898592 26065378 dup Chr13_11 chr13 17918001 18354948 dup Chr13_12 chr13 112424858 112739202 del Chr13_13 chr13 113086430 113259065 del Chr13_14 chr13 92972655 93146180 del Chr13_15 chr13 74102052 74275589 dup Chr13_16 chr13 75219611 75440004 del Chr13_17 chr13 107090320 107274703 del Chr13_18 chr13 82592802 82779067 del Chr13_19 chr13 48181984 48370518 del Chr13_20 chr13 19918915 20122478 del Chr13_21 chr13 82956558 83175698 del Chr13_22 chr13 82035430 82280653 del Chr13_23 chr13 110872855 111151995 del Chr13_24 chr13 108719614 109007551 del Chr13_25 chr13 62097238 62520980 del Chr13_26 chr13 88209082 88673975 dup Chr14_1 chr14 82105460 82216550 del Chr14_2 chr14 41933545 42078579 del Chr14_3 chr14 86259051 86411966 dup Chr14_4 chr14 45863402 46018276 dup Chr14_5 chr14 83206211 83363593 del Chr14_6 chr14 31928231 32086193 dup Chr14_7 chr14 20285948 20541454 del/dup Chr14_8 chr14 44775832 45052160 del WGTP event CNV_id chromosome start end call Chr14_9 chr14 18732531 19626027 complex Chr14_10 chr14 73030050 73196823 dup Chr14_11 chr14 59477247 59652794 del Chr14_12 chr14 25297720 25474958 del/dup Chr14_13 chr14 47329907 47516073 dup Chr14_14 chr14 77143933 77332325 dup Chr14_15 chr14 19215884 19626027 complex Chr14_16 chr14 27134939 27513082 del/dup Chr14_17 chr14 41115623 41329261 del Chr14_18 chr14 43468955 43714231 del Chr14_19 chr14 44127583 44383416 del Chr14_20 chr14 103217278 103482566 del Chr14_21 chr14 85228067 85495155 del Chr14_22 chr14 77973363 78243281 del Chr14_23 chr14 104584391 105020471 del Chr15_1 chr15 20231618 20285790 del Chr15_2 chr15 80676701 81107580 del/dup Chr15_3 chr15 35618861 35759779 dup Chr15_4 chr15 82506626 82870925 del/dup Chr15_5 chr15 32330313 32775539 del/dup Chr15_6 chr15 83063933 83217534 del Chr15_7 chr15 46296330 46451070 del Chr15_8 chr15 18263733 21066294 complex Chr15_9 chr15 67421806 67579253 del Chr15_10 chr15 100089153 100248597 dup Chr15_11 chr15 18747225 19014108 del Chr15_12 chr15 38619837 38782403 del Chr15_13 chr15 77142292 77305824 dup Chr15_14 chr15 26599827 26763830 del Chr15_15 chr15 21805431 22452007 del/dup Chr15_16 chr15 19791326 20428072 multiallelic Chr15_17 chr15 99707205 99872978 dup Chr15_18 chr15 26086062 26763830 complex Chr15_19 chr15 63967839 64137439 del Chr15_20 chr15 20762791 21365850 complex Chr15_21 chr15 93267980 93447142 del Chr15_22 chr15 19050502 19484504 complex Chr15_23 chr15 99298613 99478425 dup Chr15_24 chr15 99550339 99734009 complex Chr15_25 chr15 20197558 20428072 complex Chr15_26 chr15 41610450 41935933 del/dup Chr15_27 chr15 30191187 30773871 del/dup Chr15_28 chr15 74957605 75160503 dup Chr15_29 chr15 29981051 30184543 del/dup Chr15_30 chr15 29553592 29932359 del Chr15_31 chr15 89632854 89841316 dup Chr15_32 chr15 18263733 18473371 dup Chr15_33 chr15 94219335 94439704 del Chr15_34 chr15 30191187 30412040 del/dup Chr15_35 chr15 88366960 88590229 dup Chr15_36 chr15 28080236 28939783 del/dup Chr15_37 chr15 83451942 83685716 complex Chr15_38 chr15 72002167 72251969 complex Chr15_39 chr15 25060215 25335769 del Chr15_40 chr15 66325126 66601717 del Chr15_41 chr15 79728575 80011124 dup Chr15_42 chr15 70606839 70907613 complex Chr15_43 chr15 95508704 95833748 del Chr15_44 chr15 28605178 28939783 del Chr15_45 chr15 20253909 20704897 del/dup Chr15_46 chr15 42756160 43210134 dup Chr15_47 chr15 98091816 98574562 dup WGTP event CNV_id chromosome start end call Chr15_48 chr15 29725770 30375195 dup Chr15_49 chr15 49069549 49617631 dup Chr16_1 chr16 32140874 32205188 complex Chr16_2 chr16 31658070 33715261 complex Chr16_3 chr16 88398233 88495450 del Chr16_4 chr16 21052 133600 dup Chr16_5 chr16 76811430 76929139 del Chr16_6 chr16 14529556 15133811 del/dup Chr16_7 chr16 31736153 32773201 multiallelic Chr16_8 chr16 46886938 47037255 dup Chr16_9 chr16 86986673 87137417 dup Chr16_10 chr16 34215264 34627143 dup Chr16_11 chr16 21241957 21833734 del/dup Chr16_12 chr16 73977115 74134472 dup Chr16_13 chr16 28590949 28751472 del Chr16_14 chr16 804894 1111069 complex Chr16_15 chr16 72892281 73144686 complex Chr16_16 chr16 85399263 85564336 del Chr16_17 chr16 33282424 34224164 complex Chr16_18 chr16 18036757 19066807 del/dup Chr16_19 chr16 32612180 32902091 complex Chr16_20 chr16 22201625 22679810 del/dup Chr16_21 chr16 68412623 68870723 complex Chr16_22 chr16 25532212 25718755 dup Chr16_23 chr16 53121783 53309710 dup Chr16_24 chr16 86476851 86671233 del Chr16_25 chr16 9968477 10165051 del/dup Chr16_26 chr16 31736153 32205188 complex Chr16_27 chr16 87970408 88179649 dup Chr16_28 chr16 14896111 15274051 dup Chr16_29 chr16 16092718 16304613 del Chr16_30 chr16 29981456 30290781 dup Chr16_31 chr16 24850896 25094479 dup Chr16_32 chr16 18000444 18293192 dup Chr16_33 chr16 4912851 5364830 del/dup Chr16_34 chr16 16092718 16831289 del/dup Chr16_35 chr16 45874367 46163788 dup Chr16_36 chr16 6588011 6878909 del Chr16_37 chr16 57136506 57433538 del Chr16_38 chr16 70533845 70831848 dup Chr16_39 chr16 54226897 54541091 dup Chr16_40 chr16 2476826 2810537 dup Chr16_41 chr16 29181449 29609853 dup Chr16_42 chr16 69364623 69874484 dup Chr16_43 chr16 28082639 29058054 del/dup Chr16_44 chr16 17480600 18293192 dup Chr16_45 chr16 266993 1081992 del Chr17_1 chr17 31583743 31651855 multiallelic Chr17_2 chr17 65403530 65490775 del Chr17_3 chr17 343377 440727 del Chr17_4 chr17 36001826 36103630 dup Chr17_5 chr17 21191534 22014559 del/dup Chr17_6 chr17 22045526 22170456 dup Chr17_7 chr17 53997375 54149948 dup Chr17_8 chr17 55350429 55513944 complex Chr17_9 chr17 72638503 72807003 dup Chr17_10 chr17 42875373 43119955 complex Chr17_11 chr17 18175250 18387109 multiallelic Chr17_12 chr17 41439751 42632332 multiallelic Chr17_13 chr17 57650339 57826573 complex Chr17_14 chr17 31309398 31981395 complex Chr17_15 chr17 32036161 32221507 del WGTP event CNV_id chromosome start end call Chr17_16 chr17 76741026 76933757 dup Chr17_17 chr17 40977732 41171794 dup Chr17_18 chr17 20227887 20640432 dup Chr17_19 chr17 32642843 32848430 dup Chr17_20 chr17 33803799 34010545 del/dup Chr17_21 chr17 16467781 16758162 del Chr17_22 chr17 43957672 44191836 dup Chr17_23 chr17 48369345 48627779 del Chr17_24 chr17 13821966 14069281 del Chr17_25 chr17 33140728 34010545 complex Chr17_26 chr17 36554901 37123136 del Chr17_27 chr17 22902614 23201246 dup Chr17_28 chr17 568336 1008155 dup Chr17_29 chr17 42326359 42632332 dup Chr17_30 chr17 27245834 27562095 dup Chr17_31 chr17 54437361 54780416 dup Chr17_32 chr17 18771341 19132640 complex Chr17_33 chr17 22045526 22465691 dup Chr18_1 chr18 64388382 64543942 dup Chr18_2 chr18 19024430 19181612 del Chr18_3 chr18 61863327 62021348 dup Chr18_4 chr18 35736115 35903305 dup Chr18_5 chr18 14077067 14251361 dup Chr18_6 chr18 11887023 12066102 del Chr18_7 chr18 6752909 6933645 dup Chr18_8 chr18 14817332 14998645 dup Chr18_9 chr18 62157007 62341492 dup Chr18_10 chr18 28637325 28828735 del Chr18_11 chr18 74125373 74378820 dup Chr18_12 chr18 14979964 15367893 dup Chr18_13 chr18 12230681 12489525 del Chr18_14 chr18 73047414 73306926 del Chr18_15 chr18 64138015 64411132 del Chr18_16 chr18 3667422 4160252 dup Chr18_17 chr18 67703807 68125877 del Chr18_18 chr18 32304033 32733948 dup Chr18_19 chr18 13988748 15367893 dup Chr19_1 chr19 8758670 8832847 complex Chr19_2 chr19 59359391 59464094 del/dup Chr19_3 chr19 55228822 55344796 complex Chr19_4 chr19 183069 327646 dup Chr19_5 chr19 14957950 15120179 dup Chr19_6 chr19 1331124 1495933 del Chr19_7 chr19 40402918 40578953 del Chr19_8 chr19 39817858 39984175 dup Chr19_9 chr19 52549596 52717317 del Chr19_10 chr19 47734587 48590893 del/dup Chr19_11 chr19 56683708 56958512 del Chr19_12 chr19 57037904 57225638 dup Chr19_13 chr19 902641 1095485 dup Chr19_14 chr19 20321226 20637787 del Chr19_15 chr19 24142405 24349203 dup Chr19_16 chr19 45304260 45531360 dup Chr19_17 chr19 58102271 58344387 del Chr19_18 chr19 48347697 48590893 del Chr19_19 chr19 59359391 60158136 complex Chr19_20 chr19 45983467 46237908 del Chr19_21 chr19 20028401 20290544 dup Chr19_22 chr19 44919744 45212970 dup Chr19_23 chr19 32658593 32953337 dup Chr19_24 chr19 34038496 34356975 del Chr19_25 chr19 902641 1495933 del/dup WGTP event CNV_id chromosome start end call Chr19_26 chr19 22774966 23732307 dup Chr19_27 chr19 38468914 39273401 dup Chr19_28 chr19 21777328 22951313 del Chr20_1 chr20 8001 11943 del Chr20_2 chr20 60464834 60583327 del Chr20_3 chr20 26006100 26072099 dup Chr20_4 chr20 36392696 36498327 dup Chr20_5 chr20 1424781 1627256 dup Chr20_6 chr20 59894657 60016638 del/dup Chr20_7 chr20 14679344 14803457 del Chr20_8 chr20 30959468 31211827 del Chr20_9 chr20 22977404 23121240 del Chr20_10 chr20 61572793 61846811 complex Chr20_11 chr20 60733815 60897084 del Chr20_12 chr20 28033231 28267569 complex Chr20_13 chr20 26006100 26267569 dup Chr20_14 chr20 62108666 62435964 complex Chr20_15 chr20 44126322 44398283 complex Chr20_16 chr20 25649992 26072099 complex Chr20_17 chr20 45701817 45957486 dup Chr20_18 chr20 55604184 56121677 del Chr20_19 chr20 10840138 11064725 del Chr20_20 chr20 8898291 9227700 del Chr20_21 chr20 2078560 2423469 dup Chr20_22 chr20 60464834 60897084 complex Chr20_23 chr20 11638021 12381393 dup Chr20_24 chr20 8002182 8595665 dup Chr21_1 chr21 27302101 27462314 dup Chr21_2 chr21 14098750 14261623 del Chr21_3 chr21 13556403 14152724 del/dup Chr21_4 chr21 10023842 10197104 del/dup Chr21_5 chr21 15834517 16018549 dup Chr21_6 chr21 20637992 20877335 del Chr21_7 chr21 32151463 32438711 del Chr22_1 chr22 46845829 46850201 del Chr22_2 chr22 48248831 48252981 del Chr22_3 chr22 47465793 47475686 del Chr22_4 chr22 43007198 43026202 dup Chr22_5 chr22 32494349 32528033 del Chr22_6 chr22 35499654 35569272 del Chr22_7 chr22 14509865 14563401 complex Chr22_8 chr22 33068219 33107464 del Chr22_9 chr22 45891592 45931039 del Chr22_10 chr22 20693407 20733158 del Chr22_11 chr22 23382276 23422245 del Chr22_12 chr22 42968722 43026202 del/dup Chr22_13 chr22 32193499 32234100 del Chr22_14 chr22 47095130 47136752 dup Chr22_15 chr22 49392382 49495206 del Chr22_16 chr22 44975462 45018495 complex Chr22_17 chr22 17363351 17436267 complex Chr22_18 chr22 49219663 49307552 del Chr22_19 chr22 43347341 43531066 del Chr22_20 chr22 16926349 17436267 complex Chr22_21 chr22 20619657 20733158 dup Chr22_22 chr22 25223053 25354450 del Chr22_23 chr22 35231063 35366534 del Chr22_24 chr22 23691355 24281461 del/dup Chr22_25 chr22 45709833 45931039 complex Chr22_26 chr22 41091699 41407804 dup Chr22_27 chr22 35499654 35685405 del Chr22_28 chr22 36328377 36590378 del WGTP event CNV_id chromosome start end call Chr22_29 chr22 33762965 33957507 del Chr22_30 chr22 18401047 18684001 del Chr22_31 chr22 43894761 44221622 dup Chr22_32 chr22 14509865 15652016 complex ChrX_1 chrX 114768844 114795257 del ChrX_2 chrX 128423110 128467003 complex ChrX_3 chrX 125340415 125399344 dup ChrX_4 chrX 151881624 151947652 dup ChrX_5 chrX 103049195 103124000 dup ChrX_6 chrX 77031055 77115217 del ChrX_7 chrX 104109151 104221182 del ChrX_8 chrX 148422218 148687904 dup ChrX_9 chrX 134587595 134703510 complex ChrX_10 chrX 96741719 96861762 del/dup ChrX_11 chrX 118739321 118863415 dup ChrX_12 chrX 109387916 109517626 del ChrX_13 chrX 105343681 105487922 del ChrX_14 chrX 27962843 28110213 dup ChrX_15 chrX 56622090 56770769 complex ChrX_16 chrX 126868603 127019222 del ChrX_17 chrX 31123273 31278805 del ChrX_18 chrX 139711783 139870206 dup ChrX_19 chrX 9138826 9310156 complex ChrX_20 chrX 115711880 115883234 dup ChrX_21 chrX 9860872 10041747 del ChrX_22 chrX 140319722 140559532 complex ChrX_23 chrX 119183307 119364831 del ChrX_24 chrX 61984759 62329082 dup ChrX_25 chrX 122690351 122888100 dup ChrX_26 chrX 141595220 141794235 complex ChrX_27 chrX 108585146 108787037 del ChrX_28 chrX 70654274 71083437 del ChrX_29 chrX 313529 532251 dup ChrX_30 chrX 28107442 28359884 del ChrX_31 chrX 57515394 57773429 dup ChrX_32 chrX 128423110 128689620 del ChrX_33 chrX 47523164 47902964 del/dup ChrX_34 chrX 134587595 134880261 del ChrX_35 chrX 89957981 90252381 dup ChrX_36 chrX 134328057 134703510 dup ChrX_37 chrX 133926407 134223835 dup ChrX_38 chrX 66282690 66582954 dup ChrX_39 chrX 63321820 63666298 dup ChrX_40 chrX 118739321 119110866 dup ChrX_41 chrX 102888546 103261206 dup ChrX_42 chrX 89260661 89673776 dup ChrX_43 chrX 7061134 7483618 del ChrX_44 chrX 139711783 140501009 dup ChrX_45 chrX 1865728 3187726 dup ChrY_1 chrY 9174325 9284683 dup ChrY_2 chrY 21951675 22097515 del/dup ChrY_3 chrY 25241502 25501828 del ChrY_4 chrY 10432535 10697914 complex ChrY_5 chrY 5999160 6369813 complex ChrY_6 chrY 25470410 25653680 del/dup ChrY_7 chrY 22617025 22937953 dup ChrY_8 chrY 7738992 7981359 dup ChrY_9 chrY 26835125 27123476 dup ChrY_10 chrY 19062951 19393189 del ChrY_11 chrY 22934254 26842096 del/dup ChrY_12 chrY 21771803 22937953 complex ChrY_13 chrY 23113433 24253006 del/dup WGTP event CNV_id chromosome start end call ChrY_14 chrY 9174325 10072259 complex Supplemental Table 11C: CNV regions from 500K EA

chr start end gains losses overlap with WGTP 500K EA 1 77822 1058627 4 1 yes 500K EA 1 1548033 1725888 0 2 yes 500K EA 1 3608198 3678693 1 0 500K EA 1 7505729 7622325 1 0 500K EA 1 12722672 13544763 9 22 yes 500K EA 1 14050388 14117706 2 0 500K EA 1 15872786 15900413 0 2 500K EA 1 16554000 17053464 170 10 yes 500K EA 1 25190816 25209157 0 1 500K EA 1 30375428 30410749 0 6 500K EA 1 31351473 32135424 0 1 yes 500K EA 1 38797694 38806748 0 3 500K EA 1 53200585 53244138 0 2 500K EA 1 54981672 55020630 0 4 500K EA 1 72809121 72827226 1 0 500K EA 1 75795429 75869007 0 2 yes 500K EA 1 76950439 77014906 0 1 500K EA 1 77487035 77500483 0 2 500K EA 1 81599438 81608767 0 2 500K EA 1 83315378 83656249 2 1 yes 500K EA 1 94831811 94870624 0 5 500K EA 1 102084360 102129114 0 2 500K EA 1 105856683 105936087 0 6 500K EA 1 106491085 106558195 0 1 yes 500K EA 1 107366027 107421762 0 2 yes 500K EA 1 111499437 111506775 0 1 500K EA 1 111535893 111547026 0 3 500K EA 1 112407136 112422566 0 10 500K EA 1 112958672 116411310 2 1 yes 500K EA 1 119810703 119874484 3 3 yes 500K EA 1 141480746 143032961 9 17 yes 500K EA 1 143086160 143482819 0 1 yes 500K EA 1 144917189 146809052 6 60 yes 500K EA 1 148141867 148224708 5 0 500K EA 1 149495781 149552299 1 0 yes 500K EA 1 158157328 158413210 28 23 yes 500K EA 1 158796126 159091666 3 0 yes 500K EA 1 162149184 162157194 0 3 500K EA 1 163275200 163333436 0 2 yes 500K EA 1 167046739 167144950 0 4 500K EA 1 175389239 175405731 0 3 500K EA 1 182024854 182077428 0 2 500K EA 1 186049278 186300204 0 7 yes 500K EA 1 186468490 186551144 0 2 500K EA 1 186690763 186726869 0 4 500K EA 1 188509177 188557409 0 1 500K EA 1 190363185 190441853 0 3 500K EA 1 191669736 191674561 0 2 500K EA 1 192622899 192752192 1 4 yes 500K EA 1 193440880 193797731 10 44 yes 500K EA 1 197239167 197328634 0 1 500K EA 1 204831917 204885513 2 0 500K EA 1 206967918 207009174 0 4 500K EA 1 209313824 209394792 0 1 500K EA 1 220000153 220016185 1 0 500K EA 1 221972429 222010220 4 0 500K EA 1 228033829 228134776 2 0 yes 500K EA 1 233192877 233228405 0 2 chr start end gains losses overlap with WGTP 500K EA 1 233458152 233471959 1 0 500K EA 1 234327110 235054539 1 0 yes 500K EA 1 236233461 236634188 1 0 yes 500K EA 1 239362708 239606926 16 23 500K EA 1 242354620 242442043 0 2 500K EA 1 243265897 243272062 0 1 500K EA 1 244079375 244648357 1 0 yes 500K EA 1 244921722 245143423 0 2 yes 500K EA 2 240958 295803 1 0 yes 500K EA 2 302992 848062 1 0 yes 500K EA 2 1410597 1484084 1 0 500K EA 2 3256238 3288649 1 0 500K EA 2 3730174 3770183 0 1 500K EA 2 4402072 4417591 0 1 500K EA 2 6248649 6273145 0 17 500K EA 2 10297740 10357304 1 0 500K EA 2 10546176 10639567 1 0 500K EA 2 14296389 14319566 1 0 500K EA 2 14642533 14660690 0 9 500K EA 2 16983359 16989153 0 1 500K EA 2 17809678 17896719 1 0 500K EA 2 18063761 18147135 0 3 500K EA 2 29088147 30418897 1 0 yes 500K EA 2 34596931 34666683 0 4 500K EA 2 35484210 35548857 0 4 500K EA 2 36199686 36482225 0 2 yes 500K EA 2 36534557 36568956 1 0 500K EA 2 36959004 36960602 0 1 500K EA 2 37821038 37916959 21 3 yes 500K EA 2 40842372 40878370 0 3 500K EA 2 46525886 46668082 0 2 yes 500K EA 2 50710112 50772700 0 1 500K EA 2 56618323 56722941 2 1 yes 500K EA 2 57294090 57353462 2 0 yes 500K EA 2 58306194 61252101 1 0 yes 500K EA 2 64260853 64432941 2 0 yes 500K EA 2 66041145 66060953 1 0 500K EA 2 67178358 67248668 0 1 yes 500K EA 2 71253797 71285075 0 2 500K EA 2 75275078 75294365 0 2 500K EA 2 75702144 75825556 2 0 yes 500K EA 2 76749556 76771867 0 1 500K EA 2 77097511 77120706 0 1 500K EA 2 77876528 77905870 1 0 yes 500K EA 2 78111390 78551901 0 2 yes 500K EA 2 81671346 81727952 0 1 500K EA 2 83162231 83803064 0 1 yes 500K EA 2 87017102 88135226 3 2 yes 500K EA 2 89740700 91696901 6 36 yes 500K EA 2 94780673 94972832 1 0 yes 500K EA 2 97130485 97733045 1 1 yes 500K EA 2 107969196 108681855 2 0 yes 500K EA 2 110192354 110313018 1 0 yes 500K EA 2 113185466 113195120 0 1 500K EA 2 116213758 116391580 1 0 yes 500K EA 2 117201020 117460821 0 2 yes 500K EA 2 130490748 131318354 2 0 yes 500K EA 2 131747626 132310822 4 4 yes 500K EA 2 133101579 133147577 11 0 500K EA 2 137031522 137074036 1 0 chr start end gains losses overlap with WGTP 500K EA 2 142029855 142079679 1 0 yes 500K EA 2 151328047 151575481 1 0 yes 500K EA 2 153480707 153624340 0 2 yes 500K EA 2 174352834 174370707 0 2 500K EA 2 177140714 177191106 1 0 500K EA 2 183354176 183590436 1 0 yes 500K EA 2 185036251 185196292 0 1 500K EA 2 187242105 187318248 2 0 yes 500K EA 2 194745343 194782381 0 2 500K EA 2 205168233 205174230 0 2 500K EA 2 209298057 209377458 0 1 500K EA 2 213012709 213018930 0 8 500K EA 2 216138444 216256321 0 1 yes 500K EA 2 222179557 222227609 0 1 yes 500K EA 2 228736395 228746258 0 1 500K EA 2 233037366 233133441 1 0 500K EA 2 241111015 241229702 1 0 yes 500K EA 2 242415890 242730382 1 3 yes 500K EA 3 61204 102933 1 0 yes 500K EA 3 196081 211759 1 0 yes 500K EA 3 1222123 1302426 1 0 yes 500K EA 3 1338740 1346260 0 2 yes 500K EA 3 1455555 1563919 1 0 yes 500K EA 3 2217552 2462786 1 0 yes 500K EA 3 4062787 4081495 0 2 500K EA 3 4113369 4185967 0 2 yes 500K EA 3 4241532 4252366 0 1 yes 500K EA 3 6181901 6224264 0 7 500K EA 3 7499552 7539303 1 0 500K EA 3 14933078 15026556 1 0 yes 500K EA 3 16202432 16231043 0 1 500K EA 3 21180674 21351652 1 0 500K EA 3 24700007 24788964 0 1 yes 500K EA 3 26021365 26148227 0 1 yes 500K EA 3 36258534 36290961 0 1 500K EA 3 39509276 39530501 1 0 500K EA 3 41395796 41501946 0 1 yes 500K EA 3 42335110 42378384 0 1 500K EA 3 45991468 46095404 0 2 500K EA 3 46394638 46419798 0 1 500K EA 3 52981095 53014495 0 1 500K EA 3 60650681 60689812 0 1 500K EA 3 60775739 60919051 0 3 yes 500K EA 3 60968955 61027682 0 1 yes 500K EA 3 61039472 61094963 0 1 yes 500K EA 3 61119467 61195849 1 0 yes 500K EA 3 61544597 61611196 1 0 500K EA 3 64922928 64933281 0 1 500K EA 3 65151156 65199576 1 19 500K EA 3 68971420 69018486 2 0 500K EA 3 75474768 76085726 3 13 yes 500K EA 3 78536627 78579808 1 0 500K EA 3 89343185 89353777 0 1 500K EA 3 104428032 104433385 1 0 500K EA 3 105572457 106260663 0 1 yes 500K EA 3 113587565 113596024 0 1 500K EA 3 117568368 117604638 0 2 500K EA 3 122747576 122806155 1 0 500K EA 3 126932312 126935644 1 0 500K EA 3 128898840 128916240 0 1 chr start end gains losses overlap with WGTP 500K EA 3 131192345 131422071 147 28 yes 500K EA 3 132802569 132855391 1 0 500K EA 3 134503648 134515590 0 2 500K EA 3 141491918 141942926 1 1 yes 500K EA 3 143239239 143577329 2 0 yes 500K EA 3 144388359 144447071 1 0 yes 500K EA 3 147098550 147144469 0 1 500K EA 3 152984775 153025999 0 1 yes 500K EA 3 153811704 154007851 1 1 500K EA 3 156968004 156973709 2 0 500K EA 3 161833723 161862863 0 2 500K EA 3 163666164 163709523 0 4 500K EA 3 164344341 164432687 0 1 500K EA 3 166523565 166615499 0 4 500K EA 3 174683883 174755275 0 2 yes 500K EA 3 178177234 178198620 0 3 500K EA 3 187853052 187910042 0 2 yes 500K EA 3 189069542 189083061 1 0 500K EA 3 193570453 193577446 1 0 500K EA 3 196584084 196969332 188 0 yes 500K EA 3 198778468 198808132 0 2 yes 500K EA 4 19099 56331 1 2 500K EA 4 3509131 3547567 1 0 yes 500K EA 4 3661108 3751308 1 0 yes 500K EA 4 6725902 6739063 0 2 500K EA 4 8823992 9488074 17 2 yes 500K EA 4 9728030 9740273 0 1 yes 500K EA 4 9802458 9815460 0 1 yes 500K EA 4 9947405 9952736 0 4 yes 500K EA 4 11337511 11348511 0 13 500K EA 4 12928417 12968570 1 0 500K EA 4 17211513 17264589 0 1 500K EA 4 18763789 18863091 0 3 500K EA 4 20848734 20857264 0 1 500K EA 4 21693436 21767251 0 2 yes 500K EA 4 22951435 22990481 1 0 500K EA 4 23123935 23166081 0 2 500K EA 4 25178326 25184127 0 1 500K EA 4 25382090 25416475 0 3 500K EA 4 26132536 26138154 0 1 500K EA 4 27909573 27914267 1 0 500K EA 4 28308476 28445387 0 2 yes 500K EA 4 28800351 28817794 1 0 500K EA 4 28986666 29007386 0 1 500K EA 4 33971807 34235432 2 0 yes 500K EA 4 34579485 34680339 0 56 yes 500K EA 4 42950671 43051416 1 9 500K EA 4 44801372 44874500 3 0 500K EA 4 48890029 49469842 1 2 yes 500K EA 4 57963872 58446870 1 1 yes 500K EA 4 66400764 66474947 2 0 500K EA 4 68619630 68857679 1 0 yes 500K EA 4 69007686 69812428 7 45 yes 500K EA 4 69831620 69840498 0 1 yes 500K EA 4 69865808 69928319 3 0 yes 500K EA 4 70043934 70082367 0 1 yes 500K EA 4 70200693 70479481 2 42 yes 500K EA 4 71396544 71502233 0 4 500K EA 4 73716212 73794632 0 9 500K EA 4 74048053 74135413 0 2 chr start end gains losses overlap with WGTP 500K EA 4 77749271 77812584 0 2 yes 500K EA 4 87432938 87495944 0 2 500K EA 4 87774470 88046712 0 1 500K EA 4 89025760 89072503 0 2 500K EA 4 89315671 89486435 1 0 yes 500K EA 4 103130039 103291127 1 0 yes 500K EA 4 109298778 109305695 0 1 500K EA 4 114711846 114719490 0 1 500K EA 4 115761288 115792082 0 1 yes 500K EA 4 116439195 116540304 0 22 500K EA 4 118906546 119964813 1 0 yes 500K EA 4 124596552 125610766 1 0 yes 500K EA 4 125995545 126007226 0 1 500K EA 4 132277939 132739982 2 0 yes 500K EA 4 132781976 132855491 1 0 yes 500K EA 4 132883456 132959908 1 0 yes 500K EA 4 145146248 145448965 4 13 yes 500K EA 4 153133876 153167343 0 22 500K EA 4 156964511 156968445 0 1 500K EA 4 158541701 158702897 1 0 yes 500K EA 4 161385730 161462448 0 3 500K EA 4 162141027 162312760 18 0 500K EA 4 162551407 162593480 0 2 500K EA 4 166006477 166008354 0 1 500K EA 4 169169911 169472158 0 4 yes 500K EA 4 172699064 172742341 0 3 500K EA 4 178588468 178692863 1 0 yes 500K EA 4 181842862 181847554 0 1 500K EA 4 183006629 183024960 0 1 500K EA 4 185535745 185542857 0 1 500K EA 4 189546195 189637395 0 3 yes 500K EA 4 190885813 191140586 10 6 yes 500K EA 5 690324 937439 151 12 yes 500K EA 5 7188014 7256093 0 2 500K EA 5 8754920 8843546 0 11 500K EA 5 9950967 10008044 0 1 yes 500K EA 5 13197682 13401985 0 2 yes 500K EA 5 15362984 15386853 1 0 500K EA 5 15731556 15863987 1 35 500K EA 5 17451090 17840103 0 20 yes 500K EA 5 20472731 20494555 0 5 500K EA 5 23324344 23340668 0 1 500K EA 5 24564081 24613895 0 1 500K EA 5 32137157 32213541 5 0 yes 500K EA 5 33557835 33584771 0 2 500K EA 5 40909835 41045039 0 1 500K EA 5 55016652 55094749 1 0 500K EA 5 55688830 55707856 0 2 500K EA 5 61685160 61784669 1 0 yes 500K EA 5 62067121 62138099 1 0 500K EA 5 75462619 75510536 2 0 500K EA 5 75647353 75678730 1 0 500K EA 5 95329992 95565292 1 0 yes 500K EA 5 97054185 97163903 0 6 500K EA 5 97468282 97643999 2 0 yes 500K EA 5 99452655 99911270 1 2 yes 500K EA 5 100570013 100684490 2 0 yes 500K EA 5 101207948 101233931 0 6 500K EA 5 103967573 104010013 0 2 500K EA 5 104226158 104322489 1 1 chr start end gains losses overlap with WGTP 500K EA 5 104452196 104556024 0 5 yes 500K EA 5 106255008 106286649 0 1 500K EA 5 109778421 110180038 0 1 yes 500K EA 5 114725159 114765482 0 4 500K EA 5 115543618 115571522 0 1 500K EA 5 115606709 115661373 0 7 500K EA 5 117813488 117892105 0 1 yes 500K EA 5 118583762 118695647 0 1 500K EA 5 122626041 122685098 1 0 500K EA 5 128671528 128790773 0 2 yes 500K EA 5 135329916 135380394 0 2 yes 500K EA 5 137833483 137865270 0 1 500K EA 5 144466435 144475035 0 2 500K EA 5 146410036 146519693 0 1 500K EA 5 155497577 155530680 0 13 yes 500K EA 5 160471139 160490574 0 3 yes 500K EA 5 171966705 172148018 5 0 yes 500K EA 5 173726296 173745954 0 1 500K EA 5 175279234 175696974 5 0 yes 500K EA 5 178653574 178894478 2 0 yes 500K EA 5 180012576 180177830 1 0 yes 500K EA 5 180311387 180421549 1 0 500K EA 6 162334 356954 167 15 yes 500K EA 6 896385 953488 0 1 500K EA 6 2561236 2577107 0 1 500K EA 6 2934581 2961056 1 0 500K EA 6 7384069 7448784 1 0 500K EA 6 10574157 10664858 0 2 yes 500K EA 6 15776846 15833457 0 1 500K EA 6 26806459 27004868 1 0 yes 500K EA 6 29942451 30073480 0 84 yes 500K EA 6 30893252 30896567 0 1 yes 500K EA 6 31359339 31443686 2 18 yes 500K EA 6 31461308 31650287 0 6 yes 500K EA 6 41706502 41749467 0 4 yes 500K EA 6 45061736 45097497 0 1 yes 500K EA 6 45993620 45995399 0 1 500K EA 6 47798026 47814999 0 1 500K EA 6 52730063 52774200 0 1 500K EA 6 52900813 52969163 0 4 500K EA 6 54059816 54115308 1 1 yes 500K EA 6 63781337 63929207 1 0 yes 500K EA 6 63956681 63961313 1 0 yes 500K EA 6 66411109 66510269 0 3 500K EA 6 66961128 67117117 0 7 500K EA 6 67721287 67745004 0 1 500K EA 6 67821780 67861137 0 1 500K EA 6 68326677 68583232 1 1 yes 500K EA 6 74624342 74681784 2 0 500K EA 6 75117667 75218942 0 1 yes 500K EA 6 75582459 75681971 0 5 500K EA 6 77474806 77533382 1 55 500K EA 6 79001258 79150726 0 65 yes 500K EA 6 81322214 81360930 0 7 500K EA 6 82154779 82217840 0 2 500K EA 6 84790018 84853288 0 2 500K EA 6 93127736 93161367 1 0 500K EA 6 93634138 93728395 1 0 500K EA 6 105439613 105806657 2 0 yes 500K EA 6 110496619 110611373 0 2 chr start end gains losses overlap with WGTP 500K EA 6 114671437 115749378 1 0 yes 500K EA 6 117570741 117716222 0 2 yes 500K EA 6 121008976 121071648 0 1 500K EA 6 136399747 136408668 0 1 500K EA 6 143861702 143866797 1 0 500K EA 6 154212042 154232313 0 2 yes 500K EA 6 154802849 154849989 0 1 500K EA 6 158598614 158619762 1 0 500K EA 6 158649279 158728910 1 1 500K EA 6 160402742 161041281 1 1 yes 500K EA 6 161906087 161907120 1 0 500K EA 6 162461349 162478101 0 1 500K EA 6 162706292 162710176 0 2 500K EA 6 162811333 163203672 1 0 yes 500K EA 6 167571004 167995289 1 0 yes 500K EA 6 168151009 168425764 4 0 yes 500K EA 6 169319421 169350071 0 4 500K EA 7 141322 189431 13 1 yes 500K EA 7 3132732 3233596 2 2 yes 500K EA 7 3375589 3403590 0 5 500K EA 7 4112654 4212478 1 1 500K EA 7 6537823 6750454 0 2 500K EA 7 7053302 7215015 0 3 yes 500K EA 7 8597194 8657317 0 1 500K EA 7 8893236 9015089 0 2 yes 500K EA 7 9578732 9699463 1 0 500K EA 7 11081247 11125514 0 1 500K EA 7 12278853 12369775 2 0 500K EA 7 14845100 14945514 0 1 yes 500K EA 7 15789103 15801129 1 0 500K EA 7 16009402 16107468 0 1 yes 500K EA 7 16119379 16231714 0 4 yes 500K EA 7 16856134 16878340 0 2 yes 500K EA 7 16903042 17218573 1 0 yes 500K EA 7 17273084 17297879 0 1 yes 500K EA 7 18540954 18574580 0 1 500K EA 7 19169386 19347306 2 0 yes 500K EA 7 29421593 29560689 1 0 yes 500K EA 7 37484765 37541846 0 1 yes 500K EA 7 38067319 38191405 0 1 yes 500K EA 7 39833420 40042823 1 0 500K EA 7 40157270 40270518 1 0 500K EA 7 46646975 46655440 0 2 500K EA 7 57307684 57347793 1 0 500K EA 7 57376181 57689510 3 1 yes 500K EA 7 61076556 62556415 5 0 yes 500K EA 7 64138391 64818001 0 1 yes 500K EA 7 71427575 72200171 3 0 yes 500K EA 7 75682804 76466493 16 3 yes 500K EA 7 78446039 78532576 0 10 500K EA 7 87781582 87907853 0 1 yes 500K EA 7 88201486 88268110 0 1 500K EA 7 89331811 89501295 1 0 500K EA 7 104352201 104802443 2 0 yes 500K EA 7 105179617 105181392 0 2 500K EA 7 108189596 108254349 1 0 500K EA 7 110650214 110855621 0 1 yes 500K EA 7 115112000 115149266 0 1 500K EA 7 120502410 120587277 0 1 500K EA 7 120653822 120683906 0 1 chr start end gains losses overlap with WGTP 500K EA 7 122392587 122483286 1 0 500K EA 7 133517421 133525343 0 1 500K EA 7 141686975 141718376 0 2 yes 500K EA 7 141739700 142018646 0 6 yes 500K EA 7 148984351 149343695 4 0 yes 500K EA 7 149671475 149684632 0 1 500K EA 7 152281712 152287772 0 1 500K EA 7 152584598 152662168 1 2 yes 500K EA 7 152891524 153249486 6 0 yes 500K EA 7 154322472 154327193 0 1 500K EA 7 155764762 155819766 0 4 yes 500K EA 8 177639 405401 2 1 yes 500K EA 8 2116686 2375383 3 3 yes 500K EA 8 2684771 2697799 0 1 500K EA 8 3551652 3554023 1 0 500K EA 8 3671287 5942813 4 39 yes 500K EA 8 6023403 6069687 0 3 500K EA 8 6092385 6147262 1 0 500K EA 8 6160762 6236366 0 3 500K EA 8 6799659 6814575 0 1 yes 500K EA 8 6908814 8183341 9 14 yes 500K EA 8 8375229 8448555 0 1 500K EA 8 8745049 8785304 1 0 500K EA 8 9091324 9108239 0 1 500K EA 8 11882733 12646342 65 63 yes 500K EA 8 12883370 12926648 0 1 500K EA 8 13584750 13781886 0 29 yes 500K EA 8 14300858 14321648 0 2 500K EA 8 14549778 14559616 0 1 500K EA 8 14670571 15719081 0 2 yes 500K EA 8 16303512 16949896 3 0 yes 500K EA 8 17383467 17648137 0 4 yes 500K EA 8 18893788 18924134 0 2 500K EA 8 20030851 20073883 0 1 500K EA 8 21729708 22858325 0 1 yes 500K EA 8 25026436 25049622 0 5 500K EA 8 25737239 25763131 0 1 500K EA 8 39293436 39577556 0 92 yes 500K EA 8 47534345 47684445 4 0 500K EA 8 50577786 50755257 3 0 yes 500K EA 8 51035846 51131495 0 1 yes 500K EA 8 51912593 52045960 2 0 500K EA 8 53897210 54039563 1 0 yes 500K EA 8 54090134 54163645 0 4 yes 500K EA 8 59467844 59504885 1 0 500K EA 8 61146767 61184397 0 2 500K EA 8 63318677 63422736 0 2 500K EA 8 79962967 79977663 0 2 500K EA 8 90162190 90164239 0 1 500K EA 8 90390763 90407394 0 2 500K EA 8 91159997 91304511 1 1 yes 500K EA 8 92196639 92253014 0 1 yes 500K EA 8 96892887 96916149 0 1 500K EA 8 102462222 102471681 0 1 500K EA 8 102678650 102718857 0 3 500K EA 8 114954608 115280348 1 0 yes 500K EA 8 116948684 117176086 1 0 yes 500K EA 8 117692900 117714868 0 5 500K EA 8 121834882 121898100 1 0 500K EA 8 134236863 134249655 0 1 chr start end gains losses overlap with WGTP 500K EA 8 135130463 135131756 0 5 500K EA 8 135212786 135244049 0 2 500K EA 8 137757137 137969110 0 6 yes 500K EA 8 139050457 139114328 1 0 500K EA 8 140327110 140328379 0 1 500K EA 8 141036810 141046387 0 1 500K EA 8 143460347 143679430 1 0 500K EA 8 146120191 146264218 0 1 500K EA 9 47964 352209 2 0 yes 500K EA 9 554836 728434 0 10 yes 500K EA 9 1173321 1403700 0 1 yes 500K EA 9 2955090 2975743 0 1 500K EA 9 3998954 4012297 0 1 500K EA 9 4517262 4518816 0 2 500K EA 9 5278908 5326984 0 1 yes 500K EA 9 5344558 5398358 0 2 yes 500K EA 9 6691130 6695914 0 1 yes 500K EA 9 6733440 6835561 0 1 yes 500K EA 9 7260158 7363868 0 1 yes 500K EA 9 7514075 7551271 0 5 500K EA 9 9786608 9804116 0 2 500K EA 9 9952603 9964221 0 1 500K EA 9 10502307 10576527 0 2 500K EA 9 10629445 10670025 0 1 500K EA 9 11637401 11701989 0 1 500K EA 9 11827866 12187607 0 6 yes 500K EA 9 12273944 12579068 0 1 yes 500K EA 9 12711881 12748881 0 1 yes 500K EA 9 16053191 16072467 1 0 500K EA 9 16893850 16908196 0 1 500K EA 9 17801584 17818437 0 1 500K EA 9 19116476 19151145 0 1 500K EA 9 20746547 20753840 0 1 500K EA 9 21171454 21186515 0 1 500K EA 9 21271544 21293689 0 2 500K EA 9 21489624 21516526 0 1 500K EA 9 22618931 22686345 1 0 500K EA 9 24457996 24518103 0 1 500K EA 9 25211244 25374959 0 1 500K EA 9 28577774 28769376 0 2 yes 500K EA 9 29918566 29999947 0 2 yes 500K EA 9 30245385 30379493 2 0 yes 500K EA 9 32085083 32107175 0 1 500K EA 9 33794006 33809555 1 0 500K EA 9 38493875 38673287 0 2 yes 500K EA 9 38756241 40073195 2 0 yes 500K EA 9 42050602 43951965 15 21 yes 500K EA 9 65853919 68256580 1 1 yes 500K EA 9 68520661 68583297 1 0 500K EA 9 69247800 69277652 1 0 500K EA 9 69330123 69363930 3 3 500K EA 9 71486407 71491754 0 1 500K EA 9 76999952 77020098 5 0 500K EA 9 78658863 78703638 0 3 500K EA 9 101717505 101862268 3 70 yes 500K EA 9 101918912 101963391 0 1 500K EA 9 103893020 103919961 0 1 500K EA 9 104439357 104463949 1 16 500K EA 9 106263491 106375395 0 1 yes 500K EA 9 112450952 112673663 4 0 yes chr start end gains losses overlap with WGTP 500K EA 9 112680178 112712453 1 0 yes 500K EA 9 112728012 112743854 2 0 yes 500K EA 9 112894953 112971799 2 0 yes 500K EA 9 116604215 116620188 1 0 500K EA 9 119368741 119383168 0 1 500K EA 9 125822418 125845443 0 1 500K EA 9 129679522 129702320 1 0 500K EA 9 131319462 131508504 1 0 yes 500K EA 10 1432709 1453158 0 1 500K EA 10 1842791 1913557 2 2 500K EA 10 2682793 3124681 1 0 yes 500K EA 10 3297225 3300298 0 1 500K EA 10 4276880 4313493 0 1 500K EA 10 5547024 5760518 5 0 yes 500K EA 10 6690997 6705355 0 4 500K EA 10 7136154 7179524 1 0 500K EA 10 7537823 7672510 0 1 yes 500K EA 10 13089087 13104413 0 3 500K EA 10 13718676 13726648 0 1 500K EA 10 16741412 16752674 0 1 500K EA 10 18875331 18946513 1 0 500K EA 10 19734150 19780641 0 1 yes 500K EA 10 19816916 20045002 0 1 yes 500K EA 10 20324355 20366013 1 1 500K EA 10 20739152 20949210 3 63 yes 500K EA 10 27200938 27269999 21 2 500K EA 10 32991417 33000799 0 1 500K EA 10 37971818 37998918 2 0 500K EA 10 38717029 39018686 1 1 yes 500K EA 10 41753546 42249122 1 0 yes 500K EA 10 42424074 42673001 0 1 yes 500K EA 10 45364098 48037264 41 19 yes 500K EA 10 52665980 52685589 0 1 500K EA 10 52967781 52992342 0 1 500K EA 10 54778135 54807367 0 3 500K EA 10 55027142 55201043 0 2 yes 500K EA 10 56106514 56143760 12 0 yes 500K EA 10 56849158 56853483 0 3 500K EA 10 56872041 56988850 0 1 500K EA 10 58237729 58314518 0 1 yes 500K EA 10 58492250 58618213 0 15 500K EA 10 59242689 59439185 0 1 yes 500K EA 10 60506139 60566271 2 0 yes 500K EA 10 60994141 61003145 0 1 500K EA 10 67987416 68078527 0 1 yes 500K EA 10 70708723 70722894 0 1 500K EA 10 72907909 72956161 0 1 500K EA 10 77206052 77406628 1 0 yes 500K EA 10 79039280 79263477 1 0 yes 500K EA 10 81772720 81779567 0 1 yes 500K EA 10 84034612 84048907 0 1 500K EA 10 84390694 84427173 2 0 500K EA 10 84561902 84608631 0 1 500K EA 10 88886420 89274999 1 4 yes 500K EA 10 92891080 92922917 0 1 500K EA 10 99824786 99883943 0 2 500K EA 10 102193061 102265632 2 0 yes 500K EA 10 107602546 107689620 0 2 yes 500K EA 10 109121712 109123622 0 1 500K EA 10 117404858 117461605 0 1 chr start end gains losses overlap with WGTP 500K EA 10 123426455 123451644 0 1 500K EA 10 128881619 129008874 1 0 yes 500K EA 10 133485668 133634871 0 7 500K EA 10 134542100 134648239 1 0 yes 500K EA 10 134907049 135321566 20 1 yes 500K EA 11 3376078 3569739 1 1 yes 500K EA 11 4119053 4282368 1 0 yes 500K EA 11 4466861 4519034 0 2 500K EA 11 4918489 4948858 0 1 yes 500K EA 11 5373198 5448609 0 1 500K EA 11 5733199 5798932 0 68 yes 500K EA 11 5824631 5964189 8 0 yes 500K EA 11 7376191 7402481 0 1 500K EA 11 11250242 11269413 0 1 500K EA 11 16871867 16890706 0 1 500K EA 11 18886391 18939210 27 25 yes 500K EA 11 19439936 19450983 0 1 500K EA 11 21112669 21194273 0 6 500K EA 11 21740206 21805311 0 2 500K EA 11 25045288 25279174 1 3 yes 500K EA 11 25520766 25595288 0 6 yes 500K EA 11 25651185 25684737 0 10 yes 500K EA 11 30121848 30136966 0 2 500K EA 11 32749360 32915185 1 0 yes 500K EA 11 34177080 34326812 0 2 500K EA 11 34869891 34920304 0 2 500K EA 11 35024058 35195154 0 1 yes 500K EA 11 37079701 37100001 0 1 500K EA 11 38401344 38437928 0 4 500K EA 11 41075935 41157340 0 1 yes 500K EA 11 48322333 49025210 0 3 yes 500K EA 11 49238492 49355549 0 3 yes 500K EA 11 49538501 49820388 0 27 500K EA 11 50128453 50405768 2 0 yes 500K EA 11 55096278 55394688 19 83 yes 500K EA 11 55446439 55605732 0 2 500K EA 11 58502814 58662594 15 0 yes 500K EA 11 61505378 61650609 1 0 500K EA 11 62801568 62883430 0 1 500K EA 11 67229481 67647865 0 8 yes 500K EA 11 73520257 74223536 1 0 yes 500K EA 11 74875928 74878739 0 1 500K EA 11 79645152 79693784 0 7 500K EA 11 80076875 80080035 0 1 500K EA 11 80553027 80556842 0 1 500K EA 11 80665959 80695621 0 2 500K EA 11 80996713 81471485 0 16 yes 500K EA 11 84234326 84271303 0 1 500K EA 11 85114516 85150995 0 1 yes 500K EA 11 85547592 85583161 0 1 500K EA 11 87287865 87304787 0 1 500K EA 11 89105700 89525014 0 1 yes 500K EA 11 90605720 90702192 0 1 500K EA 11 91456251 91464123 0 1 500K EA 11 92537990 92573785 0 1 500K EA 11 93315872 93354598 1 20 500K EA 11 96355736 96549641 0 1 yes 500K EA 11 97120050 97249540 0 1 500K EA 11 97309468 97384974 0 1 500K EA 11 98266953 98310378 0 1 chr start end gains losses overlap with WGTP 500K EA 11 98674719 98707009 0 6 yes 500K EA 11 99309814 99358487 1 2 500K EA 11 102541001 102720677 0 1 500K EA 11 104224803 104303755 0 1 500K EA 11 104401086 104484927 2 19 500K EA 11 106829486 106849778 0 3 500K EA 11 120978808 121045852 1 0 500K EA 11 122339246 122372360 1 0 500K EA 11 124580498 124605648 0 1 500K EA 11 126701966 126709174 0 1 500K EA 11 129633534 129715211 0 1 yes 500K EA 11 130484613 130489555 0 1 500K EA 11 134085801 134147144 7 0 500K EA 12 205271 413467 1 2 yes 500K EA 12 656499 834812 1 0 yes 500K EA 12 6358711 6521697 2 0 yes 500K EA 12 7791451 8033850 11 0 yes 500K EA 12 8172022 8472071 14 7 yes 500K EA 12 9474722 9702031 132 61 yes 500K EA 12 9747225 9779820 0 2 yes 500K EA 12 11404579 11444635 0 1 yes 500K EA 12 25125048 25143445 0 1 500K EA 12 25540624 25545712 0 1 500K EA 12 27539678 27542418 0 2 500K EA 12 31125435 31335485 12 2 yes 500K EA 12 31882773 31963864 7 0 500K EA 12 33417622 34727104 3 20 yes 500K EA 12 36177141 37243569 2 0 yes 500K EA 12 37328102 37332250 1 0 500K EA 12 38586180 38618120 0 3 500K EA 12 40067025 40102269 1 0 500K EA 12 46833395 47065829 1 1 yes 500K EA 12 50962670 51071786 1 0 yes 500K EA 12 57477996 57520339 1 0 yes 500K EA 12 59797263 59898818 2 1 500K EA 12 60060452 60082655 0 1 500K EA 12 62188068 62438880 2 0 yes 500K EA 12 65191672 65266447 0 1 500K EA 12 70459038 70558246 1 0 yes 500K EA 12 71368737 71494315 0 1 yes 500K EA 12 71660953 71703530 0 1 500K EA 12 73396068 73500176 1 0 500K EA 12 81670581 81704083 0 1 yes 500K EA 12 92175967 92188663 0 1 500K EA 12 114691670 114713454 0 1 500K EA 12 117692414 117757043 0 1 500K EA 12 122635002 122720736 2 0 500K EA 12 125324021 125362245 0 2 500K EA 12 128536856 129618333 1 0 yes 500K EA 12 130248171 130915718 2 6 yes 500K EA 12 132249701 132344463 0 1 yes 500K EA 13 17960319 18358616 8 8 yes 500K EA 13 19870722 20078247 0 1 yes 500K EA 13 20717264 20796168 1 0 500K EA 13 23927295 23948923 0 1 500K EA 13 30423174 30476563 0 1 500K EA 13 36209331 36273415 0 2 500K EA 13 36968044 37011260 0 1 500K EA 13 38938036 38988742 0 2 500K EA 13 41649707 41674117 0 1 chr start end gains losses overlap with WGTP 500K EA 13 42098764 42130996 0 3 500K EA 13 53231210 53319335 1 0 500K EA 13 53590033 53609237 0 1 500K EA 13 56601020 56824435 0 9 yes 500K EA 13 62179940 62619249 0 2 yes 500K EA 13 63201508 63285508 0 1 500K EA 13 65128608 65255649 1 0 yes 500K EA 13 65903813 66017201 0 3 500K EA 13 66129506 66217983 0 1 500K EA 13 68253637 68290580 0 1 500K EA 13 69634065 69687992 0 3 500K EA 13 72712442 72713960 0 1 500K EA 13 83009774 83030766 0 2 yes 500K EA 13 83063628 83156897 0 1 yes 500K EA 13 84446595 84452592 0 2 500K EA 13 88337416 88662594 1 2 yes 500K EA 13 97712694 97753390 0 1 500K EA 13 101459508 101483261 0 1 500K EA 13 103073528 103079107 0 6 500K EA 13 103201047 103222979 1 0 500K EA 13 103783832 103787454 0 1 500K EA 13 104466931 104540789 1 0 yes 500K EA 13 107093227 107130924 0 1 yes 500K EA 13 110474921 110590297 1 0 yes 500K EA 14 19272965 19608948 156 0 yes 500K EA 14 20422939 20503182 1 2 yes 500K EA 14 21462543 21466983 0 1 500K EA 14 22011989 22057862 0 1 500K EA 14 25833467 25854753 0 1 500K EA 14 37858356 37874184 0 1 500K EA 14 40541848 40562301 0 2 500K EA 14 40646835 40769154 0 48 500K EA 14 40836311 40950477 0 1 500K EA 14 41920404 42044446 0 2 yes 500K EA 14 43558078 43608847 0 11 yes 500K EA 14 44239152 44324634 0 1 yes 500K EA 14 44871455 45041032 0 3 yes 500K EA 14 45120624 45190488 0 1 500K EA 14 52872802 52890807 0 1 500K EA 14 53759574 53803592 0 1 500K EA 14 59496524 59545703 0 1 yes 500K EA 14 64324218 64341533 0 1 500K EA 14 71872489 71889437 0 2 500K EA 14 73620134 73676171 1 0 500K EA 14 77174650 77282215 1 0 yes 500K EA 14 77448909 77571772 0 1 500K EA 14 77945360 77982720 1 0 yes 500K EA 14 78125151 78210289 0 1 yes 500K EA 14 78728484 78735438 0 1 500K EA 14 84633513 84635740 0 1 500K EA 14 85252320 85260552 0 1 yes 500K EA 14 85520078 85568590 0 3 500K EA 14 87460869 87500047 0 2 500K EA 14 93382087 93414055 2 0 500K EA 14 94007639 94015670 0 1 500K EA 14 97199755 97224576 0 2 500K EA 14 98604476 98636221 0 1 500K EA 14 106210547 106295344 61 29 500K EA 15 18403665 21241985 204 24 yes 500K EA 15 21606530 21610088 0 1 chr start end gains losses overlap with WGTP 500K EA 15 21877877 22380634 3 14 yes 500K EA 15 22606371 22689056 0 3 500K EA 15 28393128 28964768 0 7 yes 500K EA 15 29762552 30740356 3 0 yes 500K EA 15 32447708 32687764 7 51 yes 500K EA 15 32688453 32729249 0 1 yes 500K EA 15 39834465 39909909 0 1 500K EA 15 41619215 41845926 0 5 yes 500K EA 15 42888144 43170912 3 2 yes 500K EA 15 49139541 49571273 1 0 yes 500K EA 15 51557013 51572775 0 1 500K EA 15 54523770 54577372 0 1 500K EA 15 59467652 59487950 0 1 500K EA 15 68815452 68834724 0 1 500K EA 15 77337962 77340626 0 1 500K EA 15 77737577 77850372 0 1 500K EA 15 79788150 79874464 1 0 yes 500K EA 15 82330480 82359162 0 1 500K EA 15 82618970 82904075 5 1 yes 500K EA 15 84140970 84162590 0 4 500K EA 15 84946745 84954786 0 1 500K EA 15 85706849 85711119 0 2 500K EA 15 88424056 88610637 5 0 yes 500K EA 15 90382555 90416250 0 2 500K EA 15 91597772 91620597 1 1 500K EA 15 95654446 95716640 0 1 yes 500K EA 15 98175492 98422157 1 0 yes 500K EA 15 99537666 99839857 1 0 yes 500K EA 16 4149842 4198092 0 2 500K EA 16 4995942 5310411 1 0 yes 500K EA 16 5542095 5551122 0 1 500K EA 16 6448405 6449672 0 1 500K EA 16 6594720 6632981 2 0 yes 500K EA 16 6713809 6752649 0 3 yes 500K EA 16 6973749 7021963 0 1 500K EA 16 7855056 7915358 0 1 500K EA 16 9721050 9729949 0 1 500K EA 16 12554682 12561909 0 5 500K EA 16 12584246 12619700 0 9 500K EA 16 16260667 16653145 1 4 yes 500K EA 16 17441601 18990536 3 0 yes 500K EA 16 20352824 20506848 0 15 500K EA 16 21212772 21856623 2 1 yes 500K EA 16 22313312 22631165 2 22 yes 500K EA 16 24976087 25044753 1 1 yes 500K EA 16 31918174 33744011 1 3 yes 500K EA 16 34293686 34900436 19 0 yes 500K EA 16 45819013 46152506 1 0 yes 500K EA 16 52965305 52987359 0 2 500K EA 16 53310669 53336408 0 1 500K EA 16 62639947 62714192 0 3 500K EA 16 68609885 68745051 1 0 yes 500K EA 16 69391450 69757550 3 0 yes 500K EA 16 72330599 72332356 0 1 500K EA 16 74567282 74579010 0 1 500K EA 16 74819177 74829497 0 1 500K EA 16 76848674 76974815 0 3 yes 500K EA 16 77607617 77626238 0 7 500K EA 16 78452465 78480811 1 0 500K EA 16 79529780 79584643 1 32 chr start end gains losses overlap with WGTP 500K EA 16 82340616 82351735 0 1 500K EA 16 84834231 84849716 0 1 500K EA 16 85079026 85094533 1 1 500K EA 16 85539033 85558564 0 2 yes 500K EA 17 595817 897708 2 0 yes 500K EA 17 6034605 6087870 0 2 500K EA 17 13900781 13965204 0 1 yes 500K EA 17 16512229 16705555 2 7 yes 500K EA 17 19426327 19504358 0 4 500K EA 17 21246313 21641572 1 0 yes 500K EA 17 31429427 32016863 112 1 yes 500K EA 17 32018706 32104672 3 0 yes 500K EA 17 32210529 32219667 0 1 yes 500K EA 17 36906648 37150369 3 0 yes 500K EA 17 40813669 41089766 76 22 yes 500K EA 17 41518102 42223353 61 1 yes 500K EA 17 44093882 44118402 1 0 yes 500K EA 17 48396906 48413228 0 1 yes 500K EA 17 51506859 51535723 0 9 500K EA 17 53175939 53180824 0 1 500K EA 17 69252400 69258719 0 1 500K EA 17 74743681 74774728 0 2 500K EA 17 75752791 75790078 1 0 500K EA 18 277648 306558 0 3 500K EA 18 667302 695598 0 1 500K EA 18 3784119 4112410 2 0 yes 500K EA 18 9733326 9743992 0 1 500K EA 18 14198563 14548050 1 0 yes 500K EA 18 14731611 14855985 4 0 yes 500K EA 18 24413258 24450849 0 2 500K EA 18 26068546 26073661 0 4 500K EA 18 27886747 27928990 1 0 500K EA 18 32241210 32272575 1 0 500K EA 18 32364761 32735865 1 0 yes 500K EA 18 37638408 37686676 0 2 500K EA 18 38183758 38194401 0 2 500K EA 18 49503791 49532928 0 1 500K EA 18 54081842 54095115 0 5 500K EA 18 55803729 55838153 3 0 500K EA 18 56251349 56278547 0 1 500K EA 18 59700021 59742065 0 5 500K EA 18 60558805 60600790 0 1 500K EA 18 62053230 62087598 1 15 500K EA 18 63098485 63123732 0 1 500K EA 18 64126718 64284813 0 2 yes 500K EA 18 64888576 64912007 0 29 500K EA 18 67700021 68122628 0 1 yes 500K EA 18 68579533 68585381 0 1 500K EA 19 12350726 12410655 1 0 500K EA 19 15641041 15712261 14 1 500K EA 19 20079226 20152327 1 0 yes 500K EA 19 20360525 20566187 0 35 yes 500K EA 19 21847093 23448260 2 4 yes 500K EA 19 23474937 23534946 0 1 yes 500K EA 19 24131560 24297477 1 0 yes 500K EA 19 34447521 34456548 0 1 500K EA 19 38568301 39224079 3 0 yes 500K EA 19 40345482 40365173 0 27 500K EA 19 42486690 42743446 0 1 500K EA 19 46123775 46220507 1 2 yes chr start end gains losses overlap with WGTP 500K EA 19 47856258 48562727 146 30 yes 500K EA 19 49585942 49639284 0 2 500K EA 19 56834443 56856939 1 2 yes 500K EA 19 56951383 57296437 2 0 yes 500K EA 19 58002524 58037133 5 4 500K EA 19 58162326 58246052 0 1 yes 500K EA 19 58604054 58696751 0 2 500K EA 19 59374787 59491567 27 27 yes 500K EA 19 59850663 60118592 7 23 yes 500K EA 19 60229274 60342499 1 0 500K EA 19 60927349 61018118 12 0 500K EA 19 62684998 62694776 1 0 500K EA 19 63590775 63596527 0 2 500K EA 20 2152811 2307429 1 0 yes 500K EA 20 8022116 8536318 1 0 yes 500K EA 20 11742014 12235765 2 0 yes 500K EA 20 12581827 12609944 0 2 500K EA 20 14653888 14792049 0 2 yes 500K EA 20 14825886 14863051 0 1 500K EA 20 15230448 15279007 0 9 500K EA 20 17305806 17338095 0 2 500K EA 20 18197877 18221632 0 1 500K EA 20 23094607 23127604 0 4 yes 500K EA 20 28106854 28244356 0 1 yes 500K EA 20 35736026 35759976 0 1 500K EA 20 36367793 36539571 1 0 yes 500K EA 20 40686319 40710511 0 2 500K EA 20 44681417 44722596 1 0 500K EA 20 45195752 45227374 0 1 500K EA 20 49756024 49852802 0 1 500K EA 20 52112544 52118615 0 1 500K EA 20 58995933 59023990 2 0 500K EA 21 9941889 10105718 4 6 yes 500K EA 21 13354570 14258658 3 4 yes 500K EA 21 19561892 19565214 0 1 500K EA 21 19626353 19677375 0 1 500K EA 21 20716906 20811712 0 3 yes 500K EA 21 22433789 22596775 0 62 500K EA 21 23320362 23512054 0 2 500K EA 21 24483440 24515887 1 0 500K EA 21 29161064 29191388 1 0 500K EA 21 39779393 39888026 1 0 500K EA 21 46067460 46144196 0 1 500K EA 21 46811098 46902240 1 0 500K EA 22 14461115 15431692 2 7 yes 500K EA 22 17005919 17412089 3 0 yes 500K EA 22 22581891 22727762 1 4 500K EA 22 23932716 24371067 16 10 yes 500K EA 22 24460443 24475138 1 0 500K EA 22 33785204 33902969 0 1 yes 500K EA 22 41160225 41364932 0 1 yes 500K EA 22 42695340 42716298 0 1 500K EA 22 43951199 44245703 1 0 yes 500K EA 22 46758244 46775212 0 1 500K EA 22 47780805 47808278 0 1 500K EA 23 4010786 4023267 2 0 500K EA 23 6249179 6726074 2 0 500K EA 23 7211131 7355904 0 1 yes 500K EA 23 47575078 47825476 10 3 yes 500K EA 23 63292574 63919710 1 0 yes chr start end gains losses overlap with WGTP 500K EA 23 75852421 75934438 0 2 500K EA 23 90003377 90134018 1 0 yes 500K EA 23 103056216 103111418 2 0 yes 500K EA 23 115553046 115809368 1 0 yes 500K EA 23 134466048 134673554 5 0 yes 500K EA 23 140036126 140469418 2 0 yes 500K EA 23 148590921 148800374 8 0 yes 500K EA 23 151900926 152045136 1 0 yes 500K EA 23 2696752 3169853 2 0 yes 500K EA 23 7830174 7901660 1 0 500K EA 23 15418427 15483661 0 1 500K EA 23 16946317 16971335 0 1 500K EA 23 22628358 22749222 0 2 500K EA 23 27751188 31356624 1 1 yes 500K EA 23 66354058 67102115 1 0 yes 500K EA 23 78897478 78910649 0 1 500K EA 23 88800734 89069512 1 0 500K EA 23 115037017 115175870 1 0 500K EA 23 139767019 139785882 2 0 yes 500K EA 23 145829455 146494249 1 0 500K EA 23 146718150 146857358 1 0 500K EA 23 151572622 151688320 1 0 Supplemental Table 11D: CNV events from 500K EA 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 1 1 77822 1058627 77822 839326 41del/dup 2 1 1548033 1725888 1678951 1713113 02del 3 1 3608198 3678693 3608198 3671502 10dup 4 1 7505729 7622325 7567410 7617039 10dup 5 1 12722672 13544763 12790412 13520332 921del/dup 6 1 12790412 12845695 12790412 12792711 01del 7 1 14050388 14117706 14059886 14115674 20dup 8 1 15872786 15900413 15872786 15900413 02del 9 1 16554000 17053464 16669641 17013635 112 4 multiallelic 10 1 16560300 17045289 16609393 16961637 19 2 complex 11 1 16609393 17045033 16775020 17013635 27 0 dup 12 1 16573097 17016443 16609393 16705004 52complex 13 1 16609393 16979949 16704768 16775020 40dup 14 1 16690664 17045033 16801212 17016443 12complex 15 1 16668554 17016443 16669641 17016443 10dup 16 1 16609393 16801212 16768709 16775020 10dup 17 1 25190816 25209157 25190816 25204738 01del 18 1 30375428 30410749 30406466 30410589 06del 19 1 31351473 32135424 31376950 31990049 01del 20 1 38797694 38806748 38797694 38804841 03del 21 1 53226518 53242389 53226749 53242044 01del 22 1 53200585 53244138 53200585 53206900 01del 23 1 54981672 55020630 55008254 55016857 04del 24 1 72809121 72827226 72809121 72821190 10dup 25 1 75795429 75869007 75806255 75833759 02del 26 1 76950439 77014906 76966158 77004970 01del 27 1 77487035 77500483 77487035 77491857 02del 28 1 81599438 81608767 81599438 81608767 02del 29 1 83315378 83656249 83552294 83645277 21complex 30 1 94831811 94870624 94846203 94863834 05del 31 1 102084360 102129114 102116268 102123899 02del 32 1 105856683 105936087 105883462 105936087 06del 33 1 106491085 106558195 106512095 106558195 01del 34 1 107366027 107421762 107367901 107372891 02del 35 1 111499437 111506775 111503176 111504937 01del 36 1 111535893 111547026 111540506 111547026 03del 37 1 112407136 112422566 112407136 112421327 010del 38 1 115433285 115819379 115446133 115808292 10dup 39 1 112988198 113162419 112988198 113130876 10dup 40 1 112958672 116411310 112958672 116388710 01del 41 1 119822116 119874484 119822299 119862528 13del/dup 42 1 119810703 119869808 119810703 119839032 20dup 43 1 141480746 142385363 141480746 142357871 10dup 44 1 142378509 143032961 142445417 142694585 414complex 45 1 142440042 142592972 142445417 142503097 12complex 46 1 142592972 142744108 142592972 142732360 20dup 47 1 142440042 142589430 142504034 142530060 11multiallelic 48 1 143086160 143482819 143115023 143479630 01del 49 1 144917189 146809052 145700996 146039625 660del/dup 50 1 148141867 148224708 148150861 148224708 50dup 51 1 149495781 149552299 149497939 149549653 10dup 52 1 158157328 158413210 158310272 158375651 24 18 del/dup 53 1 158291806 158405340 158310556 158361623 32del/dup 54 1 158326814 158405340 158361544 158375651 13complex 55 1 158796126 159091666 158813480 159091666 10dup 56 1 158880358 158925396 158892578 158910824 20dup 57 1 162149184 162157194 162152978 162155534 03del 58 1 163275200 163333436 163278006 163333436 01del 59 1 163304911 163332444 163325341 163326867 01del 60 1 167046739 167144950 167057723 167118792 04del 61 1 175389239 175405731 175389239 175405731 03del 62 1 182024854 182077428 182054146 182077428 02del 63 1 186049278 186300204 186078811 186267341 07del 64 1 186468490 186551144 186468490 186513163 02del 65 1 186690763 186726869 186702057 186716570 04del 66 1 188509177 188557409 188515832 188557409 01del 67 1 190363185 190441853 190399448 190441853 03del 68 1 191669736 191674561 191669736 191674561 02del 69 1 192622899 192752192 192631476 192745668 10dup 70 1 192669359 192673684 192669983 192672977 04del 71 1 193440880 193648016 193462805 193614160 534del/dup 72 1 193440880 193797731 193533269 193618427 27del/dup 73 1 193441814 193555270 193462805 193533269 33complex 74 1 197239167 197328634 197289424 197327920 01del 76 1 204831917 204885513 204834754 204843574 20dup 77 1 206967918 207009174 206976435 207000923 04del 78 1 209313824 209394792 209357523 209394792 01del 79 1 220000153 220016185 220000153 220016185 10dup 80 1 221972429 222010220 221972429 221983065 40dup 81 1 228033829 228134776 228033829 228119443 20dup 82 1 233192877 233228405 233207744 233219640 02del 83 1 233458152 233471959 233458152 233470554 10dup 84 1 234327110 235054539 234338811 235051546 10dup 85 1 236233461 236634188 236243287 236623071 10dup 86 1 239362708 239606926 239380743 239477544 16 23 complex 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 87 1 242354620 242442043 242354620 242429210 02del 88 1 243265897 243272062 243265897 243272062 01del 89 1 244079375 244648357 244194154 244605525 10dup 90 1 244921722 245143423 245058074 245136687 02del 91 2 240958 295803 249296 272736 10dup 92 2 302992 848062 345504 833960 10dup 93 2 1410597 1484084 1411021 1453138 10dup 94 2 3256238 3288649 3265707 3288065 10dup 95 2 3730174 3770183 3735847 3750661 01del 96 2 4402072 4417591 4402072 4412293 01del 97 2 6248649 6273145 6250738 6270652 017del 98 2 10297740 10357304 10297740 10334361 10dup 99 2 10546176 10639567 10598488 10626147 10dup 100 2 14296389 14319566 14304508 14319566 10dup 101 2 14642533 14660690 14655988 14660690 09del 102 2 16983359 16989153 16983359 16989153 01del 103 2 17809678 17896719 17854903 17880390 10dup 104 2 18063761 18147135 18097748 18113898 03del 105 2 29088147 30418897 29142046 30402093 10dup 106 2 34596931 34666683 34596931 34663454 04del 107 2 35484210 35548857 35494119 35497580 04del 108 2 36199686 36482225 36264765 36477101 01del 109 2 36287067 36364113 36287067 36332219 01del 110 2 36534557 36568956 36536019 36543603 10dup 111 2 36959004 36960602 36959004 36960602 01del 112 2 37821038 37916959 37848232 37901092 20 3 del/dup 113 2 37853047 37910581 37860221 37898843 10dup 114 2 40842372 40878370 40842372 40861257 03del 115 2 46525886 46668082 46563275 46651334 02del 116 2 50710112 50772700 50710112 50743385 01del 117 2 56618323 56722941 56645686 56722941 21del/dup 118 2 57294090 57353462 57313976 57353462 20dup 119 2 58306194 61252101 58497341 60982303 10dup 120 2 64260853 64432941 64269471 64423937 20dup 121 2 66041145 66060953 66041145 66060953 10dup 122 2 67178358 67248668 67184771 67227901 01del 123 2 71253797 71285075 71253797 71285075 02del 124 2 75275078 75294365 75275078 75285854 02del 125 2 75702144 75825556 75733157 75825556 20dup 126 2 76749556 76771867 76749556 76771867 01del 127 2 77097511 77120706 77097511 77120706 01del 128 2 77876528 77905870 77901119 77905870 10dup 129 2 78111390 78551901 78162846 78526798 02del 130 2 81671346 81727952 81671346 81727952 01del 131 2 83162231 83803064 83162231 83734684 01del 132 2 87017102 88135226 87039100 87828118 32complex 133 2 89740700 91696901 89740700 91212000 636del 134 2 94780673 94972832 94780673 94959446 10dup 135 2 97472228 97733045 97472228 97733045 10dup 136 2 97130485 97476218 97175459 97476218 01del 137 2 107969196 108681855 107999505 108566041 20dup 138 2 110192354 110313018 110205175 110313018 10dup 139 2 113185466 113195120 113185466 113195120 01del 140 2 116213758 116391580 116251152 116391580 10dup 141 2 117201020 117460821 117238085 117447367 02del 142 2 130490748 131318354 130664117 130859366 20dup 143 2 132253678 132304569 132261583 132303772 10dup 144 2 131914844 132310822 131930048 132277430 10dup 145 2 131999940 132097444 131999940 132072532 10dup 146 2 131747626 131989151 131788979 131930171 03del 147 2 132188211 132303772 132191206 132261583 11complex 148 2 133101579 133147577 133112423 133135989 11 0 dup 149 2 137031522 137074036 137031522 137074036 10dup 150 2 142029855 142079679 142029855 142072644 10dup 151 2 151328047 151575481 151451933 151566712 10dup 153 2 153480707 153624340 153509104 153597873 02del 154 2 174352834 174370707 174366797 174370707 02del 155 2 177140714 177191106 177156474 177191106 10dup 156 2 183354176 183590436 183427514 183590436 10dup 157 2 185036251 185196292 185049902 185169692 01del 158 2 187242105 187318248 187250050 187295850 20dup 159 2 194745343 194782381 194745343 194782381 02del 160 2 205168233 205174230 205172173 205174230 02del 161 2 209298057 209377458 209298088 209355287 01del 162 2 213012709 213018930 213012709 213015500 08del 163 2 216138444 216256321 216150780 216208018 01del 164 2 222179557 222227609 222219810 222227609 01del 165 2 228736395 228746258 228736395 228740333 01del 166 2 233037366 233133441 233058556 233131916 10dup 167 2 241111015 241229702 241172058 241229702 10dup 168 2 242415890 242730382 242642787 242730382 13del/dup 169 3 61204 102933 70172 102933 10dup 170 3 196081 211759 196081 210748 10dup 171 3 1222123 1302426 1246183 1292631 10dup 172 3 1338740 1346260 1338740 1342042 02del 173 3 1455555 1563919 1455555 1555390 10dup 174 3 2217552 2462786 2249216 2462697 10dup 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 175 3 4062787 4081495 4063809 4071644 02del 176 3 4113369 4185967 4123796 4180623 02del 177 3 4241532 4252366 4241532 4248055 01del 178 3 6181901 6224264 6199872 6211442 07del 179 3 7499552 7539303 7523067 7539303 10dup 180 3 14933078 15026556 14933078 15012855 10dup 181 3 16202432 16231043 16208246 16228307 01del 182 3 21180674 21351652 21239774 21318600 10dup 183 3 24700007 24788964 24721324 24788964 01del 184 3 26021365 26148227 26021365 26122061 01del 185 3 36258534 36290961 36285414 36290671 01del 186 3 39509276 39530501 39509276 39522022 10dup 187 3 41395796 41501946 41395796 41476741 01del 188 3 42335110 42378384 42335110 42343886 01del 189 3 45991468 46095404 46009090 46095404 02del 190 3 46394638 46419798 46396842 46415076 01del 191 3 52981095 53014495 52981095 53014495 01del 192 3 60650681 60689812 60657032 60689757 01del 193 3 60775739 60919051 60900243 60914014 01del 194 3 60792362 60896747 60800692 60883053 02del 195 3 61039472 61094963 61053685 61084402 01del 196 3 60968955 61027682 60968955 61027682 01del 197 3 61119467 61195849 61127327 61191515 10dup 198 3 61544597 61611196 61555952 61588747 10dup 199 3 64922928 64933281 64922928 64933281 01del 200 3 65151156 65199576 65164684 65187319 119del/dup 201 3 68971420 69018486 68979805 69008468 20dup 202 3 75795694 76001559 75957471 75996192 01del 203 3 75474768 75864387 75476955 75784778 18del 204 3 75476420 76085726 75621533 75864387 24complex 205 3 78536627 78579808 78547485 78556912 10dup 206 3 89343185 89353777 89343185 89353777 01del 207 3 104428032 104433385 104428032 104433385 10dup 208 3 105572457 106260663 105586566 106260663 01del 209 3 113587565 113596024 113587565 113596024 01del 210 3 117568368 117604638 117581731 117595500 02del 211 3 122747576 122806155 122747576 122806127 10dup 212 3 126932312 126935644 126932312 126935644 10dup 213 3 128898840 128916240 128898840 128910608 01del 214 3 131192345 131422071 131233075 131291453 146 24 del 215 3 131276436 131416346 131291453 131396962 25multiallelic 216 3 132802569 132855391 132802569 132818685 10dup 217 3 134503648 134515590 134503648 134507275 02del 218 3 141491918 141942926 141501187 141942126 10dup 219 3 141744385 141764782 141744385 141764782 01del 220 3 143239239 143577329 143336624 143498288 20dup 221 3 144388359 144447071 144388359 144442971 10dup 222 3 147098550 147144469 147114997 147144469 01del 223 3 152984775 153025999 153012819 153025999 01del 224 3 153811704 153962892 153835300 153957410 01del 225 3 153876460 154007851 153910349 153964273 10dup 226 3 156968004 156973709 156968004 156973709 20dup 227 3 161833723 161862863 161839642 161841511 02del 228 3 163666164 163709523 163700474 163709523 04del 229 3 164344341 164432687 164344341 164428536 01del 230 3 166523565 166615499 166523818 166545470 04del 231 3 174683883 174755275 174685932 174708069 02del 232 3 178177234 178198620 178177234 178189020 03del 233 3 187853052 187910042 187870001 187897578 02del 234 3 189069542 189083061 189069542 189079722 10dup 235 3 193570453 193577446 193570453 193576735 10dup 236 3 196584084 196969332 196894481 196968445 186 0 dup 237 3 196743569 196966085 196743569 196950134 10dup 238 3 196894481 196969332 196962948 196966085 10dup 239 3 198778468 198808132 198792589 198802442 02del 240 4 19099 56331 19301 56331 12multiallelic 241 4 3509131 3547567 3509131 3524291 10dup 242 4 3661108 3751308 3674395 3736632 10dup 243 4 6725902 6739063 6737076 6739063 02del 244 4 9048572 9488074 9420860 9480793 10dup 245 4 8823992 9385067 9052835 9197880 13 0 dup 246 4 9058087 9466981 9058087 9440833 12complex 247 4 9285384 9385067 9285384 9373265 10dup 248 4 9048572 9083510 9048572 9069224 10dup 249 4 9728030 9740273 9728030 9740273 01del 250 4 9802458 9815460 9804187 9815460 01del 251 4 9947405 9952736 9949057 9952736 04del 252 4 11337511 11348511 11338292 11348511 013del 253 4 12928417 12968570 12936974 12953439 10dup 254 4 17211513 17264589 17220906 17244425 01del 255 4 18763789 18863091 18772432 18796333 03del 256 4 20848734 20857264 20848734 20857264 01del 257 4 21693436 21767251 21725939 21756631 02del 258 4 22951435 22990481 22969909 22984031 10dup 259 4 23123935 23166081 23123935 23166081 02del 260 4 25178326 25184127 25178326 25184127 01del 261 4 25382090 25416475 25390655 25406815 03del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 262 4 26132536 26138154 26132536 26138154 01del 263 4 27909573 27914267 27909573 27914052 10dup 264 4 28308476 28445387 28318995 28399097 02del 265 4 28800351 28817794 28800351 28817794 10dup 266 4 28986666 29007386 28986666 28991807 01del 267 4 33971807 34235432 34158636 34226589 20dup 268 4 34579485 34680339 34588263 34663930 056del 269 4 42950671 43051416 42965638 43051416 19del/dup 270 4 44801372 44874500 44809531 44846780 30dup 271 4 48890029 49469842 48890029 49469842 12del/dup 272 4 58430351 58446870 58444467 58445909 01del 273 4 57963872 58441889 57980325 58407549 10dup 274 4 66400764 66474947 66429951 66456027 20dup 275 4 68619630 68857679 68619630 68778682 10dup 276 4 69831620 69840498 69831620 69838659 01del 277 4 69007686 69812428 69017814 69792913 745del/dup 278 4 69865808 69928319 69865808 69890231 30dup 279 4 70043934 70082367 70044331 70063226 01del 280 4 70200693 70479481 70211033 70427072 242del 281 4 71396544 71502233 71408876 71418181 04del 282 4 73716212 73794632 73786405 73790347 09del 283 4 74048053 74135413 74064502 74123685 02del 284 4 77749271 77812584 77803860 77809330 02del 285 4 87432938 87495944 87461349 87478471 02del 286 4 87774470 88046712 87880573 88046712 01del 287 4 89025760 89072503 89026567 89029904 02del 288 4 89315671 89486435 89387066 89423254 10dup 289 4 103130039 103291127 103153250 103239370 10dup 290 4 109298778 109305695 109301226 109305695 01del 291 4 114711846 114719490 114711846 114719490 01del 292 4 115761288 115792082 115761288 115787143 01del 293 4 116439195 116540304 116506964 116533117 022del 294 4 118906546 119964813 118925444 119774042 10dup 295 4 124596552 125610766 124633235 125604771 10dup 296 4 125995545 126007226 125995545 126007226 01del 297 4 132277939 132739982 132382089 132674054 20dup 298 4 132781976 132855491 132822337 132853842 10dup 299 4 132883456 132959908 132908107 132932337 10dup 300 4 145200243 145448965 145266171 145389446 45del/dup 301 4 145146248 145389446 145199798 145278437 08del 302 4 153133876 153167343 153149138 153152305 022del 303 4 156964511 156968445 156964511 156968445 01del 304 4 158541701 158702897 158621187 158683206 10dup 305 4 161385730 161462448 161420498 161425500 03del 306 4 162141027 162312760 162222345 162303973 18 0 dup 307 4 162551407 162593480 162552144 162559877 02del 308 4 166006477 166008354 166006477 166008354 01del 309 4 169169911 169472158 169189455 169354046 04del 310 4 172699064 172742341 172708642 172741856 03del 311 4 178588468 178692863 178611551 178672207 10dup 312 4 181842862 181847554 181842862 181847554 01del 313 4 183006629 183024960 183006629 183018356 01del 314 4 185535745 185542857 185535745 185542857 01del 315 4 189546195 189637395 189590885 189605486 03del 316 4 191053255 191140586 191066299 191117889 10dup 317 4 190885813 191078580 190926253 191066299 84complex 318 4 190896474 191078580 190899090 190967344 12complex 319 5 690324 937439 738504 876715 141 12 multiallelic 320 5 690324 936065 815435 927001 50dup 321 5 697552 874726 697552 815435 40dup 322 5 751305 874726 813840 820288 10dup 323 5 7188014 7256093 7231622 7242925 02del 324 5 8754920 8843546 8755522 8800338 011del 325 5 9950967 10008044 9963876 9974374 01del 326 5 13197682 13401985 13258665 13379476 02del 327 5 15362984 15386853 15362984 15386338 10dup 328 5 15731556 15863987 15767022 15776346 135del 329 5 17451090 17736871 17556091 17704795 012del 330 5 17544212 17698277 17544212 17564713 06del 331 5 17672912 17840103 17698277 17824060 02del 332 5 20472731 20494555 20473288 20475648 05del 333 5 23324344 23340668 23338073 23340668 01del 334 5 24564081 24613895 24564081 24613895 01del 335 5 32137157 32213541 32152371 32185000 50dup 336 5 33557835 33584771 33557835 33571571 02del 337 5 40909835 41045039 40911636 41036428 01del 338 5 55016652 55094749 55016652 55062994 10dup 339 5 55688830 55707856 55688830 55707228 02del 340 5 61685160 61784669 61693714 61756731 10dup 341 5 62067121 62138099 62083435 62138099 10dup 342 5 75462619 75510536 75467455 75485751 20dup 343 5 75647353 75678730 75647353 75669623 10dup 344 5 95329992 95565292 95336927 95478080 10dup 345 5 97054185 97163903 97076449 97125076 06del 346 5 97468282 97643999 97472572 97558496 20dup 347 5 99452655 99692426 99474075 99672534 10dup 348 5 99672534 99911270 99782976 99843001 02del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 349 5 100570013 100684490 100579903 100663882 20dup 350 5 101207948 101233931 101207948 101233931 06del 351 5 103967573 104010013 103989195 104001831 02del 352 5 104301300 104322489 104301300 104322489 01del 353 5 104226158 104301325 104249142 104270952 10dup 354 5 104452196 104556024 104475298 104555970 05del 355 5 106255008 106286649 106255008 106286649 01del 356 5 109778421 110180038 109793062 110093410 01del 357 5 114725159 114765482 114736927 114748980 04del 358 5 115543618 115571522 115543618 115571522 01del 359 5 115606709 115661373 115624176 115649502 07del 360 5 117813488 117892105 117834744 117874543 01del 361 5 118583762 118695647 118678382 118688399 01del 362 5 122626041 122685098 122626041 122658252 10dup 363 5 128671528 128790773 128695732 128769684 02del 364 5 135329916 135380394 135340702 135360470 02del 365 5 137833483 137865270 137833483 137838843 01del 366 5 144466435 144475035 144466546 144474852 02del 367 5 146410036 146519693 146418228 146456183 01del 368 5 155497577 155530680 155512692 155515691 013del 369 5 160471139 160490574 160474005 160480641 03del 370 5 171966705 172148018 172015884 172091278 50dup 371 5 173726296 173745954 173726296 173730660 01del 372 5 175279234 175696974 175409168 175570975 50dup 373 5 178653574 178894478 178682862 178841576 20dup 374 5 180012576 180177830 180077813 180142099 10dup 375 5 180311387 180421549 180384879 180421549 10dup 376 6 162334 356954 202461 334319 120 7 complex 377 6 168039 342937 248121 323970 18 0 dup 378 6 168039 329546 197145 267696 14 5 complex 379 6 178750 342937 279825 334319 93complex 380 6 178750 323970 248017 273070 50dup 381 6 202461 334630 320377 334319 10dup 382 6 896385 953488 896385 953488 01del 383 6 2561236 2577107 2570100 2577107 01del 384 6 2934581 2961056 2934581 2961056 10dup 385 6 7384069 7448784 7384069 7448784 10dup 386 6 10574157 10664858 10579248 10610996 02del 387 6 15776846 15833457 15793990 15820046 01del 388 6 26806459 27004868 26812951 27004868 10dup 389 6 30006876 30025125 30013137 30024597 01del 390 6 29942451 30073480 29949000 30023128 075del 391 6 29943813 30023128 29967224 29982554 05del 392 6 29976043 30024347 29982244 30014028 04del 393 6 30025125 30073480 30045083 30072927 02del 394 6 30025125 30059783 30025125 30046756 01del 395 6 30893252 30896567 30893252 30896567 01del 396 6 31359339 31374314 31366666 31374096 01del 397 6 31370848 31443686 31377287 31392153 116del/dup 398 6 31374096 31436834 31374096 31388921 11del 399 6 31461308 31650287 31468074 31565557 06del 400 6 41706502 41749467 41727028 41734726 04del 401 6 45061736 45097497 45061736 45075468 01del 402 6 45993620 45995399 45993620 45995399 01del 403 6 47798026 47814999 47798026 47811503 01del 404 6 52730063 52774200 52734228 52770112 01del 405 6 52900813 52969163 52907308 52910282 04del 406 6 54059816 54115308 54059816 54085408 11del/dup 407 6 63781337 63929207 63786930 63888718 10dup 408 6 63956681 63961313 63957010 63961313 10dup 409 6 66411109 66510269 66428054 66510269 03del 410 6 66961128 67117117 67065532 67105350 07del 411 6 67721287 67745004 67738476 67745004 01del 412 6 67821780 67861137 67843097 67852545 01del 413 6 68474413 68583232 68522631 68565666 10dup 414 6 68326677 68474413 68326677 68474413 01del 415 6 74624342 74681784 74637168 74667157 20dup 416 6 75117667 75218942 75117667 75187456 01del 417 6 75582459 75681971 75600547 75647255 05del 418 6 77474806 77533382 77496587 77529522 155del 419 6 79001258 79150726 79036117 79109332 065del 420 6 81357777 81360930 81357777 81360930 01del 421 6 81322214 81358383 81332831 81357777 06del 422 6 82154779 82217840 82212583 82217840 02del 423 6 84790018 84853288 84792906 84795516 02del 424 6 93127736 93161367 93127736 93161367 10dup 425 6 93634138 93728395 93645408 93675648 10dup 426 6 105439613 105806657 105439613 105690080 20dup 427 6 110496619 110611373 110502884 110512363 02del 428 6 114671437 115749378 114705622 115569492 10dup 429 6 117570741 117716222 117624563 117663193 02del 430 6 121008976 121071648 121023831 121043332 01del 431 6 136399747 136408668 136399747 136408668 01del 432 6 143861702 143866797 143862472 143866797 10dup 433 6 154212042 154232313 154215450 154218825 02del 434 6 154802849 154849989 154802849 154813670 01del 435 6 158598614 158619762 158598614 158619762 10dup 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 436 6 158707220 158728910 158721095 158727148 10dup 437 6 158649279 158707220 158649279 158696603 01del 438 6 160743311 160745989 160744870 160745989 01del 439 6 160402742 161041281 160430493 161002129 10dup 440 6 161906087 161907120 161906087 161907120 10dup 441 6 162461349 162478101 162466767 162472895 01del 442 6 162706292 162710176 162706292 162710176 02del 443 6 162811333 163203672 162819340 163021517 10dup 444 6 167571004 167995289 167596280 167740810 10dup 445 6 168151009 168425764 168153834 168414475 40dup 446 6 169319421 169350071 169324345 169335736 04del 447 7 141322 189431 141322 166807 12 1 del/dup 448 7 158399 189089 158399 180194 10dup 449 7 3132732 3233596 3173099 3233596 22del/dup 450 7 3375589 3403590 3383544 3387478 05del 451 7 4112654 4174369 4149882 4158100 10dup 452 7 4172052 4212478 4174369 4212478 01del 453 7 6537823 6750454 6607117 6736929 02del 454 7 7053302 7117220 7068042 7090455 01del 455 7 7090455 7215015 7117220 7194550 02del 456 7 8597194 8657317 8602067 8632452 01del 457 7 8893236 9015089 8913477 8986454 02del 458 7 9578732 9699463 9578732 9670774 10dup 459 7 11081247 11125514 11087081 11122578 01del 460 7 12278853 12369775 12290717 12321157 20dup 461 7 14845100 14945514 14847807 14930381 01del 462 7 15789103 15801129 15789103 15801129 10dup 463 7 16009402 16107468 16024994 16096761 01del 464 7 16119379 16231714 16122404 16173062 04del 465 7 16856134 16878340 16867106 16869568 02del 466 7 16903042 17218573 16905175 17203990 10dup 467 7 17273084 17297879 17273084 17289106 01del 468 7 18540954 18574580 18573536 18574580 01del 469 7 19169386 19347306 19188783 19307076 20dup 470 7 29421593 29560689 29484629 29524699 10dup 471 7 37484765 37541846 37489748 37541846 01del 472 7 38067319 38191405 38067319 38162129 01del 473 7 39833420 40042823 39858237 39934919 10dup 474 7 40157270 40270518 40172433 40252963 10dup 475 7 46646975 46655440 46652790 46655440 02del 476 7 57307684 57347793 57307684 57347430 10dup 477 7 57376181 57689510 57466015 57689510 30dup 478 7 57611532 57678760 57611532 57668731 01del 479 7 62089596 62150336 62089596 62097757 10dup 480 7 61076556 62556415 61601581 62150336 40dup 481 7 64138391 64818001 64172228 64532124 01del 482 7 71427575 72200171 71451749 71661781 30dup 483 7 75682804 76466493 75859511 76212673 15 3 del/dup 484 7 75914938 76137701 75914938 76093009 10dup 485 7 78446039 78532576 78452005 78497209 010del 487 7 87781582 87907853 87781582 87891205 01del 488 7 88201486 88268110 88230752 88244436 01del 489 7 89331811 89501295 89351257 89392031 10dup 490 7 104352201 104802443 104385026 104737681 20dup 491 7 105179617 105181392 105179617 105181392 02del 492 7 108189596 108254349 108189596 108254349 10dup 493 7 110650214 110855621 110707542 110824769 01del 494 7 115112000 115149266 115112000 115149266 01del 495 7 120502410 120587277 120502410 120587277 01del 496 7 120653822 120683906 120653822 120675652 01del 497 7 122392587 122483286 122392587 122471588 10dup 498 7 133517421 133525343 133517421 133525343 01del 499 7 141686975 141718376 141708117 141710769 02del 500 7 141827095 142018646 141836942 141998293 02del 501 7 141778074 141813948 141778074 141811422 02del 502 7 141739700 141983328 141749838 141896797 01del 503 7 141916794 142018646 141941760 141983139 01del 504 7 148984351 149343695 149004746 149243724 40dup 505 7 149671475 149684632 149672189 149682904 01del 506 7 152281712 152287772 152283869 152287772 01del 507 7 152584598 152662168 152585267 152621728 12del/dup 508 7 152891524 153249486 152960635 153098241 60dup 509 7 154322472 154327193 154322472 154327193 01del 510 7 155764762 155819766 155764813 155808164 04del 511 8 227333 250511 227333 242717 01del 512 8 177639 405401 180568 397746 20dup 513 8 2129674 2191803 2129674 2171522 01del 514 8 2116686 2375383 2137112 2372128 10dup 515 8 2226740 2259919 2234017 2258689 22complex 516 8 2684771 2697799 2684771 2695519 01del 517 8 3551652 3554023 3551652 3554023 10dup 518 8 4654062 4688714 4658756 4663986 10dup 519 8 5561105 5595762 5588817 5595284 023del 520 8 3957010 4010219 3971564 4010219 010del 521 8 4696921 4754112 4706329 4742185 04del 522 8 3671287 5942813 3675256 5929944 30dup 523 8 4597504 4707779 4607132 4696921 02del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 524 8 6023403 6069687 6051516 6054664 03del 525 8 6092385 6147262 6095306 6133731 10dup 526 8 6160762 6236366 6165620 6211403 03del 527 8 6799659 6814575 6802441 6814575 01del 528 8 6908814 8149069 6925431 8106541 614del/dup 529 8 6965809 8183341 8145978 8183317 20dup 530 8 7212059 8106541 7212059 7361701 10dup 531 8 8375229 8448555 8411447 8423837 01del 532 8 8745049 8785304 8759788 8785304 10dup 533 8 9091324 9108239 9091324 9100437 01del 534 8 11882733 12634940 11941938 12517929 52 35 complex 535 8 11897149 12575194 11941938 12264620 613complex 536 8 11941938 12646342 12291610 12575194 28del/dup 537 8 12025186 12487533 12264620 12291512 76del/dup 538 8 12285367 12596928 12286403 12487533 13complex 539 8 11933744 12596928 12029748 12526350 01del 540 8 12883370 12926648 12900672 12922389 01del 541 8 13642515 13781886 13642515 13772572 01del 542 8 13631654 13722323 13643904 13696428 027del 543 8 13584750 13693864 13631654 13676763 01del 544 8 14300858 14321648 14303019 14317510 02del 545 8 14549778 14559616 14549919 14559616 01del 546 8 14670571 15719081 14675298 15708398 02del 547 8 16387088 16428215 16387088 16427843 10dup 548 8 16303512 16949896 16330262 16932710 20dup 549 8 17480455 17493999 17482758 17486481 01del 550 8 17383467 17648137 17404697 17625435 01del 551 8 17585213 17599309 17585213 17595342 02del 552 8 18893788 18924134 18900123 18902791 02del 553 8 20030851 20073883 20030851 20056363 01del 554 8 21729708 22858325 22422587 22540213 01del 555 8 25026436 25049622 25026922 25040250 05del 556 8 25737239 25763131 25737239 25761125 01del 557 8 39293436 39577556 39326152 39440685 092del 558 8 47534345 47624665 47548174 47618480 10dup 559 8 47609486 47684445 47609486 47684445 30dup 560 8 50577786 50755257 50594566 50692706 30dup 561 8 51035846 51131495 51037075 51109255 01del 562 8 51912593 52045960 51932442 52045960 20dup 563 8 53897210 54039563 53913268 54024038 10dup 564 8 54090134 54163645 54109449 54153567 04del 565 8 59467844 59504885 59467844 59471312 10dup 566 8 61146767 61184397 61165748 61170422 02del 567 8 63318677 63422736 63345848 63421892 02del 568 8 79962967 79977663 79962967 79977663 02del 569 8 90162190 90164239 90162190 90164239 01del 570 8 90390763 90407394 90392844 90403153 02del 571 8 91159997 91304511 91219902 91279648 11del/dup 572 8 92196639 92253014 92196639 92253014 01del 573 8 96892887 96916149 96892887 96916149 01del 574 8 102462222 102471681 102462222 102471681 01del 575 8 102678650 102718857 102689866 102693736 03del 576 8 114954608 115280348 115077159 115132774 10dup 577 8 116948684 117176086 116984146 117138117 10dup 578 8 117692900 117714868 117699864 117702438 05del 579 8 121834882 121898100 121834882 121898100 10dup 580 8 134236863 134249655 134236863 134249655 01del 581 8 135130463 135131756 135130463 135131756 05del 582 8 135212786 135244049 135217181 135234954 02del 583 8 137757137 137969110 137757137 137931617 06del 584 8 139050457 139114328 139106414 139114328 10dup 585 8 140327110 140328379 140327110 140328379 01del 586 8 141036810 141046387 141036810 141046387 01del 587 8 143460347 143679430 143483686 143639778 10dup 588 8 146120191 146264218 146229553 146264218 01del 589 9 47964 352209 176603 279061 20dup 590 9 554836 622131 581610 597901 08del 591 9 592204 728434 603260 695168 02del 592 9 1173321 1403700 1192371 1392080 01del 593 9 2955090 2975743 2955090 2959061 01del 594 9 3998954 4012297 3998954 4011867 01del 595 9 4517262 4518816 4517262 4518816 02del 596 9 5278908 5326984 5292095 5326984 01del 597 9 5344558 5398358 5375783 5382330 02del 598 9 6691130 6695914 6691130 6695914 01del 599 9 6733440 6835561 6759429 6788091 01del 601 9 7260158 7363868 7275482 7358850 01del 602 9 7514075 7551271 7514485 7537216 05del 603 9 9786608 9804116 9789050 9804116 02del 604 9 9952603 9964221 9956113 9962241 01del 605 9 10502307 10576527 10536257 10571373 02del 606 9 10629445 10670025 10629445 10669912 01del 607 9 11637401 11701989 11637401 11701824 01del 608 9 11827866 12187607 11858796 12172768 04del 609 9 11895556 12021984 11903220 11997006 02del 610 9 12273944 12579068 12278197 12571785 01del 611 9 12711881 12748881 12725666 12738818 01del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 612 9 16053191 16072467 16058991 16072467 10dup 613 9 16893850 16908196 16893850 16908196 01del 614 9 17801584 17818437 17801584 17818437 01del 615 9 19116476 19151145 19135435 19145134 01del 616 9 20746547 20753840 20746547 20753840 01del 617 9 21171454 21186515 21171454 21181684 01del 618 9 21271544 21293689 21279320 21293689 02del 619 9 21489624 21516526 21504364 21516526 01del 620 9 22618931 22686345 22618931 22673792 10dup 621 9 24457996 24518103 24457996 24505111 01del 622 9 25211244 25374959 25258867 25339769 01del 623 9 28577774 28769376 28578575 28751593 01del 624 9 28705838 28724248 28709759 28724248 01del 625 9 29918566 29999947 29918566 29981403 02del 626 9 30245385 30379493 30245385 30365986 20dup 627 9 32085083 32107175 32096034 32107175 01del 628 9 33794006 33809555 33794006 33809365 10dup 629 9 38493875 38673287 38493875 38673287 02del 630 9 38756241 40073195 38758168 40073195 20dup 631 9 42050602 43951965 42050602 43863873 12 19 del/dup 632 9 42050602 43951965 42937560 43951965 22del/dup 633 9 42050602 43617278 42050602 42936442 10dup 634 9 65853919 68256580 65853919 68245287 11complex 635 9 68520661 68583297 68534019 68561794 10dup 636 9 69247800 69277652 69247800 69277652 10dup 637 9 69330123 69363930 69330123 69346360 33del/dup 638 9 71486407 71491754 71486407 71488378 01del 639 9 76999952 77020098 76999952 77002169 50dup 640 9 78658863 78703638 78664404 78692682 03del 641 9 101717505 101862268 101796515 101802243 370del/dup 642 9 101918912 101963391 101918912 101947665 01del 643 9 103893020 103919961 103893020 103919961 01del 644 9 104439357 104463949 104439569 104445674 116del/dup 645 9 106263491 106375395 106263491 106370752 01del 646 9 112680178 112712453 112694580 112699582 10dup 647 9 112450952 112673663 112462808 112661008 40dup 648 9 112728012 112743854 112736252 112742023 20dup 649 9 112894953 112971799 112938777 112967666 20dup 650 9 116604215 116620188 116604215 116612811 10dup 651 9 119368741 119383168 119372787 119383168 01del 652 9 125822418 125845443 125834210 125845443 01del 653 9 129679522 129702320 129679522 129702320 10dup 654 9 131319462 131508504 131332236 131449717 10dup 655 10 1432709 1453158 1432709 1442786 01del 656 10 1842791 1913557 1856108 1907354 21del/dup 657 10 1888756 1898328 1888782 1892670 01del 658 10 2682793 3124681 2685566 3104994 10dup 659 10 3297225 3300298 3297225 3300298 01del 660 10 4276880 4313493 4284071 4297011 01del 661 10 5547024 5760518 5713333 5756864 50dup 662 10 6690997 6705355 6697781 6704674 04del 663 10 7136154 7179524 7136154 7175215 10dup 664 10 7537823 7672510 7545032 7614772 01del 665 10 13089087 13104413 13096593 13098163 03del 666 10 13718676 13726648 13718676 13726648 01del 667 10 16741412 16752674 16741412 16752674 01del 668 10 18875331 18946513 18875331 18926267 10dup 669 10 19734150 19780641 19750097 19780641 01del 670 10 19816916 20045002 19849680 20045002 01del 671 10 20324355 20366013 20331611 20359851 11del/dup 672 10 20739152 20949210 20786206 20949210 01del 673 10 20822154 20949210 20891019 20895478 362del/dup 674 10 27200938 27269999 27232770 27268445 21 2 del/dup 675 10 32991417 33000799 32991417 33000799 01del 676 10 37971818 37998918 37974972 37997426 20dup 677 10 38717029 39018686 38943702 39018686 11complex 678 10 41753546 42249122 41753546 42235836 10dup 679 10 42424074 42673001 42424074 42631395 01del 680 10 46529485 46575501 46529485 46575501 10dup 681 10 45367462 45530757 45368924 45468756 01del 682 10 45364098 47067457 45530757 46557002 17 6 complex 683 10 45392878 48037264 45536421 47212082 16 10 del/dup 684 10 45367462 47030119 46363383 46510142 60dup 685 10 46422763 47062478 46510142 46529485 33complex 686 10 52665980 52685589 52665980 52685589 01del 687 10 52967781 52992342 52967781 52992342 01del 688 10 54778135 54807367 54789048 54807367 03del 689 10 55027142 55201043 55053174 55127514 02del 690 10 56106514 56143760 56127179 56138051 12 0 dup 691 10 56849158 56853483 56849158 56853055 03del 692 10 56872041 56988850 56880374 56943114 01del 693 10 58237729 58314518 58247992 58285889 01del 694 10 58516581 58618213 58575853 58618213 09del 695 10 58492250 58535262 58516581 58531544 06del 696 10 59242689 59439185 59242689 59439185 01del 697 10 60506139 60566271 60525908 60566271 20dup 698 10 60994141 61003145 60994141 61003145 01del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 699 10 67987416 68078527 67998550 68078527 01del 700 10 70708723 70722894 70713787 70722894 01del 701 10 72907909 72956161 72907909 72956161 01del 702 10 77206052 77406628 77218182 77370241 10dup 703 10 79039280 79263477 79041145 79263057 10dup 704 10 81772720 81779567 81776666 81779567 01del 705 10 84034612 84048907 84034612 84048907 01del 706 10 84390694 84427173 84401882 84421159 20dup 707 10 84561902 84608631 84561902 84608631 01del 708 10 88886420 89274999 88905087 89150364 14complex 709 10 92891080 92922917 92898244 92922917 01del 710 10 99824786 99883943 99824786 99842138 02del 711 10 102193061 102265632 102212947 102246486 20dup 712 10 107602546 107689620 107608010 107673992 02del 713 10 109121712 109123622 109121712 109122628 01del 714 10 117404858 117461605 117404858 117461605 01del 715 10 123426455 123451644 123426455 123450896 01del 716 10 128881619 129008874 128921233 128974317 10dup 717 10 133485668 133634871 133485668 133503143 07del 718 10 134542100 134648239 134568024 134640172 10dup 719 10 134907049 135321566 135143333 135319691 14 1 del/dup 720 10 135079451 135293417 135143333 135261191 40dup 721 10 135240018 135321566 135259748 135318176 20dup 722 11 3376078 3569739 3480060 3569172 11complex 723 11 4119053 4282368 4125217 4192351 10dup 724 11 4466861 4519034 4466861 4518966 02del 725 11 4918489 4948858 4923637 4930561 01del 726 11 5373198 5448609 5388562 5448609 01del 727 11 5733199 5798932 5734586 5774897 068del 728 11 5824631 5964189 5842287 5890620 80dup 729 11 7376191 7402481 7397977 7401442 01del 730 11 11250242 11269413 11250242 11269413 01del 731 11 16871867 16890706 16873795 16883598 01del 732 11 18886391 18939210 18905796 18915387 27 25 del/dup 733 11 19439936 19450983 19448881 19450983 01del 734 11 21112669 21194273 21133448 21172421 06del 735 11 21740206 21805311 21779213 21791089 02del 736 11 25204553 25229775 25204553 25229775 10dup 737 11 25045288 25279174 25090644 25250127 03del 738 11 25520766 25595288 25537641 25581002 06del 739 11 25651185 25684737 25657046 25673125 010del 740 11 30121848 30136966 30121848 30136966 02del 741 11 32749360 32915185 32752668 32879476 10dup 742 11 34177080 34326812 34198182 34300059 01del 743 11 34294918 34315052 34294918 34309802 01del 744 11 34869891 34920304 34870713 34876877 02del 745 11 35024058 35195154 35030628 35193380 01del 746 11 37079701 37100001 37082765 37090747 01del 747 11 38401344 38437928 38414672 38417833 04del 748 11 41075935 41157340 41085436 41124659 01del 749 11 48940894 49025210 48956881 49025210 01del 750 11 48322333 48956881 48373597 48886497 02del 751 11 49238492 49355549 49267528 49317177 03del 752 11 49538501 49820388 49670299 49716508 027del 753 11 50256441 50405768 50256441 50339013 10dup 754 11 50128453 50332876 50174761 50259255 10dup 755 11 55096278 55230803 55130549 55201444 19 76 del/dup 756 11 55130549 55394688 55217364 55346872 05del 757 11 55446439 55605732 55446439 55580152 02del 758 11 55130549 55364837 55232246 55252198 02del 759 11 58502814 58662594 58535219 58610745 15 0 dup 760 11 61505378 61650609 61526164 61602562 10dup 761 11 62801568 62883430 62801568 62883430 01del 762 11 67229481 67647865 67241130 67488532 08del 763 11 73520257 74223536 73673344 74211100 10dup 764 11 74875928 74878739 74875928 74878739 01del 765 11 79645152 79693784 79650581 79660988 07del 766 11 80076875 80080035 80076875 80080035 01del 767 11 80553027 80556842 80553027 80556842 01del 768 11 80665959 80695621 80669801 80689139 02del 769 11 80996713 81126163 81001232 81107016 01del 770 11 81175188 81208645 81175188 81208645 013del 771 11 81124533 81471485 81131219 81437753 02del 772 11 84234326 84271303 84234326 84247054 01del 773 11 85114516 85150995 85114516 85148541 01del 774 11 85547592 85583161 85560951 85583161 01del 775 11 87287865 87304787 87287865 87292778 01del 776 11 89105700 89525014 89471689 89483126 01del 777 11 90605720 90702192 90605720 90686554 01del 778 11 91456251 91464123 91456251 91464123 01del 779 11 92537990 92573785 92537990 92573785 01del 780 11 93315872 93354598 93318623 93327428 120del 781 11 96355736 96549641 96480303 96549641 01del 782 11 97120050 97249540 97128585 97193277 01del 783 11 97309468 97384974 97323161 97379032 01del 784 11 98266953 98310378 98274111 98310378 01del 785 11 98674719 98707009 98679357 98691890 06del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 786 11 99309814 99358487 99324506 99358487 12complex 787 11 102541001 102720677 102572670 102720677 01del 788 11 104224803 104303755 104224803 104264756 01del 789 11 104401086 104442581 104428916 104436443 019del 790 11 104442581 104484927 104455217 104477768 20dup 791 11 106829486 106849778 106843727 106849778 03del 792 11 120978808 121045852 120988611 121040148 10dup 793 11 122339246 122372360 122339246 122371312 10dup 794 11 124580498 124605648 124582578 124584904 01del 795 11 126701966 126709174 126701966 126709174 01del 796 11 129633534 129715211 129633534 129715211 01del 797 11 130484613 130489555 130484613 130489555 01del 798 11 134113081 134147144 134121027 134131333 50dup 799 11 134085801 134113081 134085801 134106222 20dup 800 12 303412 413467 303412 409299 10dup 801 12 205271 303412 248990 255353 02del 802 12 656499 834812 705335 834812 10dup 803 12 6358711 6521697 6415872 6446982 20dup 804 12 7791451 8033850 7908745 7971597 11 0 dup 805 12 8172022 8472071 8220967 8382584 13 7 del/dup 806 12 8259480 8283630 8259480 8269466 10dup 807 12 9474722 9702031 9532468 9622904 132 61 multiallelic 808 12 9631521 9702031 9634553 9685932 20dup 809 12 9747225 9779820 9753603 9765661 02del 810 12 11404579 11444635 11404579 11444635 01del 811 12 25125048 25143445 25131747 25135693 01del 812 12 25540624 25545712 25540624 25545712 01del 813 12 27539678 27542418 27539678 27542418 02del 814 12 31125435 31335485 31169298 31298174 12 0 dup 815 12 31169298 31247316 31169298 31244416 02del 816 12 31882773 31963864 31904362 31953020 70dup 817 12 33417622 34727104 33417622 34374200 10dup 818 12 34445062 34650850 34445062 34571980 10dup 819 12 33467973 33524866 33467973 33524866 01del 820 12 34051454 34277165 34103379 34209618 020del 821 12 34051454 34727104 34266146 34651598 20dup 822 12 36177141 36255461 36177141 36228889 10dup 823 12 36177141 37243569 36225372 37243569 10dup 824 12 37328102 37332250 37330303 37332250 10dup 825 12 38586180 38618120 38589898 38609908 03del 826 12 40067025 40102269 40067902 40102269 10dup 827 12 46833395 47065829 46833395 47011045 10dup 828 12 46958573 46989789 46962305 46989789 01del 829 12 50962670 51071786 50978740 51062234 10dup 830 12 57477996 57520339 57477996 57502524 10dup 831 12 59846251 59898818 59868562 59889777 20dup 832 12 59797263 59888595 59821513 59882103 01del 833 12 60060452 60082655 60073924 60079806 01del 834 12 62188068 62438880 62261464 62431798 20dup 835 12 65191672 65266447 65250071 65256523 01del 836 12 70459038 70558246 70459657 70558246 10dup 837 12 71368737 71494315 71368737 71486624 01del 838 12 71660953 71703530 71660953 71703530 01del 839 12 73396068 73500176 73408264 73498062 10dup 840 12 81670581 81704083 81670581 81704083 01del 841 12 92175967 92188663 92184021 92188663 01del 842 12 114691670 114713454 114699283 114713454 01del 843 12 117692414 117757043 117705082 117746020 01del 844 12 122635002 122720736 122640691 122720736 20dup 845 12 125324021 125362245 125348559 125354085 02del 846 12 128536856 129618333 128542193 129600046 10dup 847 12 130274439 130915718 130353185 130910158 10dup 848 12 130769865 130845280 130781044 130786816 10dup 849 12 130425003 130457297 130425003 130455366 01del 850 12 130248171 130353185 130272940 130350635 05del 851 12 132249701 132344463 132249701 132344463 01del 852 13 18204524 18348905 18204524 18342039 48complex 853 13 17960319 18342039 18110262 18253166 30dup 854 13 18253166 18358616 18253166 18351458 10dup 855 13 19870722 20078247 19870722 19994681 01del 856 13 20717264 20796168 20719242 20794843 10dup 857 13 23927295 23948923 23927401 23939187 01del 858 13 30423174 30476563 30427814 30439657 01del 859 13 36209331 36273415 36212286 36249756 02del 860 13 36968044 37011260 36969135 37011260 01del 861 13 38938036 38988742 38960329 38968118 02del 862 13 41649707 41674117 41657971 41674117 01del 863 13 42098764 42130996 42102766 42123721 03del 864 13 53231210 53319335 53259380 53319335 10dup 865 13 53590033 53609237 53590033 53593895 01del 866 13 56601020 56824435 56714907 56790236 09del 867 13 62179940 62619249 62223170 62527158 02del 868 13 63201508 63285508 63201508 63285508 01del 869 13 65128608 65255649 65132921 65255649 10dup 870 13 65903813 66017201 65912427 65971657 03del 871 13 66129506 66217983 66129506 66206672 01del 872 13 68253637 68290580 68284287 68290580 01del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 873 13 69634065 69687992 69634065 69670716 03del 874 13 72712442 72713960 72712511 72713960 01del 875 13 83009774 83030766 83022480 83030587 02del 876 13 83063628 83156897 83080600 83156897 01del 877 13 84446595 84452592 84446595 84452592 02del 878 13 88337416 88620754 88337416 88620754 10dup 879 13 88594137 88662594 88601868 88631816 02del 880 13 97712694 97753390 97712694 97740231 01del 881 13 101459508 101483261 101459508 101465763 01del 882 13 103073528 103079107 103073528 103077233 06del 883 13 103201047 103222979 103201375 103222979 10dup 884 13 103783832 103787454 103783832 103787454 01del 885 13 104466931 104540789 104513756 104537908 10dup 886 13 107093227 107130924 107099660 107126149 01del 887 13 110474921 110590297 110478211 110549062 10dup 888 14 19502641 19543920 19502828 19525147 10dup 889 14 19590226 19608948 19590795 19608948 10dup 890 14 19272965 19580947 19272965 19492423 147 0 dup 891 14 19272965 19492423 19402695 19435240 40dup 892 14 19444633 19488997 19447566 19483641 30dup 893 14 19272965 19608948 19272965 19608948 10dup 894 14 20422939 20503182 20422939 20443497 12del/dup 895 14 21462543 21466983 21462543 21466983 01del 897 14 22011989 22057862 22012459 22048175 01del 898 14 25833467 25854753 25833467 25854753 01del 899 14 37858356 37874184 37858356 37874007 01del 900 14 40541848 40562301 40541848 40555190 02del 901 14 40646835 40769154 40684005 40706033 048del 902 14 40836311 40950477 40894132 40916646 01del 903 14 41920404 42044446 41940713 42022286 02del 904 14 43558078 43608847 43570867 43604910 011del 905 14 44239152 44324634 44255590 44277315 01del 906 14 44871455 45041032 44898979 45041032 03del 907 14 45120624 45190488 45153107 45190488 01del 908 14 52872802 52890807 52872802 52890807 01del 909 14 53759574 53803592 53759574 53803592 01del 910 14 59496524 59545703 59496524 59508928 01del 911 14 64324218 64341533 64331515 64338358 01del 912 14 71872489 71889437 71872489 71884406 02del 913 14 73620134 73676171 73640811 73667602 10dup 914 14 77174650 77282215 77174650 77275608 10dup 915 14 77448909 77571772 77478438 77566340 01del 916 14 77945360 77982720 77945360 77960804 10dup 917 14 78125151 78210289 78134215 78180904 01del 918 14 78728484 78735438 78728484 78735438 01del 919 14 84633513 84635740 84633513 84635740 01del 920 14 85252320 85260552 85252320 85260552 01del 921 14 85520078 85568590 85530668 85550949 03del 922 14 87460869 87500047 87470106 87485253 02del 923 14 93382087 93414055 93388913 93400847 20dup 924 14 94007639 94015670 94007639 94013865 01del 925 14 97199755 97224576 97199824 97210433 02del 926 14 98604476 98636221 98621848 98633625 01del 927 14 106210547 106294783 106210547 106264422 56 21 del/dup 928 14 106210547 106295344 106210547 106238538 08del 929 14 106215123 106294783 106231839 106253619 40dup 930 14 106223861 106264422 106223861 106231735 10dup 931 15 19139947 21207965 20329239 20688804 10dup 932 15 18403665 20545323 18671277 20274130 61 1 complex 933 15 18427103 20335459 18671277 20274130 37 0 dup 934 15 18427103 20351309 18809823 19465661 10 10 complex 935 15 18711364 20335459 19788495 20059872 23 1 multiallelic 936 15 18427103 20329239 18432722 19788495 11 3 multiallelic 937 15 18427103 20335459 19257253 19465661 24 2 complex 938 15 18432722 20274130 18671277 19164076 14 0 dup 939 15 18427103 21241985 18671277 20773725 11 1 complex 940 15 18824589 20335459 19886462 20335459 62multiallelic 941 15 18711364 20329239 19841990 19915944 50dup 942 15 20457011 20584281 20457011 20556643 60dup 943 15 19128165 19258683 19128165 19187727 12complex 944 15 18432722 19431424 18432722 18838769 30dup 945 15 18432722 20329239 19821421 19876834 30dup 946 15 18711364 20329239 19877365 19943185 20dup 947 15 18753439 20274130 19368490 19465661 11complex 948 15 19244796 19385558 19244796 19385558 30dup 949 15 18873156 19178275 19139947 19162588 20dup 950 15 18812205 18850150 18812205 18850150 11complex 951 15 20422689 20588961 20555858 20588961 20dup 952 15 19464675 20774374 20335459 20498385 11del/dup 953 15 19923127 19951198 19923127 19951198 10dup 954 15 19164450 19199509 19164450 19199509 10dup 955 15 19257253 20077554 19970690 20045333 10dup 956 15 18427103 20274130 18809892 18824546 10dup 957 15 19157015 19244796 19162768 19164450 01del 958 15 19349313 20329239 19368490 19915944 10dup 959 15 18875952 19164450 18875952 19164450 10dup 960 15 19178339 20274130 19886462 19911606 10dup 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 961 15 21606530 21610088 21606530 21610088 01del 962 15 21892118 21931984 21892118 21928046 01del 963 15 22011887 22131052 22011887 22098514 01del 964 15 21877877 22380634 22098514 22300674 48del/dup 965 15 21892118 22072791 21931984 22022195 04del 966 15 22011887 22289332 22072791 22217599 11del/dup 967 15 22232921 22339434 22232921 22300674 01del 968 15 22606371 22689056 22622873 22659931 03del 969 15 28393128 28964768 28393128 28864940 07del 970 15 29762552 30740356 29806023 30298847 30dup 971 15 32688453 32729249 32717043 32720053 01del 972 15 32447708 32687764 32498326 32602617 751del/dup 973 15 39834465 39909909 39834465 39909909 01del 974 15 41619215 41845926 41676268 41840909 05del 975 15 42888144 43170912 42893168 43037184 32del/dup 976 15 49139541 49571273 49143403 49540148 10dup 977 15 51557013 51572775 51557013 51572775 01del 978 15 54523770 54577372 54523770 54577372 01del 979 15 59467652 59487950 59470349 59481935 01del 980 15 68815452 68834724 68821323 68834724 01del 981 15 77337962 77340626 77337962 77340626 01del 982 15 77737577 77850372 77754188 77803419 01del 983 15 79788150 79874464 79802725 79844345 10dup 985 15 82330480 82359162 82330480 82334689 01del 986 15 82618970 82904075 82618970 82904057 51complex 987 15 84140970 84162590 84142636 84151512 04del 988 15 84946745 84954786 84946745 84954786 01del 989 15 85706849 85711119 85706849 85711119 02del 990 15 88589888 88610637 88589912 88610637 10dup 991 15 88424056 88601412 88448992 88579335 40dup 992 15 90382555 90416250 90390344 90403622 02del 993 15 91597772 91620597 91605992 91620597 11del/dup 994 15 95654446 95716640 95654446 95711422 01del 995 15 98175492 98422157 98175516 98403957 10dup 996 15 99537666 99839857 99583955 99821546 10dup 997 16 4149842 4198092 4162240 4185910 02del 998 16 4995942 5310411 4995942 5300635 10dup 999 16 5542095 5551122 5548414 5551122 01del 1000 16 6448405 6449672 6448405 6449672 01del 1001 16 6594720 6632981 6603645 6622204 20dup 1002 16 6713809 6752649 6717197 6740651 03del 1003 16 6973749 7021963 7004037 7021963 01del 1004 16 7855056 7915358 7855056 7915358 01del 1005 16 9721050 9729949 9721050 9729949 01del 1006 16 12554682 12561909 12555559 12561909 05del 1007 16 12584246 12619700 12599033 12614880 09del 1008 16 16260667 16653145 16260667 16653145 14complex 1009 16 17441601 18072199 17516769 18072199 10dup 1010 16 18152877 18700411 18513898 18700411 10dup 1011 16 18072199 18990536 18874875 18982692 10dup 1012 16 20437119 20506848 20454385 20504059 01del 1013 16 20352824 20478276 20407950 20438354 014del 1014 16 21212772 21856623 21446837 21647775 21del/dup 1015 16 22313312 22631165 22466298 22612021 222del/dup 1016 16 24976087 25044753 24976087 25044753 11complex 1017 16 31918174 33744011 31918174 33572339 13multiallelic 1018 16 34667702 34820192 34708422 34802728 10dup 1019 16 34293686 34900436 34307201 34614572 19 0 dup 1020 16 45819013 46152506 45948101 46078672 10dup 1021 16 52965305 52987359 52967948 52977133 02del 1022 16 53310669 53336408 53325665 53332843 01del 1023 16 62639947 62714192 62639947 62696633 03del 1024 16 68609885 68745051 68622514 68681914 10dup 1025 16 69391450 69757550 69411882 69669602 30dup 1026 16 72330599 72332356 72330599 72332356 01del 1027 16 74567282 74579010 74567282 74578601 01del 1028 16 74819177 74829497 74819177 74829497 01del 1029 16 76929719 76974815 76929719 76974815 01del 1030 16 76848674 76948718 76857692 76918650 02del 1031 16 77607617 77626238 77618863 77620657 07del 1032 16 78452465 78480811 78452465 78480811 10dup 1033 16 79539177 79584643 79557783 79584643 01del 1034 16 79529780 79564259 79536934 79544102 131del/dup 1035 16 82340616 82351735 82340616 82351597 01del 1036 16 84834231 84849716 84836802 84848317 01del 1037 16 85539033 85558564 85539033 85549215 02del 1038 16 85079026 85094533 85079026 85084370 11complex 1039 17 800382 897708 827403 883601 10dup 1040 17 595817 827403 714985 787555 10dup 1041 17 6034605 6087870 6047210 6076840 02del 1042 17 13900781 13965204 13905369 13945992 01del 1043 17 16512229 16705555 16658950 16705555 27del/dup 1044 17 19426327 19504358 19426327 19500060 04del 1045 17 21246313 21641572 21308957 21437192 10dup 1046 17 31429427 32016863 31460821 31501499 112 0 dup 1047 17 32018706 32104672 32060753 32096773 30dup 1048 17 31460821 31895171 31461042 31473221 01del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 1049 17 32210529 32219667 32214012 32219667 01del 1050 17 36906648 37150369 36920120 37019240 30dup 1051 17 40813669 41089766 40897617 41015758 76 22 multiallelic 1052 17 41518102 42223353 41521621 41719833 41 0 dup 1053 17 41569871 42177829 41623640 41707463 20 0 dup 1054 17 41521621 41719833 41560151 41587103 21dup 1055 17 44093882 44118402 44093882 44118402 10dup 1056 17 48396906 48413228 48396906 48413228 01del 1057 17 51506859 51535723 51518243 51522852 09del 1058 17 53175939 53180824 53175939 53180824 01del 1059 17 69252400 69258719 69252400 69258719 01del 1060 17 74743681 74774728 74743681 74774728 02del 1061 17 75752791 75790078 75758221 75780106 10dup 1062 18 277648 306558 284021 294180 03del 1063 18 667302 695598 671962 675574 01del 1064 18 3784119 4112410 3784119 4095490 20dup 1065 18 9733326 9743992 9734353 9743992 01del 1066 18 14198563 14548050 14246531 14342852 10dup 1067 18 14731611 14855985 14743891 14845278 40dup 1068 18 24413258 24450849 24420573 24450128 02del 1069 18 26068546 26073661 26068546 26069966 04del 1070 18 27886747 27928990 27886747 27928990 10dup 1071 18 32241210 32272575 32241586 32272575 10dup 1072 18 32364761 32735865 32370299 32683125 10dup 1073 18 37638408 37686676 37638408 37686676 02del 1074 18 38183758 38194401 38185219 38194401 02del 1075 18 49503791 49532928 49503791 49520817 01del 1076 18 54081842 54095115 54081842 54086942 05del 1077 18 55803729 55838153 55803729 55813766 30dup 1078 18 56251349 56278547 56251380 56267422 01del 1079 18 59700021 59742065 59701163 59732876 05del 1080 18 60558805 60600790 60569424 60600790 01del 1081 18 62053230 62087598 62059541 62063708 115del/dup 1082 18 63098485 63123732 63111650 63119574 01del 1083 18 64126718 64284813 64156973 64267431 02del 1084 18 64888576 64912007 64888576 64903434 029del 1085 18 67700021 68122628 67738002 68033409 01del 1086 18 68579533 68585381 68579533 68582952 01del 1087 19 12350726 12410655 12381305 12400878 10dup 1088 19 15641041 15712261 15641615 15686739 13 1 del/dup 1089 19 15641747 15686739 15655727 15686739 10dup 1090 19 20079226 20152327 20101049 20152327 10dup 1091 19 20360525 20566187 20424240 20513074 035del 1092 19 21847093 22982374 21881415 22864259 01del 1093 19 22310497 22372715 22325357 22362462 03del 1094 19 22783426 23448260 22788956 23418867 20dup 1095 19 23474937 23534946 23497074 23534946 01del 1096 19 24131560 24297477 24132342 24254249 10dup 1097 19 34447521 34456548 34447521 34456548 01del 1098 19 38899057 38945239 38913190 38924012 10dup 1099 19 38568301 39224079 38633344 39205753 20dup 1100 19 40345482 40365173 40350568 40364911 027del 1102 19 42486690 42743446 42557205 42707549 01del 1103 19 46123775 46220507 46174582 46195917 12del/dup 1104 19 48230781 48511244 48362435 48481823 138 16 del 1105 19 47929604 48496602 47997284 48435623 55del/dup 1106 19 47856258 48314448 47997284 48231029 26del/dup 1107 19 48029945 48481823 48197824 48427094 32del/dup 1108 19 48435623 48562727 48461673 48511244 03del 1109 19 48373067 48462406 48413354 48461673 20dup 1110 19 48024719 48171792 48024719 48159695 10dup 1111 19 48395295 48461673 48403432 48413354 01del 1112 19 48316888 48445318 48370928 48403432 10dup 1113 19 49585942 49639284 49591313 49622643 02del 1114 19 56834443 56856939 56834443 56854528 12del/dup 1115 19 56951383 57296437 56989937 57293752 20dup 1116 19 58002524 58037133 58002621 58037133 54del/dup 1117 19 58162326 58246052 58169921 58201490 01del 1118 19 58604054 58651380 58604054 58640596 01del 1119 19 58620723 58696751 58620723 58696751 01del 1120 19 59374787 59491567 59416447 59457974 27 27 del/dup 1121 19 59850663 59886999 59850663 59865309 01del 1122 19 59878067 60118592 59944016 60040503 423del 1123 19 59939919 60048834 59940064 59971780 30dup 1124 19 60229274 60342499 60243956 60311272 10dup 1125 19 60927349 61018118 60959616 60988051 12 0 dup 1126 19 62684998 62694776 62684998 62694631 10dup 1127 19 63590775 63596527 63590775 63592252 02del 1128 20 2152811 2307429 2173481 2307429 10dup 1129 20 8022116 8536318 8082140 8517422 10dup 1130 20 11742014 12235765 11754621 12230658 20dup 1131 20 12581827 12609944 12599422 12607751 02del 1132 20 14653888 14792049 14729684 14771472 02del 1133 20 14825886 14863051 14825886 14863051 01del 1134 20 15230448 15279007 15239552 15265978 09del 1135 20 17305806 17338095 17306430 17338095 02del 1136 20 18197877 18221632 18197877 18201538 01del 500K CNV start (10% density end (10% density start (90% density end (90% density chr gain loss CNV type event ID boundary*) boundary) boundary) boundary) 1137 20 23094607 23127604 23094607 23127604 04del 1138 20 28106854 28244356 28106854 28154290 01del 1139 20 35736026 35759976 35736459 35759976 01del 1140 20 36367793 36539571 36373059 36515559 10dup 1141 20 40686319 40710511 40689219 40702735 02del 1142 20 44681417 44722596 44681417 44709070 10dup 1143 20 45195752 45227374 45211053 45219040 01del 1144 20 49756024 49852802 49756024 49848066 01del 1145 20 52112544 52118615 52112562 52115926 01del 1146 20 58995933 59023990 59002551 59023478 20dup 1147 21 9941889 10105718 9941889 10105718 46multiallelic 1148 21 13354570 14258658 13613238 14103113 23del/dup 1149 21 13829460 14077407 13829460 14070001 11complex 1150 21 19561892 19565214 19561892 19565214 01del 1151 21 19626353 19677375 19626353 19668806 01del 1152 21 20716906 20811712 20722676 20799079 03del 1153 21 22433789 22596775 22577771 22586139 062del 1154 21 23400864 23430325 23414584 23430325 01del 1155 21 23320362 23512054 23320362 23372706 01del 1156 21 24483440 24515887 24483440 24515887 10dup 1157 21 29161064 29191388 29161231 29180955 10dup 1158 21 39779393 39888026 39826812 39887600 10dup 1159 21 46067460 46144196 46114298 46127605 01del 1160 21 46811098 46902240 46842971 46894358 10dup 1161 22 15327532 15431692 15327532 15431692 01del 1162 22 14461115 15364974 14461115 15311685 25complex 1163 22 15252977 15431692 15268818 15327532 01del 1164 22 17005919 17412089 17265521 17404890 30dup 1165 22 22581891 22727762 22608070 22656453 14complex 1166 22 23932716 24371067 23988962 24244331 16 8 del/dup 1167 22 23969381 24249266 24228811 24231702 02del 1168 22 24460443 24475138 24460547 24472111 10dup 1169 22 33785204 33902969 33785892 33891967 01del 1170 22 41160225 41364932 41209495 41271378 01del 1171 22 42695340 42716298 42695340 42716135 01del 1172 22 43951199 44245703 43976381 44237216 10dup 1173 22 46758244 46775212 46759423 46775212 01del 1174 22 47780805 47808278 47780870 47808278 01del X1-1 23 4010786 4020384 103065326 103111418 10dup X1-10 23 75852421 75934438 7830174 7901660 01del X1-11 23 78897478 78910649 15427789 15472610 01del X1-12 23 88800734 89069512 16946317 16954313 10dup X1-13 23 103056216 103111418 27803965 31286986 10dup X1-14 23 115037017 115175870 47627524 47726981 10dup X1-15 23 134466048 134673554 63353045 63601613 30dup X1-16 23 139767019 139785882 66602201 67076354 20dup X1-17 23 140078981 140469418 75918345 75934438 10dup X1-18 23 145829455 146494249 75918345 75923773 10dup X1-19 23 146718150 146857358 78907724 78910649 10dup X1-2 23 6249179 6726074 115063910 115172405 20dup X1-20 23 148590921 148800374 88834519 88962384 30dup X1-21 23 151572622 151688320 90110689 90119084 10dup X1-3 23 7830174 7901660 134483002 134631588 10dup X1-4 23 15418427 15483661 134483002 134635914 01del X1-5 23 16946317 16971335 139767019 139785882 01del X1-6 23 22628358 22749222 140099749 140279716 02del X1-7 23 27751188 31356624 2696752 3169853 01del X1-8 23 47575078 47825476 4010786 4020384 72del/dup X1-9 23 66354058 67102115 7211131 7355904 10dup X2-1 23 2696752 2815614 2696752 2796637 10dup X2-10 23 103056216 103111418 148590921 148658261 10dup X2-11 23 115553046 115809368 47627524 47726981 10dup X2-12 23 134466048 134673554 148590921 148658261 20dup X2-13 23 140036126 140469418 151658014 151683554 10dup X2-14 23 148590921 148800374 151920735 152042746 50dup X2-15 23 151900926 152045136 103065326 103111418 10dup X2-2 23 2696752 3169853 28019567 28082720 10dup X2-3 23 4010786 4023267 140078981 140280724 10dup X2-4 23 7211131 7355904 115727036 115809368 01del X2-5 23 27959578 28189157 4010786 4020384 10dup X2-6 23 47575078 47760428 145882623 146435480 31del/dup X2-7 23 63292574 63919710 6341828 6687431 10dup X2-8 23 75918345 75923773 146718150 146857358 01del X2-9 23 90003377 90134018 22718153 22745968 10dup * 10% and 90% boundaries are based on comparisons with the reference set. The 90% boundary is the most stringent boundary. The 10% boundary is used for all analyses unless otherwise noted (see Supplementary Methods for more details) Supplementary Table 12: Merged CNV regions from WGTP and 500K EA with validation evidence and feaures overlap

Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged WGTP chr1 2408416 2412411 6 CNV_ID_4 Merged WDR8|NM_017818\ PRDM16|NM_199454\ PRDM16|NM_022114\ WGTP chr1 3312095 3572010 121 CNV_ID_5 ARHGEF16|NM_014448\ EGFL3|NM_001409\ FAM79A|NM_182752 Merged 500K EA chr1 3608198 3678693 TP73|NM_005427\ KIAA0495|NM_207306 601990 40 CNV_ID_6 Merged WGTP chr1 5200140 5470944 AY282806_BC050076 68 CNV_ID_7 Merged 500K EA chr1 7505729 7622325 CAMTA1|NM_015215 67 CNV_ID_8 Merged WGTP chr1 8822507 8850906 Variation_0003 V 8 CNV_ID_9 Variation_0993\ PEX14|NM_004565\ KIF1B|NM_183416\ DFFA|NM_213566\ Merged DFFA|NM_004401\ APITD1|NM_199295\ CORT|NM_001302\ 605995\ 605995\ WGTP chr1 10172336 10516820 Variation_0994\ √ VF 175 CNV_ID_10 UBE4B|NM_006048\ APITD1|NM_199294\ KIF1B|NM_015074\ 601791 Variation_1535 APITD1|NM_198544\ PGD|NM_002631 Merged uc.3\ uc.4\ uc.5\ uc.6\ WGTP chr1 10676768 10989413 QPCR √ EF CASZ1|NM_017766\ C1orf127|NM_173507 340 CNV_ID_11 uc.7\ uc.8\ uc.9\ uc.10 PRAMEF5|NM_001013407\ PRAMEF8|NM_001012276_copy_2\ Variation_0379\ PRAMEF7|NM_001012277\ PRAMEF4|NM_001009611\ Variation_1537\ PRAMEF2|NM_023014\ PRAMEF8|NM_001012276_copy_3\ DC0028\ DC0029\ DC0032\ DC0030\ Merged Variation_0004\ C1orf158|NM_152290\ PRAMEF9|NM_001010890\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr1 12533434 13622361 QPCR √ PVEF PRAMEF3|NM_001013692\ PRAMEF1|NM_023013\ DHRS3|NM_004753\ DC0033\ DC0034\ DC0035\ DC0036\ 134 CNV_ID_12 Variation_0678\ Intra\ Intra PRAMEF6|NM_001010889_copy_2\ HNRPCL1|NM_001013631\ DC0031 Variation_2043\ PRAMEF7|NM_001012277_copy_2\ PRAMEF6|NM_001010889\ RP11- Variation_0256\ 474O21.1|NM_001013630\ PRAMEF9|NM_001010890_copy_2\ Variation_0677 PRAMEF8|NM_001012276 Merged 500K EA chr1 14050388 14117706 √ F U17838_AB028949 33 CNV_ID_13 Merged 500K EA chr1 15872786 15900413 √ F 4 CNV_ID_14 Variation_0380\ Variation_0995\ Variation_1538\ Variation_0996\ Variation_0997\ LOC440570|NM_001013708\ ATP13A2|NM_022089\ DC0041\ DC0043\ DC0045\ DC0046\ Merged LOC440570|NM_001013708_copy_2\ SDHB|NM_003000\ Intra\ Intra\ Both\ Intra\ Intra\ Intra\ Intra\ both chr1 16509639 17229287 Variation_0998\ QPCR √ PVEF 185470 DC0048\ DC0049\ DC0050\ DC0042\ 289 CNV_ID_15 MFAP2|NM_002403\ NECAP2|NM_018090\ MFAP2|NM_017459\ Both\ Intra\ Both Variation_0679\ CROCC|NM_014675\ PADI2|NM_007365 DC0044\ DC0047 Variation_2044\ Variation_0005\ Variation_0999\ Variation_1539 Merged WGTP chr1 21481490 21687720 QPCR √ EF ALPL|NM_000478\ NBPF3|NM_032264\ RAP1GA1|NM_002885 171760 DC0053\ DC0054 Both\ Both 95 CNV_ID_16 Merged ELA3B|NM_007352\ CDC42|NM_044472\ CDC42|NM_001791\ WGTP chr1 21967827 22158163 Variation_2045 QPCR E 142461 DC0055\ DC0056 Intra\ Intra 124 CNV_ID_17 HSPG2|NM_005529\ ELA3A|NM_005747 Merged 500K EA chr1 25190816 25209157 14 CNV_ID_18 Merged 500K EA chr1 30375428 30410749 QPCR √ EF X97198_M55683 10 CNV_ID_19 SPOCD1|NM_144569\ BAI2|NM_001703\ ZCCHC17|NM_016505\ Merged TINAGL1|NM_022164\ SERINC2|NM_178865\ PTP4A2|NM_080392\ both chr1 31351473 32135424 P WDR57|NM_004814\ HCRTR1|NM_001525\ PTP4A2|NM_080391\ 538 CNV_ID_20 PEF1|NM_012392\ PTP4A2|NM_003479\ COL16A1|NM_001856\ FABP3|NM_004102 Merged C1orf78|NM_018166\ C1orf102|NM_145047\ STK40|NM_032017\ WGTP chr1 36289232 36556181 C1orf113|NM_024676\ LSM10|NM_032881\ THRAP3|NM_005119\ 138 CNV_ID_21 RPRC1|NM_018067 Merged 500K EA chr1 38797694 38806748 √ F L26494_AK023373 7 CNV_ID_22 OXCT2|NM_022120\ MFSD2|NM_032793\ BMP8B|NM_001720\ Merged CAP1|NM_006367\ PPIE|NM_203456\ MYCL1|NM_005376\ WGTP chr1 39894236 40329525 600722 DC0065\ DC0064 Intra\ Intra 239 CNV_ID_23 PPT1|NM_000310\ TRIT1|NM_017646\ MYCL1|NM_001033081\ MYCL1|NM_001033082\ RLF|NM_012421 Merged WGTP chr1 52838036 53001202 ZYG11B|NM_024646\ MGC52498|NM_182621\ C1orf163|NM_023077 50 CNV_ID_24 Merged SCP2|NM_001007250\ PODN|NM_153703\ SCP2|NM_001007100\ 500K EA chr1 53200585 53244138 √ F 28 CNV_ID_25 SCP2|NM_002979\ SCP2|NM_001007099 Merged WGTP chr1 53630573 53741257 √ F DMRTB1|NM_033067\ GLIS1|NM_147193 72 CNV_ID_26 Merged 500K EA chr1 54981672 55020630 √ F C1orf177|NM_152607 5 CNV_ID_27 Merged WGTP chr1 64389169 64488417 UBE2U|NM_152489 50 CNV_ID_28 Variation_1009\ Variation_1011\ Variation_1005\ Variation_1007\ Merged WGTP chr1 72454417 72598834 Variation_0383\ √ F NEGR1|NM_173808 AY358132_AF083119 57 CNV_ID_29 Variation_1006\ Variation_1008\ Variation_1010\ Variation_1543 Merged 500K EA chr1 72809121 72827226 AY358132_AF083119 14 CNV_ID_30 Merged WGTP chr1 72893633 73019191 AY358132_AF083119 31 CNV_ID_31 Merged WGTP chr1 73325120 73487705 AF083119_BC062795 26 CNV_ID_32 Merged both chr1 75698925 75899769 √ PF SLC44A5|NM_152697 36 CNV_ID_33 Merged 500K EA chr1 76950439 77014906 40 CNV_ID_34 Merged 500K EA chr1 77487035 77500483 √ F AK5|NM_012093\ AK5|NM_174858 7 CNV_ID_35 Merged 500K EA chr1 81599438 81608767 √ F AY358360_AF104266 25 CNV_ID_36 Merged both chr1 83040583 83720332 Variation_0010 √ PVF AF104266_AK128604 DC0089\ DC0090\ DC0091\ DC0092 Inter\ Inter\ Inter\ Inter 489 CNV_ID_37 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged RP11-82K18.3|NM_001008662\ RBMXL1|NM_019610\ GBP1|NM_002053\ WGTP chr1 89124089 89272744 √ F DC0099 Intra 12 CNV_ID_38 GBP3|NM_018284\ RP11-82K18.3|NM_001008661 Merged WGTP chr1 90532013 90695320 √ F BC052645_AY338397 92 CNV_ID_39 Variation_1012\ Merged 500K EA chr1 94831811 94870624 Variation_1013\ PCR √ VEF 13 CNV_ID_40 Variation_1548 Merged WGTP chr1 96127772 96258135 BC010936_AB051232 77 CNV_ID_41 232400\ 232400\ Merged AGL|NM_000643\ AGL|NM_000645\ AGL|NM_000028\ WGTP chr1 100071676 100210363 SLC35A3|NM_012243\ AGL|NM_000642\ AGL|NM_000644\ 232400\ 232400\ 24 CNV_ID_42 AGL|NM_000646 232400\ 232400 Merged 500K EA chr1 102084360 102129114 √ F OLFM3|NM_058170 31 CNV_ID_43 AMY1B|NM_001008218\ AMY1B|NM_001008218_copy_3\ Variation_0872\ AMY1A|NM_001008221_copy_2\ AMY1A|NM_004038_copy_3\ Merged Variation_0012\ AMY2A|NM_000699\ AMY1B|NM_001008218_copy_2\ AMY1A|NM_004038\ DC0107\ DC0108\ DC0109\ DC0106\ WGTP chr1 103702380 104164023 QPCR √ EF AMY1C|NM_001008219\ RNPC3|NM_017619\ BC063129_BC031278 Intra\ Intra\ Intra\ Intra\ Intra\ Intra 107 CNV_ID_44 Variation_0681\ AMY1C|NM_001008219_copy_2\ AMY1A|NM_004038_copy_2\ DC0110\ DC0111 Variation_2048 AMY1C|NM_001008219_copy_3\ AMY1A|NM_001008221\ AMY2B|NM_020978\ AMY1A|NM_001008221_copy_3 Merged Variation_0682\ 500K EA chr1 105856683 105936087 √ VF BC063129_BC031278 7 CNV_ID_45 Variation_0258 Merged both chr1 106472604 106593624 P BC031278_AY043278 28 CNV_ID_46 Merged both chr1 107195670 107552925 √ PF NTNG1|NM_014917\ HRMT1L6|NM_018137 BC031278_AY043278 281 CNV_ID_47 Merged WGTP chr1 108330916 108808720 Variation_2049 QPCR √ VEF SLC25A24|NM_013386\ SLC25A24|NM_213651\ NBPF4|NM_152488 DC0115\ DC0114\ DC0116 Both\ Both\ Both 98 CNV_ID_48 Merged 500K EA chr1 111499437 111506775 3 CNV_ID_49 Merged 500K EA chr1 111535893 111547026 √ F RP11-165H20.1|NM_001013621\ CHIA|NM_201653\ CHIA|NM_021797 22 CNV_ID_50 Merged Variation_0386\ 500K EA chr1 112407136 112422566 √ VF 4 CNV_ID_51 Variation_1322

Merged WGTP chr1 116876957 116986717 √ F C1orf137|NM_001013643\IGSF3|NM_001542\IGSF3|NM_001007237 DC0143 Inter 108 CNV_ID_53 Merged Variation_1015\ both chr1 119728738 119926619 √ PVF HSD3B1|NM_000862 DC0145\ DC0146\ DC0147\ DC0148\ DC0149 Intra\ Intra\ Intra\ Intra\ Intra 116 CNV_ID_54 Variation_1552 DC0151\ DC0152\ DC0156\ DC0157\ DC0159\ Merged REG4|NM_032044\NOTCH2|NM_024408\LOC440607|NM_001004340\PHGD Intra\ Intra\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ WGTP chr1 119979355 120958392 QPCR √ EF H|NM_006623\HMGCS2|NM_005518\LOC440607|NM_001017986\ADAM30|N 606879\ 600234 L03420_AB084917 DC0160\ DC0161\ DC0162\ DC0164\ DC0150\ 554 CNV_ID_55 Inter\ Both\ Intra\ Both\ Both\ Inter\ Inter M_021794 DC0153\ DC0154\ DC0155\ DC0158\ DC0163 Variation_1553\ Variation_0388\ PDE4DIP|NM_022359\PDE4DIP|NM_014644\RBM8A|NM_005105\PDE4DIP|N Variation_0389\ M_001002810\NOTCH2NL|NM_203458\ITGA10|NM_003637\PPIAL4|NM_178 DC0176\ DC0167\ DC0170\ DC0171\ DC0172\ Merged 230\POLR3GL|NM_032305\HFE2|NM_202004\SEC22L1|NM_004892\PEX11B 608374\ 608374\ 608374\ Inter\ Intra\ Intra\ Both\ Both\ Both\ Intra\ Both\ both chr1 141387477 143032961 Variation_0387\ QPCR √ PEF L03420_AB084917 DC0174\ DC0177\ DC0165\ DC0166\ DC0168\ 712 CNV_ID_56 |NM_003846\TXNIP|NM_006472\PDE4DIP|NM_001002811\HFE2|NM_213653 608374 Inter\ Both\ Both\ Both\ Both\ Intra\ Both Variation_0260\ \HFE2|NM_145277\LIX1L|NM_153713\HFE2|NM_213652\PDE4DIP|NM_0010 DC0169\ DC0173\ DC0175\ DC0178\ DC0179 Variation_0685\ 02812 Variation_2050 DC0180\ DC0181\ DC0184\ DC0186\ DC0187\ Merged FMO5|NM_001461\ZNF364|NM_014455\CD160|NM_007053\NBPF11|NM_183 Intra\ Intra\ Intra\ Intra\ Intra\ Both\ Intra\ Intra\ both chr1 143086160 143922358 Variation_1326 √ PVF DC0190\ DC0191\ DC0182\ DC0183\ DC0185\ 363 CNV_ID_57 372\PRKAB2|NM_005399\PDZK1|NM_002614\POLR3C|NM_006468 Intra\ Both\ Intra\ Both DC0188\ DC0189 Variation_0390\ Variation_1016\ Variation_1017\ Variation_2051\ LOC388692|NM_001013644\H4/o|NM_001034077\HIST2H2AA|NM_003516_c Variation_1327\ opy_2\H4/o|NM_001034077_copy_2\MTMR11|NM_181873\HIST2H3C|NM_02 DC0202\ DC0193\ DC0194\ DC0195\ DC0196\ Variation_1331\ 1059_copy_2\HIST2H4|NM_003548_copy_2\PPIAL4|NM_178230_copy_2\HIS DC0197\ DC0198\ DC0199\ DC0200\ DC0201\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Variation_1329\ T2H2AC|NM_003517\HIST2H2AA|NM_003516\HIST2H4|NM_003548\RP5- Merged 998N21.6|NM_001025303\NBPF15|NM_173638\MTMR11|NM_006697\SV2A| DC0209\ DC0210\ DC0212\ DC0214\ DC0217\ Intra\ Intra\ Both\ Both\ Intra\ Intra\ Inter\ Intra\ both chr1 144800023 146809052 Variation_1554\ QPCR √ PVEF 146760 604 CNV_ID_58 NM_014849\RP11- DC0219\ DC0204\ DC0205\ DC0206\ DC0207\ Both\ Both\ Both\ Both\ Both\ Both\ Both\ Both\ Variation_1334\ 196G18.6|NM_001024599\H3/o|NM_001005464\HIST2H3C|NM_021059\SF3B DC0208\ DC0211\ DC0215\ DC0216\ DC0218\ Intra\ Intra\ Intra Variation_1555\ 4|NM_005850\PPIAL4|NM_178230_copy_3\NBPF14|NM_015383\HIST2H2BE| DC0203\ DC0213 Variation_1330\ NM_003528\H3/o|NM_001005464_copy_2\ZA20D1|NM_020205\HIST2H2AB|N M_175065\FLJ39739|NM_207400\FCGR1A|NM_000566\BOLA1|NM_016074 Variation_1328\ Variation_1332\ Variation_2052\ Variation_1333 Merged PSMB4|NM_002796\POGZ|NM_145796\POGZ|NM_207171\POGZ|NM_01510 500K EA chr1 148141867 148224708 Variation_1556 √ F 23 CNV_ID_59 0\SELENBP1|NM_003944 Variation_1019\ Variation_1337\ LCE3A|NM_178431\C1orf42|NM_019060\LCE2B|NM_014357\LCE2A|NM_178 Variation_1558\ 428\LCE1A|NM_178348\LCE2D|NM_178430\LCE1C|NM_178351\LCE3C|NM_ Merged Variation_1018\ 178434\SMCP|NM_030663\C1orf45|NM_001025231\LCE1F|NM_178354\LCE1 both chr1 149285912 149711226 MassSpec √ PVEF 103 CNV_ID_60 Variation_1020\ D|NM_178352\LCE3B|NM_178433\LCE1B|NM_178349\LCE4A|NM_178356\L Variation_0394\ CE5A|NM_178438\IVL|NM_005547\LCE3D|NM_032563\LCE3E|NM_178435\L CE1E|NM_178353\LCE2C|NM_178429 Variation_1559\ Variation_0393

FCGR2C|NM_001005411\FCGR2B|NM_001002274\FCGR2B|NM_001002273\ FCGR2C|NM_001005410_copy_2\FCGR3B|NM_000570\FCRLM1|NM_032738 Merged Variation_0261\ \FCGR2C|NM_201563_copy_2\FCGR3A|NM_000569\HSPA6|NM_002155\FC 604590\ 604590\ 146790\ both chr1 158157328 158413210 QPCR √ PEF DC0240\ DC0241 Intra\ Intra 44 CNV_ID_62 Variation_1339 GR2A|NM_021642\FCGR2B|NM_004001\FCGR2C|NM_001005411_copy_2\F 146740\ 604590\ 604590 CGR2B|NM_001002275\FCGR2C|NM_001005412\FCGR2C|NM_201563\FCG R2C|NM_001005410 Merged UHMK1|NM_175866\SH2D1B|NM_053282\C1orf111|NM_182581\NOS1AP|N both chr1 158796126 159235014 √ PF 201 CNV_ID_63 M_014697 Merged 500K EA chr1 162149184 162157194 √ F 8 CNV_ID_64 Merged both chr1 163223537 163382643 QPCR √ PEF LOC116123|NM_138784 AK055347_BC014341 61 CNV_ID_65 Merged WGTP chr1 166513664 166616844 √ F SCYL3|NM_020423\SCYL3|NM_181093\C1orf112|NM_018186 15 CNV_ID_66 Merged 500K EA chr1 167046739 167144950 √ F 37 CNV_ID_67 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

U74/1/170568468/170568540/100.000000, U75/1/170567673/170567733/100.000000, U76/1/170567429/170567510/100.000000, U77/1/170567102/170567166/100.000000, Merged ZBTB37|NM_032522\DARS2|NM_018122\SERPINC1|NM_000488\RC3H1|NM U44/1/170566760/170566823/100.000000, WGTP chr1 170542299 170687600 107300 104 CNV_ID_68 _172071 U78/1/170566420/170566481/100.000000, U79/1/170566144/170566225/100.000000, U80/1/170565627/170565698/100.000000, U47/1/170565164/170565239/100.000000, U81/1/170564947/170565012/100.000000 Merged WGTP chr1 171200938 171301433 Variation_0014 V RABGAP1L|NM_014857 DC0247 Inter 38 CNV_ID_69 Merged 500K EA chr1 175389239 175405731 √ F 6 CNV_ID_70 Merged 500K EA chr1 182024854 182077428 √ F 18 CNV_ID_71 Merged both chr1 185978190 186380985 √ PF M68874_AB111893 52 CNV_ID_72 Merged Variation_1344\ 500K EA chr1 186468490 186551144 √ VF M68874_AB111893 17 CNV_ID_73 Variation_1561 Merged 500K EA chr1 186690763 186726869 √ F M68874_AB111893 27 CNV_ID_74 Merged 500K EA chr1 188509177 188557409 AB111893_BC020632 12 CNV_ID_75 Merged 500K EA chr1 190363185 190441853 √ F AF312865_AK127807 DC0254 Inter 48 CNV_ID_76 Merged 500K EA chr1 191669736 191674561 √ F AF312865_AK127807 2 CNV_ID_77 Merged WGTP chr1 191987584 192311869 QPCR E AF312865_AK127807 32 CNV_ID_78 Merged both chr1 192535421 192851111 √ PF AF312865_AK127807 48 CNV_ID_79 Variation_1345\ Variation_1021\ Merged Variation_0686\ ZBTB41|NM_194314\F13B|NM_001994\CFHL1|NM_002113\ASPM|NM_01813 605481\ 134370\ 134370\ DC0255\ DC0257\ DC0258\ DC0259\ DC0260\ both chr1 193322494 193901429 PCR √ PEF 6\CFHL5|NM_030787\CFHL4|NM_006684\CFH|NM_001014975\CFHL2|NM_0 Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra 69 CNV_ID_80 Variation_2054\ 05666\CFH|NM_000186\CFHL3|NM_021023 134580 DC0261\ DC0256 Variation_0687\ Variation_2055 Merged 500K EA chr1 197239167 197328634 DDX59|NM_031306\KIF14|NM_014875 26 CNV_ID_81 Merged WGTP chr1 199299046 199455863 QPCR E JARID1B|NM_006618\SYT2|NM_177402 DC0267 Inter 60 CNV_ID_83 DC0274\ DC0275\ DC0277\ DC0271\ DC0272\ Merged Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ WGTP chr1 203946290 204313462 Variation_0398 √ F CR1|NM_000573\CR1|NM_000651\CR2|NM_001877\CR2|NM_001006658 120620\ 120620 DC0276\ DC0278\ DC0279\ DC0280\ DC0281\ 66 CNV_ID_84 Intra\ Intra\ Intra\ Intra DC0282\ DC0273 Merged 500K EA chr1 204831917 204885513 √ F 55 CNV_ID_85 Merged 500K EA chr1 206967918 207009174 √ F HHAT|NM_018194 3 CNV_ID_86 Merged FAM71A|NM_153606\ATF3|NM_004024\ATF3|NM_001030287\ATF3|NM_001 WGTP chr1 209036538 209231498 100 CNV_ID_87 674 Merged 500K EA chr1 209313824 209394792 LOC149643|NM_001024601\C1orf48|NM_015471 19 CNV_ID_88 Merged WGTP chr1 218684362 218846708 √ F BC031405_AK126238 DC0287 Both 59 CNV_ID_89 Merged 500K EA chr1 220000153 220016185 2 CNV_ID_90 Merged TP53BP2|NM_001031685\CAPN2|NM_001748\FBXO28|NM_015176\TP53BP WGTP chr1 220241955 220669898 √ F DC0291\ DC0289\ DC0290 Both\ Both\ Both 136 CNV_ID_91 2|NM_005426 Merged WGTP chr1 221394659 221560009 8 CNV_ID_92 Merged WGTP chr1 221711686 221833513 √ F 6 CNV_ID_93 Merged 500K EA chr1 221972429 222010220 √ F ENAH|NM_001008493\ENAH|NM_018212 8 CNV_ID_94 Merged DISC1|NM_001012957\DISC1|NM_001012959\DISC1|NM_001012958\DISC1| 605210\ 605210\ 605210\ both chr1 227931495 228222731 √ PF 68 CNV_ID_95 NM_018662\TSNAX|NM_005999 605210 Merged WGTP chr1 231180061 231434698 √ F DC0298 Intra 165 CNV_ID_96 Merged 500K EA chr1 233192877 233228405 √ F ACTN2|NM_001103 25 CNV_ID_97 Merged 500K EA chr1 233458152 233471959 1 CNV_ID_98 Merged both chr1 234267835 235094143 Variation_0982 PV ZP4|NM_021186\RYR2|NM_001035 180,902,600,996 NM_021186_AF279779 243 CNV_ID_99 Merged both chr1 236092135 236715545 Variation_0262 PV FMN2|NM_020066\CHRM3|NM_000740 NM_021186_AF279779 250 CNV_ID_100 Variation_1346\ Merged 500K EA chr1 239362708 239606926 Variation_1564\ QPCR √ VEF AK098092_AL161964 DC0307\ DC0309\ DC0308\ DC0310\ DC0311 Inter\ Inter\ Inter\ Both\ Inter 116 CNV_ID_101 Variation_1347 Merged 500K EA chr1 242354620 242442043 √ F SMYD3|NM_022743 30 CNV_ID_102 Merged WGTP chr1 242733187 243066985 √ F TFB2M|NM_022366\C1orf71|NM_152609\SMYD3|NM_022743 110 CNV_ID_103 Merged 500K EA chr1 243265897 243272062 12 CNV_ID_104

Merged SH3YL1|NM_015677\TMEM18|NM_152834\ACP1|NM_177554\ACP1|NM_004 both chr2 157949 915588 √ PF DC0326 Inter 99 CNV_ID_107 300\ACP1|NM_007099\LOC285016|NM_001002919 Merged TPO|NM_175720\TPO|NM_175721\TPO|NM_000547\TPO|NM_175719\TPO|N 606765\ 606765\ 606765\ 500K EA chr2 1410597 1484084 MassSpec E 3 CNV_ID_108 M_175722 606765\ 606765 Merged WGTP chr2 1866728 2035145 √ F MYT1L|NM_015025 39 CNV_ID_109 Merged 500K EA chr2 3256238 3288649 AF215924_BC002485 7 CNV_ID_110 Merged 500K EA chr2 3730174 3770183 AF215924_BC002485 1 CNV_ID_111 Merged 500K EA chr2 4402072 4417591 AF215924_BC002485 10 CNV_ID_112 Merged WGTP chr2 5448267 5618952 √ F AK001775_AB028641 55 CNV_ID_113 Merged 500K EA chr2 6248649 6273145 √ F AK123041_AK124409 6 CNV_ID_114 Merged 500K EA chr2 10297740 10357304 FLJ25102|NM_182626 19 CNV_ID_115 Merged 500K EA chr2 10546176 10639567 34 CNV_ID_116 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged D87119_AK123490\ WGTP chr2 13234898 13698420 √ F DC0331\ DC0333\ DC0332 Inter\ Inter\ Inter 93 CNV_ID_117 AK123490_AK092654 Merged 500K EA chr2 14296389 14319566 QPCR E AK123490_AK092654 17 CNV_ID_118 Merged 500K EA chr2 14642533 14660690 √ F AK123490_AK092654 10 CNV_ID_119 Merged WGTP chr2 15152787 15308457 NAG|NM_015909 AK092711_AF056195 71 CNV_ID_120 Merged 500K EA chr2 16983359 16989153 BC038971_BC022012 1 CNV_ID_121 Merged 500K EA chr2 17809678 17896719 SMC6L1|NM_024624\FLJ40869|NM_182625 24 CNV_ID_122 Merged Variation_1567\ 500K EA chr2 18063761 18147135 √ F BC004148_AY358511 21 CNV_ID_123 Variation_1028 Merged WGTP chr2 22725791 23031671 √ F AF113010_BC013982 234 CNV_ID_124 Merged RBKS|NM_022128\BRE|NM_199192\BRE|NM_199191\BRE|NM_004899\BRE| WGTP chr2 27972987 28136281 120 CNV_ID_125 NM_199193\BRE|NM_199194 Variation_1569\ Variation_1570\ Merged LOC165186|NM_199280\YPEL5|NM_016061\RSNL2|NM_024692\LBH|NM_03 both chr2 29088147 30451080 Variation_1571\ PV 1002 CNV_ID_126 0915\ALK|NM_004304\FLJ34931|NM_001029883 Variation_1572\ Variation_1573 Merged 500K EA chr2 34596931 34666683 Variation_1574 √ VF AK057470_AF167706 12 CNV_ID_127 Merged WGTP chr2 35149394 35316635 AK057470_AF167706 32 CNV_ID_128 Merged Variation_1030\ 500K EA chr2 35484210 35548857 √ F AK057470_AF167706 9 CNV_ID_129 Variation_1575 Merged WGTP chr2 35775617 36031232 Variation_0018 √ VF AK057470_AF167706 66 CNV_ID_130 Merged both chr2 36155103 36502309 Variation_0523 √ PVF CRIM1|NM_016441 AK057470_AF167706 213 CNV_ID_131 Merged 500K EA chr2 36534557 36568956 CRIM1|NM_016441 25 CNV_ID_132 Merged 500K EA chr2 36959004 36960602 4 CNV_ID_133 Merged both chr2 37708305 38050590 √ PF CDC42EP3|NM_006449 241 CNV_ID_134 Merged WGTP chr2 40459598 40645427 SLC8A1|NM_021097 114 CNV_ID_135 Merged 500K EA chr2 40842372 40878370 √ F BX537482_AF336876 3 CNV_ID_136 Variation_0985\ Merged Variation_1349\ PIGF|NM_173074\ATP6V1E2|NM_080653\RHOQ|NM_012249\PIGF|NM_0026 both chr2 46444463 46785802 √ PVF DC0340 Inter 167 CNV_ID_137 Variation_1577\ 43\EPAS1|NM_001430\CRIPT|NM_014171 Variation_0837 Merged 500K EA chr2 50710112 50772700 NRXN1|NM_004801 55 CNV_ID_138 Merged WGTP chr2 51193365 51277533 AB011150_BC009569 35 CNV_ID_139 Merged WGTP chr2 52639031 52726188 Variation_1578 V AB011150_BC009569 25 CNV_ID_140 Merged WGTP chr2 55658890 55892725 √ F MGC15407|NM_080667\PNPT1|NM_033109\SMEK2|NM_020463 66 CNV_ID_141 Merged hsa-mir-216/2/56127735/56127845/100.000000, WGTP chr2 56090090 56384045 171 CNV_ID_142 hsa-mir-217/2/56121752/56121862/100.000000 Merged both chr2 56571336 56762849 √ PF AB067499_BC027854 34 CNV_ID_143 Merged both chr2 57196182 57400047 Variation_1581 √ PF AB067499_BC027854 17 CNV_ID_144 uc.54\uc.55\uc.56\uc.58\uc Merged BCL11A|NM_018014\PEX13|NM_002618\PAPOLG|NM_022894\BCL11A|NM_ both chr2 58306194 61252101 Variation_1582 PV 138553\BCL11A|NM_138559\FLJ32312|NM_144709\REL|NM_002908\KIAA18 608111\ 601789 .59\uc.60\uc.61\uc.62\uc.5 BC054517_AJ404611 2735 CNV_ID_145 41|NM_032506\FANCL|NM_018062\BCL11A|NM_022893 3\uc.57\uc.52 Merged both chr2 64164656 64451207 √ PF PELI1|NM_020651 165 CNV_ID_146 Merged 500K EA chr2 66041145 66060953 FLJ16124|NM_001004345 AY299090_BC043503 17 CNV_ID_147 Merged WGTP chr2 66240707 66411516 AY299090_BC043503 123 CNV_ID_148 Merged both chr2 67178358 67377313 P BC043503_AJ242682 116 CNV_ID_149 Merged 500K EA chr2 71253797 71285075 Variation_1583 √ F MPHOSPH10|NM_005791\MCEE|NM_032601 DC0349 Inter 6 CNV_ID_150 STAMBP|NM_213622\STAMBP|NM_201647\STAMBP|NM_006463\CML2|NM Merged _016347\CGI- DC0355\ DC0353\ DC0354\ DC0356\ DC0357\ WGTP chr2 73628687 73990247 √ F 606844 Inter\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra 68 CNV_ID_151 121|NM_016058\ALMS1|NM_015120\DUSP11|NM_003584\NAT8|NM_003960\ DC0358\ DC0359 LOC200420|NM_145300

GCS1|NM_006302\SLC4A5|NM_033323\LOXL3|NM_032603\SLC4A5|NM_021 196\TLX2|NM_016170\AUP1|NM_012103\SLC4A5|NM_133478\WDR54|NM_0 32118\ZNHIT4|NM_031288\HTRA2|NM_013247\WBP1|NM_012477\RTKN|NM Merged _001015055\DCTN1|NM_023019\AUP1|NM_181576\NM_001534\RTKN|NM_0 WGTP chr2 74391579 74674080 √ F 601143\ 601143\ 601336 134 CNV_ID_152 33046\FLJ12788|NM_022492\AUP1|NM_181575\DQX1|NM_133637\HTRA2|N M_145074\FLJ14397|NM_032779\RTKN|NM_001015056\DCTN1|NM_004082\ PCGF1|NM_032673\SLC4A5|NM_133479\LBX2|NM_001009812\MRPL53|NM _053050 Merged 500K EA chr2 75275078 75294365 Variation_1584 √ F TACR1|NM_015727\TACR1|NM_001058 7 CNV_ID_153 Merged both chr2 75601060 75924478 Variation_1585 √ PVF MRPL19|NM_014763\C2orf3|NM_003203\FLJ13391|NM_032181 BC000853_AY358324 108 CNV_ID_154 Merged WGTP chr2 76453575 76617009 √ F BC000853_AY358324 59 CNV_ID_155 Merged 500K EA chr2 76749556 76771867 BC000853_AY358324 2 CNV_ID_156 Merged 500K EA chr2 77097511 77120706 14 CNV_ID_157 Merged both chr2 77766753 78013206 Variation_1586 √ PVF AY358324_AY359047 DC0360\ DC0361 Intra\ Intra 39 CNV_ID_158 Merged both chr2 78038044 78622687 √ PF AY358324_AY359047 109 CNV_ID_159 Merged WGTP chr2 80312976 80754119 √ F CTNNA2|NM_004389\LRRTM1|NM_178839 332 CNV_ID_160 Merged BX537769_AK075442\ 500K EA chr2 81671346 81727952 Variation_0020 V 5 CNV_ID_161 AK075442_BC067852 Merged both chr2 83160508 83876420 P AK075442_BC067852 109 CNV_ID_162 Merged WGTP chr2 84643112 84795200 FLJ37357|NM_173645 50 CNV_ID_163 Variation_1587\ Variation_0843\ Variation_0889\ DC0368\ DC0369\ DC0370\ DC0372\ DC0373\ Merged RGPD2|NM_001024457\LOC285074|NM_001012626\PLGLB1|NM_001032392 Intra\ Intra\ Intra\ Both\ Both\ Intra\ Intra\ Intra\ both chr2 87017102 88135226 Variation_1588\ QPCR √ PVEF _copy_2\PLGLB2|NM_002665\PLGLB1|NM_001032392\RGPD2|NM_0010244 DC0378\ DC0371\ DC0374\ DC0375\ DC0377\ 510 CNV_ID_164 Both\ Inter\ Both\ Inter Variation_1351\ 57_copy_2\MGC4677|NM_052871\PLGLB2|NM_002665_copy_2 DC0367\ DC0376 Variation_1352\ Variation_0266 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_1353\ Variation_1354\ Variation_1355\ Variation_0846\ AY026351_BC021716\ DC0391\ DC0394\ DC0396\ DC0389\ DC0390\ Merged Variation_2057\ Intra\ Both\ Inter\ Intra\ Intra\ Both\ Both\ Both\ both chr2 89740700 91696901 QPCR √ PEF LOC440888|NM_001032412\IFP38|NM_031943_copy_3 AB051438_CENTp\ DC0393\ DC0395\ DC0397\ DC0398\ DC0399\ 293 CNV_ID_165 Variation_2058\ Both\ Inter\ Both\ Both AB051438_AB051438 DC0400\ DC0392 Variation_1591\ Variation_0527\ Variation_0888\ Variation_0267 Merged both chr2 94780673 95041982 P TEKT4|NM_144705 AY026351_BC021716 DC0403\ DC0401\ DC0402 Inter\ Inter\ Inter 134 CNV_ID_166 Merged WGTP chr2 95392012 95574433 FAHD2A|NM_016044\CSEN|NM_001034914\CSEN|NM_013434 DC0404 Both 81 CNV_ID_167 Merged KIAA1641|NM_020970\COX5B|NM_001862\DKFZp434N062|NM_199336\ANK DC0413\ DC0420\ DC0412\ DC0414\ DC0415\ Intra\ Both\ Intra\ Both\ Both\ Intra\ Intra\ Both\ both chr2 96992983 97795025 QPCR √ PEF 176947 177 CNV_ID_168 RD36|NM_198555\ACTR1B|NM_005735\ZAP70|NM_001079 DC0416\ DC0417\ DC0418\ DC0419 Intra Merged WGTP chr2 99839409 100005193 √ F AFF3|NM_002285\AFF3|NM_001025108 127 CNV_ID_169 Merged WGTP chr2 104052123 104218620 QPCR E uc.67 AK129862_NM_006236 98 CNV_ID_170 Merged WGTP chr2 107056558 107220149 Variation_0691 V BC008680_BX537861 DC0430 Inter 30 CNV_ID_171 Variation_1593\ Merged GCC2|NM_014635\LIMS1|NM_004987\SULT1C1|NM_001056\GCC2|NM_181 both chr2 107908395 108681855 Variation_1594\ √ PVF 453\SULT1C3|NM_001008743\SULT1C2|NM_006588\SLC5A7|NM_021815\S BC008680_BX537861 DC0435\ DC0432\ DC0433\ DC0434 Intra\ Intra\ Intra\ Intra 169 CNV_ID_172 Variation_2059 ULT1C1|NM_176825 Merged NPHP1|NM_000272\NPHP1|NM_207181\MALL|NM_005434\LOC205251|NM_ 213300,607100\ both chr2 110050731 110558272 √ PF DC0442\ DC0441\ DC0443\ DC0440 Intra\ Intra\ Both\ Both 232 CNV_ID_173 174925 213300,607100 Variation_1595\ Variation_0268\ BCL2L11|NM_138621\BCL2L11|NM_207003\BCL2L11|NM_138622\BCL2L11| Merged NM_138624\ANAPC1|NM_022662\BCL2L11|NM_138627\BCL2L11|NM_00653 WGTP chr2 111616014 112463168 Variation_2060\ √ F 604705 DC0447\ DC0445\ DC0448\ DC0446 Intra\ Intra\ Intra\ Intra 363 CNV_ID_174 8\BCL2L11|NM_138623\BCL2L11|NM_138625\MERTK|NM_006343\BCL2L11| Variation_0922\ NM_138626 Variation_0952 Merged 500K EA chr2 113185466 113195120 CNV_ID_175

FKSG30|NM_001017421\PLEKHB2|NM_001031706\ARHGEF4|NM_032995\P TPN18|NM_014369\POTE2|NM_001005359\FLJ41821|NM_001001697\LOC55 Variation_0973\ 4226|NM_001024655\GPR39|NM_001508\CFC1|NM_032545_copy_2\DKFZp4 DC0459\ DC0461\ DC0462\ DC0466\ DC0467\ Variation_1597\ 34E2321|NM_207310\POTE2|NM_001005364\IMP4|NM_033416\FLJ20297|N DC0468\ DC0469\ DC0471\ DC0473\ DC0476\ Both\ Intra\ Intra\ Both\ Intra\ Intra\ Intra\ Both\ Merged Variation_0024\ M_017951\H2- DC0477\ DC0482\ DC0483\ DC0485\ DC0458\ Both\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Both\ both chr2 130063068 133031735 QPCR √ PEF ALPHA|NM_080386\ARHGEF4|NM_015320\MGC50273|NM_214461\FLJ2029 605194 AK128224_AK125976 1055 CNV_ID_183 Variation_0025\ 7|NM_017751\LOC90557|NM_138770\CFC1|NM_032545\C2orf27|NM_013310 DC0460\ DC0463\ DC0464\ DC0465\ DC0470\ Both\ Both\ Both\ Both\ Both\ Both\ Both\ Inter\ Variation_0269\ \LOC112714|NM_207312\FLJ14346|NM_025029\GPR148|NM_207364\LOC44 DC0472\ DC0474\ DC0475\ DC0478\ DC0479\ Both\ Inter\ Inter\ Inter Variation_0887 0905|NM_001013711\POTE2|NM_001004054\LOC130074|NM_001009993\M DC0480\ DC0481\ DC0484 GC12981|NM_032357\PLEKHB2|NM_017958\RAB6C|NM_032144\FLJ38377| NM_152698 Merged 500K EA chr2 133101579 133147577 √ F GPR39|NM_001508 26 CNV_ID_184 Merged 500K EA chr2 137031522 137074036 AF348491_AB051466 12 CNV_ID_185 Merged both chr2 141905123 142079679 P LRP1B|NM_018557 36 CNV_ID_186 Merged both chr2 151282785 151669718 P BC012513_AK127552 161 CNV_ID_187 Merged both chr2 153450427 153688865 √ PF BC028741_BC002908 60 CNV_ID_188 Merged WGTP chr2 154188586 154346292 √ F 55 CNV_ID_189 Merged WGTP chr2 156262297 156424935 Variation_0270 V U39196_X75918 115 CNV_ID_190 Merged WGTP chr2 168314876 168465817 AK056582_AF117222 124 CNV_ID_191 Merged 500K EA chr2 174352834 174370707 √ F 5 CNV_ID_192 Merged 500K EA chr2 177140714 177191106 60 CNV_ID_193 Merged 188840\ 188840\ 188840\ WGTP chr2 179234579 179433748 TTN|NM_133378\TTN|NM_003319\TTN|NM_133432\TTN|NM_133437 88 CNV_ID_194 188840 Merged FRZB|NM_001463\NCKAP1|NM_013436\NCKAP1|NM_205842\DNAJC10|NM both chr2 183263206 183660590 MassSpec PE 165,720,605,083 119 CNV_ID_195 _018981 Merged WGTP chr2 184193979 184384414 BC047029_AY327407 85 CNV_ID_196 Merged Variation_1041\ 500K EA chr2 185036251 185196292 V BC047029_AY327407 39 CNV_ID_197 Variation_1040 Merged both chr2 187158286 187406053 √ PF LEREPO4|NM_018471\ITGAV|NM_002210\KIAA1946|NM_177454 AK126036_AF220184 55 CNV_ID_198 Merged WGTP chr2 188205548 188328691 TFPI|NM_006287\TFPI|NM_001032281 J03225_BC001103 2 CNV_ID_199 Merged 500K EA chr2 194745343 194782381 √ F AB004064_AB033091 2 CNV_ID_200 Merged 500K EA chr2 205168233 205174230 √ F BC028210_AF428250 3 CNV_ID_201 Merged WGTP chr2 205365338 205666680 ALS2CR19|NM_057177\ALS2CR19|NM_205863\ALS2CR19|NM_152526 219 CNV_ID_202 Merged 500K EA chr2 209298057 209377458 BC036811_BC038857 14 CNV_ID_203 Merged 500K EA chr2 213012709 213018930 √ F ERBB4|NM_005235 6 CNV_ID_204 135600\ 135600\ 135600\ Merged FN1|NM_054034\FN1|NM_212482\FN1|NM_212475\FN1|NM_212478\FN1|NM both chr2 216116776 216276027 P 135600\ 135600\ 135600\ BX538045_BC032747 128 CNV_ID_205 _212476\FN1|NM_002026\FN1|NM_212474 135600 Merged both chr2 222179557 222323689 √ PF EPHA4|NM_004438 L36645_AY251280 174 CNV_ID_206 Merged 500K EA chr2 228736395 228746258 SKIP|NM_030623 AB051465_AK125359 CNV_ID_207 Merged PDE6D|NM_002601\PTMA|NM_002823\COPS7B|NM_022730\NPPC|NM_024 WGTP chr2 232362330 232831363 √ F 280 CNV_ID_208 409\MGC42174|NM_152383 Merged 500K EA chr2 233037366 233133441 Variation_1607 V ALPPL2|NM_031313\ALPP|NM_001632 DC0526\ DC0527 Intra\ Intra 71 CNV_ID_209 GPR35|NM_005301\CAPN10|NM_023083\CAPN10|NM_023088\CAPN10|NM Merged _023089\ANKMY1|NM_016552\CAPN10|NM_023087\CAPN10|NM_021251\C 605286\ 605286\ 605286\ both chr2 241085111 241308861 Variation_1609 PV APN10|NM_023084\LOC285193|NM_001033575\CAPN10|NM_023085\GPC1| hsa-mir-149/2/241115407/241115496/100.000000 36 CNV_ID_210 NM_002081\ANKMY1|NM_017844\CAPN10|NM_023086\RNPEPL1|NM_0182 605286 26 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged WGTP chr2 242139945 242221648 BOK|NM_032515\FARP2|NM_014808\STK25|NM_006374 16 CNV_ID_211 Variation_0535\ Merged Variation_1610\ FLJ40712|NM_207484\FLJ41327|NM_207485\GAL3ST2|NM_022134\NEU4|N DC0536\ DC0537\ DC0538\ DC0534\ DC0535\ both chr2 242415890 242787722 √ PVF 609186 Inter\ Inter\ Inter\ Inter\ Inter\ Inter 51 CNV_ID_212 Variation_0032\ M_080741 DC0539 Variation_0694 Merged both chr3 46156 773503 Variation_0886 √ PF CHL1|NM_006614 AF002246_AB003592 DC0831 Intra 384 CNV_ID_213 Merged both chr3 1222123 1563919 Variation_0886 √ PVF CNTN6|NM_014461 AB003592_AY090737 183 CNV_ID_214 Merged both chr3 2181272 2470417 P CNTN4|NM_175607 DC0832 Inter 166 CNV_ID_215 Merged Variation_1361\ 500K EA chr3 4062787 4081495 √ F 16 CNV_ID_216 Variation_1611 Merged both chr3 4113369 4395357 √ PF SUMF1|NM_182760\SETMAR|NM_006515 607939 133 CNV_ID_217 Variation_1050\ Merged 500K EA chr3 6181901 6224264 Variation_1051\ √ VF D86967_U92458 8 CNV_ID_218 Variation_1613 Merged 500K EA chr3 7499552 7539303 GRM7|NM_000844\GRM7|NM_181874\GRM7|NM_181875 7 CNV_ID_219 Merged WGTP chr3 12945170 13265554 Variation_0838 V IQSEC1|NM_014869 DC0842 Intra 144 CNV_ID_220 Merged NR2C2|NM_003298\MRPS25|NM_022497\ZFYVE20|NM_022340\FGD5|NM_1 both chr3 14886274 15137707 P 69 CNV_ID_221 52536 Merged 500K EA chr3 16202432 16231043 GALNTL2|NM_054110 3 CNV_ID_222 Merged WGTP chr3 20240591 20515632 QPCR √ EF BC017867_X74864 49 CNV_ID_223 Merged 500K EA chr3 21180674 21351652 BC017867_X74864 23 CNV_ID_224 Merged WGTP chr3 22052897 22231873 Variation_1616 √ F AK026072_BC022332 24 CNV_ID_225 Merged both chr3 24627517 24917930 Variation_1053 PV M26747_M62303 106 CNV_ID_226 Merged both chr3 26021365 26194166 P AK000611_BC040656 33 CNV_ID_227 Merged WGTP chr3 29158899 29670492 √ F RBMS3|NM_001003792\RBMS3|NM_014483\RBMS3|NM_001003793 AK090970_BC030290 325 CNV_ID_228 Merged WGTP chr3 33270111 33446477 FBXL2|NM_012157\UBP1|NM_014517 22 CNV_ID_229 Merged 500K EA chr3 36258534 36290961 AL133109_D86640 9 CNV_ID_230 Merged DLEC1|NM_007337\DLEC1|NM_007338\ITGA9|NM_002207\DLEC1|NM_0073 604050\ 604050\ 604050\ WGTP chr3 37806487 38079228 Variation_1365 √ F 35\CTDSPL|NM_001008392\DLEC1|NM_007336\VILL|NM_015873\DLEC1|NM hsa-mir-26a-1/3/37985898/37985975/100.000000 165 CNV_ID_231 _005106\PLCD1|NM_006225\CTDSPL|NM_005808 604050\ 604050 Merged WGTP chr3 38908752 39071102 √ F SCN11A|NM_014139\WDR48|NM_020839 35 CNV_ID_232 Merged 500K EA chr3 39509276 39530501 MOBP|NM_182934\MOBP|NM_006501\MOBP|NM_182935 3 CNV_ID_233 Merged both chr3 41314156 41748757 P 86 CNV_ID_234 Merged 500K EA chr3 42335110 42378384 QPCR E 49 CNV_ID_235 Merged 500K EA chr3 45991468 46095404 √ F FYCO1|NM_024513\XCR1|NM_001024644\XCR1|NM_005283 28 CNV_ID_236 Merged 500K EA chr3 46394638 46419798 DC0869 Inter 2 CNV_ID_237 Merged ALS2CL|NM_182775\PTHR1|NM_000316\TESSP2|NM_182702\CCDC12|NM_ WGTP chr3 46655456 46947493 Variation_1621 √ VF 144716\MYL3|NM_000258\TSP50|NM_013270\ALS2CL|NM_147129\TESSP5| 607237\ 168468\ 160790 DC0870 Inter 172 CNV_ID_238 NM_199183\TMIE|NM_147196

Merged Variation_1366\ 500K EA chr3 52981095 53014495 V SFMBT1|NM_016329\SFMBT1|NM_001005158\SFMBT1|NM_001005159 14 CNV_ID_240 Variation_1622 Merged WGTP chr3 55465669 55640833 CAST1|NM_015576\WNT5A|NM_003392 230 CNV_ID_241 Merged 500K EA chr3 60650681 60689812 FHIT|NM_002012 40 CNV_ID_242 Merged Variation_1367\ both chr3 60756983 61195849 √ PF FHIT|NM_002012 DC0876 Inter 352 CNV_ID_243 Variation_1623 Merged 500K EA chr3 61544597 61611196 PTPRG|NM_002841 53 CNV_ID_244 Merged 500K EA chr3 64922928 64933281 AF488803_AK127518 2 CNV_ID_245 Variation_1368\ Variation_1369\ Merged 500K EA chr3 65151156 65199576 Variation_1370\ √ F AF488803_AK127518 36 CNV_ID_246 Variation_1625\ Variation_1371 Merged 500K EA chr3 68971420 69018486 √ F FAM19A4|NM_001005527\FAM19A4|NM_182522 27 CNV_ID_247 DC0880\ DC0881\ DC0883\ DC0885\ DC0886\ DC0888\ DC0889\ DC0891\ DC0893\ DC0894\ Intra\ Intra\ Both\ Both\ Both\ Inter\ Inter\ Inter\ Merged Variation_0556\ AB040929_AK094187\ both chr3 75428849 76935064 √ PVF DC0895\ DC0896\ DC0897\ DC0898\ DC0882\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Both\ Both\ 653 CNV_ID_248 Variation_2061 AF226994_AB046788 DC0884\ DC0887\ DC0890\ DC0892\ DC0899\ Both\ Inter\ Inter\ Inter\ Inter DC0900 Merged WGTP chr3 77481544 77639025 √ F ROBO2|NM_002942 104 CNV_ID_249 Merged 500K EA chr3 78536627 78579808 AB046788_BC001969 22 CNV_ID_250 Merged 500K EA chr3 89343185 89353777 EPHA3|NM_182644\EPHA3|NM_005233 5 CNV_ID_251 Merged WGTP chr3 96766457 96876444 AK025762_AY358738 27 CNV_ID_252 Merged WGTP chr3 98699482 98904950 QPCR √ EF 119 CNV_ID_253 Merged WGTP chr3 102096077 102259187 ABI3BP|NM_015429 61 CNV_ID_254 Merged 500K EA chr3 104428032 104433385 BC021279_BC017840 4 CNV_ID_255 Merged WGTP chr3 104738943 104903852 BC021279_BC017840 DC0916 Inter 49 CNV_ID_256 Variation_1630\ Variation_1631\ Variation_1632\ Merged both chr3 105522067 106297806 Variation_1633\ PV BC021279_BC017840 229 CNV_ID_257 Variation_1635\ Variation_1636\ Variation_1634 Merged WGTP chr3 107633520 107818033 U26710_AK058091 31 CNV_ID_258 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged WGTP chr3 111495856 111578020 AK022698_BC067808 14 CNV_ID_259 Merged 500K EA chr3 113587565 113596024 1 CNV_ID_260 Merged 500K EA chr3 117568368 117604638 Variation_1059 √ F LSAMP|NM_002338 22 CNV_ID_261 Merged WGTP chr3 117624820 117790232 LSAMP|NM_002338 98 CNV_ID_262 Merged 500K EA chr3 122747576 122806155 ARGFX|NM_001012659\FBXO40|NM_016298\NM_006596 11 CNV_ID_263 Merged 500K EA chr3 126932312 126935644 DC0933 Both CNV_ID_264 Merged WGTP chr3 127024031 127185454 ROPN1B|NM_001012337\LOC200810|NM_001015050 DC0934\ DC0935\ DC0936\ DC0937\ DC0938 Both\ Both\ Intra\ Intra\ Intra 82 CNV_ID_265 Merged 500K EA chr3 128898840 128916240 MGLL|NM_001003794\MGLL|NM_007283 3 CNV_ID_266 Merged DNAJB8|NM_153330\RPN1|NM_002950\C3orf27|NM_007354\EEFSEC|NM_0 WGTP chr3 129540391 129920515 Variation_1374 √ F 160 CNV_ID_267 21937\GATA2|NM_032638 Merged Variation_1639\ both chr3 131142165 131422680 √ PVF TRH|NM_007117\UNQ6125|NM_001030078 275120 DC0944\ DC0945 Both\ Both 99 CNV_ID_268 Variation_1060 Merged 500K EA chr3 132802569 132855391 CPNE4|NM_130808 28 CNV_ID_269 Merged 500K EA chr3 134503648 134515590 √ F TMEM108|NM_023943 3 CNV_ID_270 Merged ARMC8|NM_213654\ARMC8|NM_014154\CLDN18|NM_016369\ARMC8|NM_0 WGTP chr3 139094487 139416533 √ F 15396\DBR1|NM_016216\DZIP1L|NM_173543\CLDN18|NM_001002026\A4GN 132 CNV_ID_271 T|NM_016161 Merged both chr3 141408462 142007428 Variation_0036 √ PVF TRIM42|NM_152616\CLSTN2|NM_022131 344 CNV_ID_272 Merged both chr3 143211568 143612534 √ PF XRN1|NM_019001\TFDP2|NM_006286\MGC40579|NM_152776 69 CNV_ID_273 Merged both chr3 144202928 144447071 P CHST2|NM_004267 196 CNV_ID_274 Merged WGTP chr3 144475395 144768677 SLC9A9|NM_173653 274 CNV_ID_275 Merged WGTP chr3 145718900 145874085 Variation_1063 V AF132204_AF116706 50 CNV_ID_276 Merged 500K EA chr3 147098550 147144469 Variation_1064 V AF132204_AF116706 2 CNV_ID_277 Merged WGTP chr3 149598961 149784837 D76435_U87591 31 CNV_ID_278 Merged WGTP chr3 152274323 152440183 P2RY14|NM_014879\GPR171|NM_013308\MED12L|NM_053002 65 CNV_ID_279 Merged both chr3 152957978 153145873 P SUCNR1|NM_033050\AADACL2|NM_207365\AADAC|NM_001086 64 CNV_ID_280 Merged Variation_1376\ 500K EA chr3 153811704 154007851 √ VF 54 CNV_ID_281 Variation_1644 Merged WGTP chr3 155740971 156041425 √ F AY255534_J03779 90 CNV_ID_282 Merged 500K EA chr3 156968004 156973709 √ F C3orf33|NM_173657 CNV_ID_283 Merged WGTP chr3 158572868 158737386 PTX3|NM_002852\VEPH1|NM_024621 68 CNV_ID_284 Merged 500K EA chr3 161833723 161862863 √ F 15 CNV_ID_285 Merged WGTP chr3 162932695 163076472 √ F AK123348_BC027488 80 CNV_ID_286 Merged 500K EA chr3 163666164 163709523 Variation_1648 √ VF AK123348_BC027488 9 CNV_ID_287 Variation_1377\ Merged WGTP chr3 163953751 164225496 Variation_0563\ √ F AK123348_BC027488 24 CNV_ID_288 Variation_1649 Merged 500K EA chr3 164344341 164432687 QPCR E AK123348_BC027488 8 CNV_ID_289 Variation_1378\ Merged WGTP chr3 165085151 165392762 Variation_1650\ QPCR VE AF109183_X63597 31 CNV_ID_290 Variation_0038 Merged 500K EA chr3 166523565 166615499 Variation_1651 √ F AB020655_M16541 21 CNV_ID_291 Merged WGTP chr3 169771716 169985812 U55853_BX640908 98 CNV_ID_292 Merged both chr3 174622697 174928079 √ PF NLGN1|NM_014932 198 CNV_ID_293 Merged WGTP chr3 177275752 177516301 Variation_1654 √ F BC057243_BC048298 66 CNV_ID_294 Merged 500K EA chr3 178177234 178198620 √ F BC057243_BC048298 4 CNV_ID_295 Merged WGTP chr3 182334298 182489344 √ F BC009702_BC013923 68 CNV_ID_296 ACA4/3/187988103/187988240/100.000000, Variation_1656\ Merged KNG1|NM_000893\ADIPOQ|NM_004797\AHSG|NM_001622\RFC4|NM_00291 E3/3/187987789/187987924/100.000000, HBI- both chr3 187819836 188050028 Variation_1381\ √ PF 6\HRG|NM_000412\EIF4A2|NM_001967\FETUB|NM_014375\RFC4|NM_1815 228960\ 142640\ 605441 57 CNV_ID_297 61/3/187987165/187987343/100.000000, Variation_1380 73 snR39B/3/187985286/187985356/100.000000 Merged WGTP chr3 188092436 188266986 ST6GAL1|NM_173217\ST6GAL1|NM_003032\ST6GAL1|NM_173216 42 CNV_ID_298 Merged 500K EA chr3 189069542 189083061 2 CNV_ID_299 Merged Variation_1068\ OSTN|NM_198184\CCDC50|NM_178335\CCDC50|NM_174908\UTS2D|NM_1 AK095107_AY573933\ WGTP chr3 192349713 192761809 √ F 107 CNV_ID_300 Variation_1659 98152 AJ416916_BC022524 Merged 500K EA chr3 193570453 193577446 FGF12|NM_021032\FGF12|NM_004113 3 CNV_ID_301 Merged Variation_0566\ WGTP chr3 194279079 194450436 V HRASLS|NM_020386 78 CNV_ID_302 Variation_1661 605290\ 605290\ 605290\ Merged OPA1|NM_130835\OPA1|NM_130834\ATP13A4|NM_032279\OPA1|NM_1308 WGTP chr3 194716602 194886348 33\OPA1|NM_130831\OPA1|NM_130837\OPA1|NM_130836\OPA1|NM_13083 605290\ 605290\ 605290\ 58 CNV_ID_303 2\OPA1|NM_015560 605290\ 605290 Variation_0042\ FLJ25996|NM_001001699\ZDHHC19|NM_144637\MUC4|NM_018406\MUC20| Variation_1383\ NM_152673\MUC4|NM_138299\MUC4|NM_004532\PCYT1A|NM_005017\MU Merged Variation_0697\ C4|NM_138297\LOC440993|NM_001013714\OSTalpha|NM_152672\TFRC|NM both chr3 196584084 197559903 QPCR √ PVEF DC0963\ DC0965\ DC0961\ DC0962\ DC0964 Inter\ Inter\ Inter\ Both\ Both 208 CNV_ID_304 Variation_2065\ _003234\TM4SF19|NM_138461\TNK2|NM_001010938\PPP1R2|NM_006241\ Variation_0696\ MGC33212|NM_152773\MUC4|NM_138298\TNK2|NM_005781\CENTB2|NM_0 12287 Variation_2064 Merged Variation_0043\ FYTTD1|NM_032288\DLG1|NM_004087\BDH1|NM_203314\BDH1|NM_20331 both chr3 198343363 198986178 √ PVF DC0966 Both 274 CNV_ID_305 Variation_0568 5\BDH1|NM_004051\FYTTD1|NM_001011537 Variation_1070\ Merged WGTP chr3 199260725 199450740 Variation_0569\ √ F LOC348840|NM_182631 DC0968\ DC0969 Inter\ Inter 50 CNV_ID_306 Variation_0044 Merged Variation_0273\ 500K EA chr4 19099 56331 √ VF ZNF595|NM_182524 DC1174 Both CNV_ID_307 Variation_0570 Merged PCGF3|NM_006315\ATP5I|NM_007100\CPLX1|NM_006651\MYL5|NM_00247 WGTP chr4 593208 921184 7\MGC4618|NM_032326\FLJ22269|NM_032219\GAK|NM_005255\PDE6B|NM 180072 62 CNV_ID_308 _000283

Merged FAM53A|NM_001013622\LOC92305|NM_138385\SLBP|NM_006527\LETM1|N WGTP chr4 1592784 1782006 134934\ 134934 83 CNV_ID_309 M_012318\FGFR3|NM_022965\TACC3|NM_006342\FGFR3|NM_000142 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

RGS12|NM_198230\LRPAP1|NM_002337\RGS12|NM_198227\FLJ35424|NM_ Merged 173661\ADRA2C|NM_000683\OTOP1|NM_177998\ZNF509|NM_145291\RGS1 DC1184\ DC1185\ DC1186\ DC1187\ DC1190\ both chr4 3431313 4469058 Variation_0346 √ PVF 2|NM_198430\FLJ33718|NM_173660\MGC13159|NM_032927\LYAR|NM_0178 104250 J03853_NM_177998 Both\ Both\ Both\ Both\ Inter\ Inter\ Both\ Both 248 CNV_ID_310 16\RGS12|NM_198229\RGS12|NM_002926\HGFAC|NM_001528\RGS12|NM_ DC1183\ DC1188\ DC1189 198587 Merged 500K EA chr4 6725902 6739063 √ F MAN2B2|NM_015274 1 CNV_ID_311 Merged GRPEL1|NM_025196\TBC1D14|NM_020773\FLJ90575|NM_153376\SORCS2| WGTP chr4 7106220 7387973 √ F 69 CNV_ID_312 NM_020777 Variation_1384\ Variation_1663\ Variation_1385\ Variation_0698\ Variation_2068\ Variation_0934\ Variation_0960\ CPZ|NM_001014448\DUB3|NM_201402_copy_8\DUB3|NM_201402_copy_2\D Variation_2069\ UB3|NM_201402_copy_3\WDR1|NM_005112\GPR78|NM_080819\DUB3|NM_ Merged 201402_copy_7\WDR1|NM_017491\DUB3|NM_201402_copy_5\DUB3|NM_20 DC1191\ DC1192\ DC1194\ DC1195\ DC1197\ both chr4 8640244 9952736 Variation_2070\ QPCR √ PVEF 126453 Intra\ Intra\ Both\ Both\ Inter\ Inter\ Both\ Both 329 CNV_ID_313 1402\SLC2A9|NM_001001290\DUB3|NM_201402_copy_6\CPZ|NM_00101444 DC1198\ DC1193\ DC1196 Variation_0699\ 7\SLC2A9|NM_020041\DRD5|NM_000798\DUB3|NM_201402_copy_4\CPZ|N Variation_0571\ M_003652 Variation_1664\ Variation_0933\ Variation_0932\ Variation_0929\ Variation_0890\ Variation_0923 Merged WGTP chr4 10019968 10222069 Variation_1665 V KIAA1729|NM_053042\MIST|NM_052964 39 CNV_ID_314 Merged 500K EA chr4 11337511 11348511 √ F BC057803_BC018067 1 CNV_ID_315 Merged WGTP chr4 12173444 12335659 BC057803_BC018067 63 CNV_ID_316 Merged 500K EA chr4 12928417 12968570 BC057803_BC018067 16 CNV_ID_317 Merged BST1|NM_004334\C1QTNF7|NM_031911\FBXL5|NM_033535\FBXL5|NM_012 WGTP chr4 15120886 15425789 √ F 87 CNV_ID_318 161 Merged 500K EA chr4 17211513 17264589 LAP3|NM_015907 15 CNV_ID_319 Merged 500K EA chr4 18763789 18863091 √ F BC037322_AF055585 29 CNV_ID_320 Merged KCNIP4|NM_147182\KCNIP4|NM_001035003\KCNIP4|NM_001035004\KCNIP 500K EA chr4 20848734 20857264 3 CNV_ID_321 4|NM_147183 Merged WGTP chr4 21549473 21656828 KCNIP4|NM_147182 AK127999_AY181243 58 CNV_ID_322 Merged both chr4 21687850 21906987 QPCR √ PEF AK127999_AY181243 71 CNV_ID_323 Merged 500K EA chr4 22951435 22990481 BC029362_AF106698 9 CNV_ID_324 Merged 500K EA chr4 23123935 23166081 √ F BC029362_AF106698 24 CNV_ID_325 Merged 500K EA chr4 25178326 25184127 12 CNV_ID_326 Merged 500K EA chr4 25382090 25416475 √ F 28 CNV_ID_327 Merged 500K EA chr4 26132536 26138154 1 CNV_ID_328 Merged 500K EA chr4 27909573 27914267 AK127623_AB006757 4 CNV_ID_329 Merged both chr4 28220227 28515706 √ PF AK127623_AB006757 107 CNV_ID_330 Merged 500K EA chr4 28800351 28817794 AK127623_AB006757 3 CNV_ID_331 Merged 500K EA chr4 28986666 29007386 Variation_0130 V AK127623_AB006757 5 CNV_ID_332 Merged WGTP chr4 29199911 29367346 AK127623_AB006757 31 CNV_ID_333 Merged WGTP chr4 29805053 29963713 AK127623_AB006757 28 CNV_ID_334 Merged WGTP chr4 31291394 31478210 AB006757_AY049733 56 CNV_ID_335 Merged WGTP chr4 32190399 32361018 AB006757_AY049733 27 CNV_ID_336 Merged both chr4 33971807 34297097 √ PF AB006757_AY049733 DC1206 Inter 68 CNV_ID_337 Variation_1074\ Variation_1670\ Variation_1075\ Merged Variation_1386\ both chr4 34459337 34779109 QPCR √ PVEF AB006757_AY049733 44 CNV_ID_338 Variation_1077\ Variation_1076\ Variation_0045\ Variation_0275 Merged WGTP chr4 40375955 40580395 82 CNV_ID_339 Merged 500K EA chr4 42950671 43051416 QPCR √ EF AB013452_AK123347 22 CNV_ID_340 Merged 500K EA chr4 44801372 44874500 √ F AF247786_BC031087 16 CNV_ID_341 Variation_0574\ Merged DC1209\ DC1210\ DC1211\ DC1213\ DC1214\ Inter\ Both\ Intra\ Inter\ Inter\ Intra\ Both\ Both\ both chr4 48890029 49501045 Variation_0575\ QPCR √ PEF FLJ21511|NM_025087 AK090412_BC053897 77 CNV_ID_342 DC1216\ DC1217\ DC1212\ DC1215 Both Variation_2071 Merged WGTP chr4 52501046 52679030 √ F DCUN1D4|NM_015115 AK090412_BC053897 48 CNV_ID_343 Merged both chr4 57894345 58495951 √ PF BC017201_AF307080 437 CNV_ID_344 Merged WGTP chr4 60959924 61146015 BC017201_AF307080 47 CNV_ID_345 Merged WGTP chr4 61623611 61796922 √ F BC017201_AF307080 87 CNV_ID_346 Merged 500K EA chr4 66400764 66474947 √ F BC017721_M95724 11 CNV_ID_347 Merged CHR415SYT|NM_001014372\TMPRSS11A|NM_182606\TMPRSS11F|NM_207 both chr4 68605772 68857679 Variation_2072 MassSpec PE 74 CNV_ID_348 407 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_1393\ Variation_1389\ Variation_1388\ Variation_1082\ Variation_1390\ Variation_1391\ Variation_1392\ DC1231\ DC1235\ DC1249\ DC1227\ DC1228\ Variation_1085\ TMPRSS11E|NM_014058_copy_2\UGT2B28|NM_053039\UGT2B15|NM_0010 DC1232\ DC1233\ DC1234\ DC1236\ DC1237\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Merged Variation_1087\ 76_copy_2\UGT2B15|NM_001076\TMPRSS11E|NM_014058\UGT2B17|NM_0 DC1238\ DC1239\ DC1240\ DC1241\ DC1242\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr4 68998845 70594932 QPCR √ PVEF 01077\UGT2B4|NM_021139\YT521|NM_133370\UGT2B10|NM_001075\YT521 346 CNV_ID_349 Variation_1394\ |NM_001031732\UGT2A3|NM_024743\UGT2B11|NM_001073\UGT2B7|NM_00 DC1243\ DC1244\ DC1245\ DC1246\ DC1248\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Variation_1083\ 1074 DC1250\ DC1251\ DC1252\ DC1253\ DC1226\ Intra\ Intra\ Intra\ Intra Variation_1084\ DC1229\ DC1230\ DC1247 Variation_1086\ Variation_0701\ Variation_2073\ Variation_1674\ Variation_1395\ Variation_1396 Merged 500K EA chr4 71396544 71502233 √ F PROL1|NM_021225\SMR3A|NM_012390\SMR3B|NM_006685 DC1256\ DC1257 Intra\ Intra 5 CNV_ID_350 Merged 500K EA chr4 73716212 73794632 √ F ADAMTS3|NM_014243 26 CNV_ID_351 Merged Variation_1397\ 500K EA chr4 74048053 74135413 √ VF 20 CNV_ID_352 Variation_1675 Merged both chr4 77621775 77812584 √ PF SHRM|NM_020859\FLJ25770|NM_178555 88 CNV_ID_353 Merged 500K EA chr4 87432938 87495944 √ F MAPK10|NM_138980\MAPK10|NM_138982\MAPK10|NM_002753 602897\ 602897\ 602897 9 CNV_ID_354 Merged PTPN13|NM_080685\PTPN13|NM_080683\PTPN13|NM_006264\PTPN13|NM 500K EA chr4 87774470 88046712 QPCR E 78 CNV_ID_355 _080684 Merged 500K EA chr4 89025760 89072503 Variation_1398 √ VF 20 CNV_ID_356 Merged both chr4 89275730 89570298 √ PF PKD2|NM_000297\ABCG2|NM_004827\PPM1K|NM_152542 173910 55 CNV_ID_357 Merged WGTP chr4 92303842 92503292 DC1265 Inter 49 CNV_ID_358 Merged WGTP chr4 97866744 98166270 BC030697_NM_183003 81 CNV_ID_359 Merged both chr4 103019877 103366118 √ PF BANK1|NM_017935 97 CNV_ID_360 Merged LOC133308|NM_178833\DHRS6|NM_020139\UBE2D3|NM_181890\LOC4938 WGTP chr4 104137960 104414925 √ F 56|NM_001008388\UBE2D3|NM_181893\LOC150159|NM_139173\CENPE|NM DC1272\ DC1274\ DC1273 Inter\ Inter\ Inter 62 CNV_ID_361 _001813 Variation_1091\ Merged Variation_1092\ WGTP chr4 104537529 104699999 √ VF 24 CNV_ID_362 Variation_1093\ Variation_0277 Merged 500K EA chr4 109298778 109305695 HADHSC|NM_005327 601609 2 CNV_ID_363 Merged 500K EA chr4 114711846 114719490 QPCR E 4 CNV_ID_364 Merged WGTP chr4 115364724 115532828 √ F AY358647_AK130458 32 CNV_ID_365 Merged both chr4 115699683 115947929 √ PF UGT8|NM_003360 AY358647_AK130458 44 CNV_ID_366 Variation_1096\ Merged 500K EA chr4 116439195 116540304 Variation_1402\ √ VF AB036429_BC030831 20 CNV_ID_367 Variation_1681 Merged WGTP chr4 116621852 116809401 AB036429_BC030831 27 CNV_ID_368 Merged WGTP chr4 117879914 117978482 √ F AB036429_BC030831 15 CNV_ID_369 Merged PRSS12|NM_003619\NDST3|NM_004784\SEC24D|NM_014822\KIAA1627|NM both chr4 118836451 120032345 Variation_1682 √ PVF 606709 BC030831_AY358852 DC1277\ DC1278\ DC1279 Inter\ Inter\ Both 384 CNV_ID_370 _020961 Merged both chr4 124568831 125736952 Variation_0050 PV SPATA5|NM_145207\SPRY1|NM_005841\SPRY1|NM_199327 BC063856_AB033049 488 CNV_ID_371 Merged 500K EA chr4 125995545 126007226 AK127496_AK026709 2 CNV_ID_372 Merged Variation_1686\ both chr4 132219682 133363089 √ PVF BC016358_AB037821 DC1282\ DC1284\ DC1286\ DC1285\ DC1283 Inter\ Both\ Inter\ Inter\ Inter 188 CNV_ID_373 Variation_0577 Merged WGTP chr4 133511465 133655754 BC016358_AB037821 35 CNV_ID_374 Variation_1405\ Merged WGTP chr4 138482863 138654737 Variation_1688\ V AL157470_AB046782 47 CNV_ID_375 Variation_1406 Merged WGTP chr4 138897853 139070702 AB046782_AB040875 102 CNV_ID_376 Merged WGTP chr4 139502133 139670493 SLC7A11|NM_014331 AB040875_AF183961 105 CNV_ID_377 Merged WGTP chr4 142423266 142725556 ZNF330|NM_014487 57 CNV_ID_378 Variation_1105\ Variation_1106\ Variation_1103\ Variation_1104\ Merged GYPE|NM_002102\SMARCA5|NM_003601\GYPA|NM_002099\GAB1|NM_002 DC1289\ DC1290\ DC1291\ DC1293\ DC1292\ both chr4 144705898 145489197 Variation_1107\ QPCR √ PVEF 039\GYPB|NM_002100\GAB1|NM_207123\GYPE|NM_198682\LOC441046|NM 111740\ 111300 L31860_AY009951 Intra\ Intra\ Intra\ Intra\ Intra\ Intra 218 CNV_ID_379 DC1294 Variation_1108\ _001011539 Variation_2074\ Variation_2075\ Variation_2076 Merged 500K EA chr4 153133876 153167343 √ F AF151033_AY008274 32 CNV_ID_380 Merged 500K EA chr4 156964511 156968445 GUCY1A3|NM_000856 CNV_ID_381 Merged both chr4 158509492 158739893 P GRIA2|NM_000826 BC028736_AF260333 85 CNV_ID_382 Variation_1407\ Merged 500K EA chr4 161385730 161462448 Variation_1692\ √ VF AB002311_BC036502 15 CNV_ID_383 Variation_0052 Merged WGTP chr4 161727569 161909769 AB002311_BC036502 30 CNV_ID_384 Variation_1693\ Merged 500K EA chr4 162141027 162312760 Variation_1112\ √ VF AB002311_BC036502 17 CNV_ID_385 Variation_1408 Merged 500K EA chr4 162551407 162593480 √ F AB002311_BC036502 6 CNV_ID_386 Merged WGTP chr4 162735374 162917315 FSTL5|NM_020116 31 CNV_ID_387 Merged WGTP chr4 163092222 163265570 Variation_0053 V FSTL5|NM_020116 25 CNV_ID_388 Merged 500K EA chr4 166006477 166008354 AL713759_AK056221 4 CNV_ID_389 Merged WGTP chr4 166159421 166333955 TRIM60|NM_152620\TRIM61|NM_001012414\FLJ31659|NM_153027 AL713759_AK056221 DC1301\ DC1302 Intra\ Intra 29 CNV_ID_390 Merged WGTP chr4 168266226 168565721 SPOCK3|NM_016950 AY358973_BC007320 35 CNV_ID_391 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_1410\ Merged Variation_1695\ both chr4 169109321 169472158 QPCR √ PVEF ANXA10|NM_007193 AY358973_BC007320 66 CNV_ID_392 Variation_1409\ Variation_1694 Merged WGTP chr4 172641989 172669987 AF481738_BC044793 5 CNV_ID_393 Merged 500K EA chr4 172699064 172742341 √ F AF481738_BC044793 11 CNV_ID_394 Merged BC035212_AK001720\ both chr4 178540618 178780523 P AGA|NM_000027\NEIL3|NM_018248 208400 112 CNV_ID_395 X55330_BC033172 Merged 500K EA chr4 181842862 181847554 X55330_BC033172 1 CNV_ID_396 Merged 500K EA chr4 183006629 183024960 X55330_BC033172 9 CNV_ID_397 Merged WGTP chr4 183933465 184117496 166 CNV_ID_398 Merged 500K EA chr4 185535745 185542857 2 CNV_ID_399 Merged KM-HN- WGTP chr4 186688274 186849845 1|NM_152775\PDLIM3|NM_014476\ANKRD37|NM_181726\FLJ11200|NM_018 57 CNV_ID_400 359 Merged WGTP chr4 187636479 187797491 Variation_0055 √ VF 13 CNV_ID_401 Merged both chr4 189459436 189638677 Variation_1699 √ PF BC015684_BC053997 68 CNV_ID_402 Merged Variation_0702\ WGTP chr4 189753545 189837970 V BC015684_BC053997 22 CNV_ID_403 Variation_0582 Merged WGTP chr4 190398953 190641305 Variation_0056 V BC015684_BC053997 DC1312 Inter 56 CNV_ID_404 Merged both chr4 190658160 191140586 Variation_0057 QPCR √ PEF BC015684_BC053997 DC1313\ DC1314 Inter\ Inter 235 CNV_ID_405

Merged PDCD6|NM_013232\KIAA1909|NM_052909\EXOC3|NM_007277\SDHA|NM_0 WGTP chr5 70263 648955 Variation_0855 √ VF 600857 DC1654\ DC1656\ DC1657\ DC1653\ DC1655 Both\ Both\ Both\ Inter\ Both 185 CNV_ID_406 04168\AHRR|NM_020731\LOC133957|NM_145265\SLC9A3|NM_004174 Variation_0704\ Variation_2077\ Variation_0705\ Variation_2078\ Variation_0706\ Merged BRD9|NM_023924\BRD9|NM_001009877\TPPP|NM_007030\NKD2|NM_0331 both chr5 673163 1214476 Variation_2079\ QPCR √ PVEF 20\ZDHHC11|NM_024786\TRIP13|NM_004237\CEP72|NM_018140\SLC12A7| DC1658\ DC1660\ DC1659\ DC1661 Intra\ Intra\ Intra\ Intra 122 CNV_ID_407 Variation_0279\ NM_006598 Variation_0707\ Variation_2080\ Variation_2081\ Variation_0855 Merged AY249325_AY335938\ WGTP chr5 3629619 3840514 √ F IRX1|NM_024337 95 CNV_ID_408 AY335938_AB095949 Merged WGTP chr5 5033876 5237615 ADAMTS16|NM_139056 AY335938_AB095949 21 CNV_ID_409 Merged WGTP chr5 5500098 5817620 Variation_0968 V AB023164_AK090679 53 CNV_ID_410 Merged 500K EA chr5 7188014 7256093 √ F 8 CNV_ID_411 Merged Variation_1411\ 500K EA chr5 8754920 8843546 √ VF BC054816_U52840 12 CNV_ID_412 Variation_1412 Merged both chr5 9850992 10044066 P NM_019599_U52830 113 CNV_ID_413 Merged WGTP chr5 12087304 12261440 U96136_AK026756 34 CNV_ID_414 Merged WGTP chr5 12839321 13039901 QPCR E U96136_AK026756 DC1668\ DC1669 Inter\ Inter 13 CNV_ID_415 Merged both chr5 13197682 13456575 Variation_1413 √ PVF U96136_AK026756 DC1669 Inter 74 CNV_ID_416 Merged 500K EA chr5 15362984 15386853 AB046801_AB020647 9 CNV_ID_417 Merged 500K EA chr5 15731556 15863987 Variation_0975 √ VF FBXL7|NM_012304 29 CNV_ID_418 Merged both chr5 17417700 17972161 Variation_0061 QPCR √ PVEF AF039656_U59325 DC1671\ DC1673\ DC1674\ DC1672 Intra\ Intra\ Intra\ Intra 225 CNV_ID_419 Merged WGTP chr5 19066044 19245996 Variation_0921 V AF039656_U59325 21 CNV_ID_420 Merged 500K EA chr5 20472731 20494555 Variation_0921 √ VF U59325_AK123308 5 CNV_ID_421 Variation_0583\ Variation_0584\ Variation_0282\ Merged Variation_0709\ WGTP chr5 21184910 21748947 √ VF U59325_AK123308 DC1677\ DC1678 Both\ Both 89 CNV_ID_422 Variation_2083\ Variation_2084\ Variation_2085\ Variation_0911 Merged WGTP chr5 21814498 22199675 Variation_0911 √ F CDH12|NM_004061\PMCHL1|NM_031887 DC1680\ DC1679 Intra\ Both 112 CNV_ID_423 Merged 500K EA chr5 23324344 23340668 Variation_0911 V L33477_AF275816 DC1681 Inter 18 CNV_ID_424 Merged 500K EA chr5 24564081 24613895 CDH10|NM_006727 14 CNV_ID_425 Merged WGTP chr5 26791054 26970598 CDH9|NM_016279 AF039747_AB035302 28 CNV_ID_426 Merged WGTP chr5 31332034 31505885 RNASEN|NM_013235\CDH6|NM_004932 164 CNV_ID_427 Merged both chr5 32047775 32239257 √ PF PDZK3|NM_015022\PDZK3|NM_178140\GOLPH3|NM_022130 45 CNV_ID_428 Merged WGTP chr5 32281118 32774401 QPCR E SUB1|NM_006713\NPR3|NM_000908\MTMR12|NM_019061\ZFR|NM_016107 108962 uc.151 188 CNV_ID_429 Merged 500K EA chr5 33557835 33584771 √ F ADAMTS12|NM_030955 15 CNV_ID_430 Variation_0587\ Merged Variation_0586\ WGTP chr5 34134806 34405626 √ VF NM_001015071 DC1688\ DC1690\ DC1689\ DC1691\ DC1692 Both\ Both\ Both\ Intra\ Intra 19 CNV_ID_431 Variation_2086\ Variation_2087 Merged 500K EA chr5 40909835 41045039 QPCR E FLJ40243|NM_173489\C7|NM_000587 217070 44 CNV_ID_432 Merged DC1701\ DC1707\ DC1702\ DC1703\ DC1704\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ WGTP chr5 49784109 50093939 √ F PARP8|NM_024615 114 CNV_ID_433 DC1705\ DC1706\ DC1708\ DC1709 Inter Merged 500K EA chr5 55016652 55094749 DDX4|NM_024415\FLJ90709|NM_173514\DDX4|NM_019039 25 CNV_ID_434 Merged 500K EA chr5 55688830 55707856 √ F 13 CNV_ID_435 Merged both chr5 61438895 61784669 √ PF IPO11|NM_016338\KIF2|NM_004520\HSA9761|NM_014473 AK127800_AF119867 DC1716 Inter 209 CNV_ID_436 Merged 500K EA chr5 62067121 62138099 AY499149_AF498978 23 CNV_ID_437 Merged WGTP chr5 66393681 66586635 CD180|NM_005582 D83597_M61906 143 CNV_ID_438 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_0064\ Variation_0711\ Variation_2089\ Variation_0955\ SERF1A|NM_021967\SMA5|NM_021036\BIRC1|NM_004536\SMN1|NM_0228 74\PMCHL2|NM_153381\SMN1|NM_000344\BDP1|NM_018429\SMA3|NM_00 Variation_0710\ 6780_copy_2\LOC153561|NM_207331_copy_2\SMN2|NM_017411\SMN2|NM_ Merged Variation_2088\ 022876\SMA4|NM_021652_copy_2\SMN2|NM_022877_copy_2\SERF1B|NM_ WGTP chr5 69109876 70831640 QPCR √ VEF 600354\ 600354 DC1718\ DC1719\ DC1717 Intra\ Both\ Both 412 CNV_ID_439 Variation_0869\ 022978\SERF1B|NM_022978_copy_2\SMN2|NM_022877\LOC153561|NM_20 Variation_0870\ 7331\GTF2H2|NM_001515_copy_3\SMN2|NM_022875_copy_2\SERF1A|NM_ 021967_copy_2\PMCHL2|NM_031888\SMN2|NM_022875\GTF2H2|NM_00151 Variation_0283\ 5_copy_2 Variation_0926\ Variation_0927\ Variation_0902 Merged WGTP chr5 71935078 72108737 DC1721\ DC1720 Inter\ Inter 70 CNV_ID_440 Merged WGTP chr5 74469516 74647470 28 CNV_ID_441 Merged 500K EA chr5 75462619 75510536 √ F SV2C|NM_014979 17 CNV_ID_442 Merged 500K EA chr5 75647353 75678730 SV2C|NM_014979 7 CNV_ID_443 Merged WGTP chr5 81245981 81550493 √ F ATG10|NM_031482 194 CNV_ID_444 Merged WGTP chr5 93790961 94067957 QPCR √ EF ANKRD32|NM_032290\MGC34713|NM_173665 204 CNV_ID_445 Merged both chr5 95257462 95566189 P ELL2|NM_012081 197 CNV_ID_446 Merged 500K EA chr5 97054185 97163903 √ F AK002021_BC067736 40 CNV_ID_447 Merged both chr5 97421264 97643999 √ PF AK002021_BC067736 57 CNV_ID_448 Merged WGTP chr5 98633225 98917493 Variation_0712 V AF006513_AY359108 DC1728\ DC1729 Intra\ Both 84 CNV_ID_449 Merged Variation_2090\ both chr5 99235573 99911270 √ PF UNQ1912|NM_198507 AF006513_AY359108 DC1732\ DC1733\ DC1735\ DC1734 Both\ Intra\ Both\ Intra 213 CNV_ID_450 Variation_0713 Merged both chr5 100535625 100788621 √ PF BC053657_AF119865 32 CNV_ID_451 Variation_1119\ Merged 500K EA chr5 101207948 101233931 Variation_1118\ √ VF BC053657_AF119865 2 CNV_ID_452 Variation_1117 Merged BC041099_AF067801\ WGTP chr5 103511683 103661467 √ F 49 CNV_ID_453 AF067801_U26403 Merged 500K EA chr5 103967573 104010013 √ F AF067801_U26403 22 CNV_ID_454 Merged 500K EA chr5 104226158 104322489 √ F AF067801_U26403 23 CNV_ID_455 Merged Variation_1415\ both chr5 104334472 104660077 √ PF AF067801_U26403 82 CNV_ID_456 Variation_1416 Merged WGTP chr5 104685688 104853617 √ F AF067801_U26403 24 CNV_ID_457 Merged 500K EA chr5 106255008 106286649 AF067801_U26403 13 CNV_ID_458 Merged WGTP chr5 106519625 106579710 √ F AF067801_U26403 38 CNV_ID_459 Merged both chr5 109669759 110180038 P LOC91137|NM_138773 132 CNV_ID_460 Merged 500K EA chr5 114725159 114765482 √ F 23 CNV_ID_461 Merged 500K EA chr5 115543618 115571522 COMMD10|NM_016144 5 CNV_ID_462 Merged 500K EA chr5 115606709 115661373 √ F COMMD10|NM_016144 26 CNV_ID_463 Merged both chr5 117692624 117970146 P AB037789_AK091296 183 CNV_ID_464 Merged 500K EA chr5 118583762 118695647 DMXL1|NM_005509 42 CNV_ID_465 Merged 500K EA chr5 122626041 122685098 30 CNV_ID_466 Merged WGTP chr5 125078762 125315808 AB033107_AK024966 95 CNV_ID_467 Merged both chr5 128623637 128862751 √ PF ADAMTS19|NM_133638 58 CNV_ID_468 Merged WGTP chr5 130098933 130316104 AJ504664_BC007090 71 CNV_ID_469 Merged WGTP chr5 130466896 130619811 √ F HINT1|NM_005340\LOC90624|NM_181705 AJ504664_BC007090 22 CNV_ID_470 Merged SMAD5|NM_001001419\LOC153328|NM_145282\IL9|NM_000590\LECT2|NM_ both chr5 135193500 135502898 √ PF 002302\TGFBI|NM_000358\SMAD5|NM_001001420\FBXL21|NM_012159\SM 601,692,602,082 142 CNV_ID_471 AD5|NM_005903 Merged 500K EA chr5 137833483 137865270 24 CNV_ID_472

Merged WGTP chr5 144153983 144340436 AB037738_AK095695 45 CNV_ID_474 Merged 500K EA chr5 144466435 144475035 √ F AB037738_AK095695 4 CNV_ID_475 Merged PPP2R2B|NM_181678\PPP2R2B|NM_181676\PPP2R2B|NM_181677\PPP2R 604325\ 604325\ 604325\ 500K EA chr5 146410036 146519693 AY351676_BC021666 39 CNV_ID_476 2B|NM_181674 604325 Merged DCTN4|NM_016221\RPS14|NM_005617\RPS14|NM_001025070\SYNPO|NM_ WGTP chr5 149804786 150265935 √ F 007286\MST150|NM_032947\MYOZ3|NM_133371\RPS14|NM_001025071\ZN 250 CNV_ID_477 F300|NM_052860\RBM22|NM_018047\NDST1|NM_001543 Merged WGTP chr5 153062206 153273106 GRIA1|NM_000827 87 CNV_ID_478 Merged both chr5 155313275 155548476 Variation_0594 √ PVF AF161507_BX537948 DC1753 Inter 113 CNV_ID_479

Merged ENTH|NM_014666\ADAM19|NM_033274\SOX30|NM_178424\SOX30|NM_007 WGTP chr5 156930186 157165622 607265 120 CNV_ID_480 017\ICF45|NM_017872\ADAM19|NM_023038\LSM11|NM_173491 Merged both chr5 160471139 160626797 √ PF AB018258_S67368 46 CNV_ID_481 Merged WGTP chr5 165155278 165334527 Variation_0069 √ VF BC011998_AB032953 226 CNV_ID_482 Merged WGTP chr5 171473028 171667877 √ F DC-UbP|NM_152277\FLJ40453|NM_001007542\STK10|NM_005990 74 CNV_ID_483 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged both chr5 171913937 172148018 √ PF DUSP1|NM_004417 100 CNV_ID_484 Merged 500K EA chr5 173726296 173745954 BC002619_D89377 14 CNV_ID_485 Merged both chr5 175279234 175696974 √ PF THOC3|NM_032361\NY-REN-7|NM_173663\FLJ44216|NM_198567 DC1764\ DC1767\ DC1768\ DC1765\ DC1766 Intra\ Intra\ Intra\ Both\ Intra 89 CNV_ID_486 Merged PX19|NM_013237\LMAN2|NM_006816\RAB24|NM_001031677\NSD1|NM_022 WGTP chr5 176550923 176735050 √ F 455\RGS14|NM_006480\RAB24|NM_130781\MXD3|NM_031300\NSD1|NM_17 606681\ 606681 63 CNV_ID_487 2349 Merged both chr5 178593872 178970135 √ PF ADAMTS2|NM_014244\RUFY1|NM_025158\ADAMTS2|NM_021599 604539\ 604539 DC1779\ DC1780\ DC1781 Intra\ Intra\ Intra 167 CNV_ID_488 Merged RASGEF1C|NM_001031799\GFPT2|NM_005110\RASGEF1C|NM_175062\MA WGTP chr5 179467083 179662550 PK9|NM_139070\MAPK9|NM_002752\MAPK9|NM_139068\MAPK9|NM_13906 67 CNV_ID_489 9 Variation_0372\ Merged both chr5 180012576 180214082 Variation_2093\ PV OR2Y1|NM_001001657\MGAT1|NM_002406 DC1784 Inter 77 CNV_ID_490 Variation_2094 Merged 500K EA chr5 180311387 180421549 Variation_2094 V BTNL3|NM_197975\BTNL3|NM_006707\BTNL9|NM_152547 DC1784 Inter 33 CNV_ID_491 Variation_0070\ Variation_0071\ Merged IRF4|NM_002460\EXOC2|NM_018303\DUSP22|NM_020185\HUS1B|NM_148 both chr6 5001 720274 Variation_0284\ QPCR √ PEF 601900 DC1928\ DC1929 Both\ Inter 271 CNV_ID_492 959 Variation_0374\ Variation_1121 Merged 500K EA chr6 896385 953488 16 CNV_ID_493 Merged 500K EA chr6 2561236 2577107 C6orf195|NM_152554 14 CNV_ID_494 Merged 500K EA chr6 2934581 2961056 DKFZp686I15217|NM_207495\NQO2|NM_000904 1 CNV_ID_495 Merged 500K EA chr6 7384069 7448784 23 CNV_ID_496 Variation_1419\ Merged both chr6 10551783 10751118 Variation_1418\ √ PVF GCNT2|NM_145655\GCNT2|NM_145649\GCNT2|NM_001491 600429\ 600429\ 600429 57 CNV_ID_497 Variation_1704 Merged WGTP chr6 11787739 11930337 C6orf105|NM_032744 58 CNV_ID_498 Merged 500K EA chr6 15776846 15833457 12 CNV_ID_499 Merged WGTP chr6 16981250 17020517 X79204_AK095016 20 CNV_ID_500 Variation_0715\ Variation_0717\ Merged Variation_0716\ both chr6 26801198 27203693 √ PF GUSBL1|NM_001033523 DC1949\ DC1947\ DC1948 Inter\ Intra\ Both 45 CNV_ID_501 Variation_2097\ Variation_2095\ Variation_2096

Merged BTNL2|NM_019602\HLA-DQA1|NM_002122\HLA-DRB5|NM_002125\HLA- WGTP chr6 32479731 32813412 Variation_1710 √ F 142857\ 606000 DC1967\ DC1968\ DC1969 Intra\ Intra\ Intra 37 CNV_ID_507 DRA|NM_019111\HLA-DRB1|NM_002124 Merged WGTP chr6 32973767 33072074 Variation_0076 √ VF HLA-DMB|NM_002118\BRD2|NM_005104\HLA-DMA|NM_006120 40 CNV_ID_508 Merged C6orf106|NM_024294\SPDEF|NM_012391\RPS10|NM_001014\PACSIN1|NM_ WGTP chr6 34490470 34822655 110 CNV_ID_509 020804\C6orf106|NM_022758 Merged WGTP chr6 35276094 35398980 ZNF76|NM_003427\SCUBE3|NM_152753\DEF6|NM_022047 70 CNV_ID_510 RP3- Merged 510O8.5|NM_207409\TULP1|NM_003322\SRPK1|NM_003137\FKBP5|NM_00 WGTP chr6 35571719 35914482 Variation_0286 √ VF 602623\ 602280 137 CNV_ID_511 4117\CLPS|NM_001832\LHFPL5|NM_182548\TEAD3|NM_003214\C6orf81|N M_145028 Merged WGTP chr6 38696947 38819063 √ F GLO1|NM_006708\DNAH8|NM_001371 138,750,209,850 39 CNV_ID_512 Merged both chr6 41696767 41807431 √ PF TFEB|NM_007162\MDFI|NM_005586 98 CNV_ID_513 Merged both chr6 44987769 45164736 P SUPT3H|NM_003599\SUPT3H|NM_181356 87 CNV_ID_514 Merged 500K EA chr6 45993620 45995399 CLIC5|NM_016929 2 CNV_ID_515 Merged WGTP chr6 46808141 47036030 √ F PLA2G7|NM_005084\GPR116|NM_015234\MEP1A|NM_005588 147,050,600,807,601,000 DC1973 Inter 68 CNV_ID_516 Merged 500K EA chr6 47798026 47814999 2 CNV_ID_517 Merged WGTP chr6 50627298 50775800 AY122469_AY028376 77 CNV_ID_518 Merged WGTP chr6 51472475 51548810 BC037225_AY074797 65 CNV_ID_519 Merged 500K EA chr6 52730063 52774200 GSTA2|NM_000846\GSTA1|NM_145740 DC1976\ DC1977 Intra\ Intra 15 CNV_ID_520 Merged 500K EA chr6 52900813 52969163 √ F GSTA4|NM_001512 14 CNV_ID_521 Merged both chr6 53947332 54115308 Variation_1421 √ PF C6orf142|NM_138569 91 CNV_ID_522 Merged X74331_CENTp\ WGTP chr6 57292500 57670563 PRIM2A|NM_000947 149 CNV_ID_523 X74331_BC034043 Merged X74331_CENTp\ WGTP chr6 58442668 58587658 Variation_0287 V DC1985\ DC1986\ DC1987 Intra\ Intra\ Intra 93 CNV_ID_524 X74331_BC034043 Merged BC034043_AF242388\ both chr6 63764581 64043848 Variation_0289 PV 103 CNV_ID_525 CENTq_AF242388 Merged 500K EA chr6 66411109 66510269 √ F AY358133_BC014322 23 CNV_ID_526 Merged 500K EA chr6 66961128 67117117 √ F AY358133_BC014322 19 CNV_ID_527 Merged 500K EA chr6 67721287 67745004 AY358133_BC014322 3 CNV_ID_528 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged 500K EA chr6 67821780 67861137 Variation_1128 V AY358133_BC014322 7 CNV_ID_529 Merged both chr6 68213162 68583232 √ PF AY358133_BC014322 58 CNV_ID_530 Merged WGTP chr6 69652213 69655072 BAI3|NM_001704 CNV_ID_531 Merged 500K EA chr6 74624342 74681784 √ F AF410459_BC050587 16 CNV_ID_532 Merged both chr6 75018716 75218942 P AF410459_BC050587 66 CNV_ID_533 Merged 500K EA chr6 75582459 75681971 √ F AF410459_BC050587 53 CNV_ID_534 Merged 500K EA chr6 77474806 77533382 PCR √ EF AF047492_M81590 10 CNV_ID_535 Merged WGTP chr6 78156739 78339761 √ F HTR1B|NM_000863 AF047492_M81590 63 CNV_ID_536 Merged WGTP chr6 78393674 78637549 AY395525_AF064597 49 CNV_ID_537 Variation_1423\ Variation_1714\ Variation_1130\ Merged Variation_1715\ both chr6 78852599 79250187 QPCR √ PVEF AY395525_AF064597 83 CNV_ID_538 Variation_1131\ Variation_1132\ Variation_1424\ Variation_0290 Merged 500K EA chr6 81322214 81360930 √ F U51016_AF130064 25 CNV_ID_539 Merged WGTP chr6 81870395 81891996 U51016_AF130064 CNV_ID_540 Merged 500K EA chr6 82154779 82217840 √ F U51016_AF130064 25 CNV_ID_541 Merged 500K EA chr6 84790018 84853288 √ F C6orf117|NM_138409 13 CNV_ID_542 Merged WGTP chr6 87513222 87701933 √ F BC032643_M91467 16 CNV_ID_543 Merged WGTP chr6 87874602 88049676 GJB7|NM_198568 60 CNV_ID_544 Merged WGTP chr6 88415707 88498192 √ F ORC3L|NM_012381\C6orf166|NM_018064\ORC3L|NM_181837 43 CNV_ID_545 Merged WGTP chr6 89147456 89318637 √ F 98 CNV_ID_546 Merged 500K EA chr6 93127736 93161367 BC017715_L36642 13 CNV_ID_547 Merged Variation_1134\ 500K EA chr6 93634138 93728395 V BC017715_L36642 46 CNV_ID_548 Variation_1716 Merged WGTP chr6 95264814 95451409 BC027940_BX640869 51 CNV_ID_549 Merged WGTP chr6 103255429 103412632 AJ301608_AY499148 25 CNV_ID_550 Variation_0602\ Merged Variation_1717\ WGTP chr6 103834514 104012090 √ VF AJ301608_AY499148 25 CNV_ID_551 Variation_1137\ Variation_1425 Merged HACE1|NM_020771\BVES|NM_147147\POPDC3|NM_022361\LIN28B|NM_00 both chr6 105302783 105806657 √ PF 164 CNV_ID_552 1004317\BVES|NM_007073 Merged WASF1|NM_001024935\WASF1|NM_001024936\CDC40|NM_015891\WASF1 500K EA chr6 110496619 110611373 √ F 40 CNV_ID_553 |NM_003931\WASF1|NM_001024934 Merged both chr6 114671437 115749378 MassSpec PE AF503292_U00803 DC2010 Inter 350 CNV_ID_554 Merged WGTP chr6 115895071 116068349 AF503292_U00803 48 CNV_ID_555 Merged both chr6 117537917 117733968 √ PF VGLL2|NM_153453\ROS1|NM_002944\VGLL2|NM_182645 91 CNV_ID_556 Merged 500K EA chr6 121008976 121071648 BC065827_AK055461 18 CNV_ID_557 Merged WGTP chr6 122765634 122925836 HSF2|NM_004506\SERINC1|NM_020755\PKIB|NM_181794 36 CNV_ID_558 Merged WGTP chr6 128883885 128886524 3 CNV_ID_559 Merged WGTP chr6 129315361 129484648 √ F LAMA2|NM_000426 156225 90 CNV_ID_560 Merged 603550\ 603550\ 603550\ WGTP chr6 133486412 133669057 EYA4|NM_172104\EYA4|NM_172103\EYA4|NM_004100\EYA4|NM_172105 112 CNV_ID_561 603550 Merged WGTP chr6 134665824 134752836 BX537882_AF303134 49 CNV_ID_562 Merged 500K EA chr6 136399747 136408668 PDE7B|NM_018945 15 CNV_ID_563 Merged IL22RA2|NM_181310\IL22RA2|NM_052962\IL22RA2|NM_181309\IFNGR1|NM WGTP chr6 137501221 137615031 107470 12 CNV_ID_564 _000416 Merged WGTP chr6 137914018 137962674 13 CNV_ID_565 Merged 500K EA chr6 143861702 143866797 FUCA2|NM_032020 CNV_ID_566 Merged WGTP chr6 143958314 144121669 PHACTR2|NM_014721 115 CNV_ID_567 Merged WGTP chr6 151380322 151546953 MTHFD1L|NM_015440 DC2027 Inter 78 CNV_ID_568 Merged WGTP chr6 153155406 153326844 VIP|NM_003381\VIP|NM_194435 43 CNV_ID_569 Merged both chr6 154212042 154386563 √ PF BC013117_L25119 36 CNV_ID_570 Merged 500K EA chr6 154802849 154849989 CNKSR3|NM_173515 23 CNV_ID_571 Merged 500K EA chr6 158598614 158619762 6 CNV_ID_572 Merged 500K EA chr6 158649279 158728910 √ F TULP4|NM_001007466\TULP4|NM_020245 11 CNV_ID_573

LPAL2|NM_145727\SLC22A1|NM_153187\LPA|NM_005577_copy_2\IGF2R|N Merged M_000876\PLG|NM_000301\LPAL2|NM_024492\SLC22A1|NM_003057\LPA|N DC2035\ DC2041\ DC2036\ DC2037\ DC2038\ both chr6 160342655 161205076 Variation_0604 √ PVF 173350\ 152200\ 147280 Inter\ Intra\ Intra\ Intra\ Intra\ Intra\ Inter\ Intra 165 CNV_ID_575 M_005577_copy_3\LPA|NM_005577\SLC22A2|NM_003058\SLC22A3|NM_021 DC2039\ DC2040\ DC2042 977\SLC22A2|NM_153191 602544,607572\ Merged 500K EA chr6 161906087 161907120 PARK2|NM_004562\PARK2|NM_013987\PARK2|NM_013988 602544,607572\ 1 CNV_ID_576 602544,607572 602544,607572\ Merged WGTP chr6 162161167 162381661 PARK2|NM_004562\PARK2|NM_013987\PARK2|NM_013988 602544,607572\ 95 CNV_ID_577 602544,607572 602544,607572\ Merged 500K EA chr6 162461349 162478101 PARK2|NM_004562\PARK2|NM_013987\PARK2|NM_013988 602544,607572\ 1 CNV_ID_578 602544,607572 602544,607572\ Merged 500K EA chr6 162706292 162710176 Variation_0371 √ F PARK2|NM_004562\PARK2|NM_013987\PARK2|NM_013988 602544,607572\ CNV_ID_579 602544,607572 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

602544,607572\ Merged PACRG|NM_152410\PARK2|NM_004562\PARK2|NM_013987\PARK2|NM_01 both chr6 162811333 163203672 Variation_0371 PV 602544,607572\ 197 CNV_ID_580 3988 602544,607572 Merged WGTP chr6 163962475 164132314 QKI|NM_006775 AB067798_BC026278 87 CNV_ID_581 Merged WGTP chr6 166112052 166269346 32 CNV_ID_582 Merged LOC401286|NM_001023565\UNC93A|NM_018974\CCR6|NM_031409\CCR6| DC2047\ DC2045\ DC2046\ DC2048\ DC2050\ both chr6 167471615 167995289 Variation_2098 QPCR PVE NM_004367\GPR31|NM_005299\TCP10|NM_004610\LOC441178|NM_001025 Intra\ Both\ Intra\ Intra\ Both\ Inter\ Intra\ Inter 99 CNV_ID_583 489\TTLL2|NM_031949\TCP10L2|NM_001013683 DC2051\ DC2049\ DC2052 Merged MLLT4|NM_005936\DACT2|NM_214462\KIF25|NM_030615\C6orf54|NM_0143 both chr6 168055424 168533940 √ PF DC2052 Inter 72 CNV_ID_584 54\FRMD1|NM_024919\KIF25|NM_005355 Merged WGTP chr6 168701943 168857249 √ F SMOC2|NM_022138 18 CNV_ID_585 Merged 500K EA chr6 169319421 169350071 √ F AF176778_L12350 CNV_ID_586 Merged WGTP chr6 169563923 169651825 √ F 10 CNV_ID_587 Merged PDCD2|NM_002598\PDCD2|NM_144781\PSMB1|NM_002793\KIAA1838|NM_ WGTP chr6 170499383 170927551 √ F 600075 DC2053 Both 86 CNV_ID_588 032448\TBP|NM_003194\DLL1|NM_005618 Merged both chr7 106471 298664 Variation_1720 √ PVF FAM20C|NM_020223 DC2096\ DC2095 Inter\ Both 40 CNV_ID_589 Merged MICAL- WGTP chr7 972336 1463188 Variation_0093 QPCR VE L2|NM_024723\MGC10911|NM_032302\MGC9712|NM_152689\MAFK|NM_00 uc.204 287 CNV_ID_590 2360\MICAL-L2|NM_182924\ZFAND2A|NM_182491 Merged Variation_1721\ both chr7 3059866 3333470 √ PF SDK1|NM_152744 189 CNV_ID_591 Variation_1141 Merged 500K EA chr7 3375589 3403590 QPCR √ EF SDK1|NM_152744 15 CNV_ID_592 Merged 500K EA chr7 4112654 4212478 √ F 21 CNV_ID_593 Merged WGTP chr7 4365856 4519892 Variation_0605 √ F ERVK6|NM_001007236\ERVK6|NM_001007236_copy_2 16 CNV_ID_594 Merged 500K EA chr7 6537823 6750454 √ F C7orf28B|NM_198097\LOC222967|NM_173565_copy_2 DC2119\ DC2121\ DC2123\ DC2120\ DC2122 Both\ Both\ Inter\ Intra\ Inter 56 CNV_ID_595 Variation_1142\ Merged both chr7 6983151 7267141 Variation_1722\ √ PVF C1GALT1|NM_020156 DC2126 Inter 112 CNV_ID_596 Variation_2099 Merged 500K EA chr7 8597194 8657317 AB047362_AF201077 20 CNV_ID_597 Merged both chr7 8846889 9015089 √ PF AB047362_AF201077 54 CNV_ID_598 Merged 500K EA chr7 9578732 9699463 AB047362_AF201077 42 CNV_ID_599 Merged 500K EA chr7 11081247 11125514 Variation_1144 V 16 CNV_ID_600 Merged WGTP chr7 11700479 11882659 AB023177_BC033901 35 CNV_ID_601 Merged 500K EA chr7 12278853 12369775 √ F 39 CNV_ID_602 Merged both chr7 14670117 15073026 P FLJ16237|NM_001004320 AB018261_BC017021 130 CNV_ID_603 Merged 500K EA chr7 15789103 15801129 1 CNV_ID_604 Merged both chr7 16009402 16300630 √ PF SOSTDC1|NM_015464 103 CNV_ID_605 Merged both chr7 16783293 17304719 √ PF AHR|NM_001621 166 CNV_ID_606 Merged HDAC9|NM_178425\HDAC9|NM_058177\HDAC9|NM_178423\HDAC9|NM_05 500K EA chr7 18540954 18574580 Variation_0094 V 18 CNV_ID_607 8176 Merged both chr7 19169386 19394202 √ PF AF517122_BC030104 132 CNV_ID_608 Merged WGTP chr7 22528824 22694150 IL6|NM_000600\TOMM7|NM_019059 147620 HBII-336/7/22669471/22669545/100.000000 71 CNV_ID_609 Merged WGTP chr7 23493296 23653562 STK31|NM_031414\MGC72075|NM_199136\STK31|NM_032944 36 CNV_ID_610 Merged WGTP chr7 27566856 27746109 JAZF1|NM_175061\TAX1BP1|NM_006024 606246 93 CNV_ID_611 Merged both chr7 29421593 29708612 P DC2132\ DC2134\ DC2135\ DC2133 Intra\ Both\ Both\ Both 94 CNV_ID_612 Merged WGTP chr7 35597466 35893678 QPCR E SEPT7|NM_001011553\SEPT7|NM_001788 DC2154\ DC2156\ DC2157\ DC2155 Intra\ Intra\ Intra\ Both 108 CNV_ID_613 Merged both chr7 37371953 37631800 P GPR141|NM_181791 51 CNV_ID_614

Merged CDC2L5|NM_031267\C7orf11|NM_138701\CDC2L5|NM_003718\C7orf10|NM_ 500K EA chr7 39833420 40042823 QPCR E 609188 67 CNV_ID_616 024728 Merged 500K EA chr7 40157270 40270518 QPCR E C7orf10|NM_024728 40 CNV_ID_617 Merged WGTP chr7 43725779 43830031 √ F UBE2D4|NM_015983\WBSCR19|NM_175064 DC2164 Both 19 CNV_ID_618 Merged 500K EA chr7 46646975 46655440 √ F 1 CNV_ID_619 Merged WGTP chr7 53107233 53259225 AK097768_AK127870 17 CNV_ID_620 Merged WGTP chr7 53749523 53910569 AK127870_BC028404 24 CNV_ID_621 Merged 500K EA chr7 57307684 57347793 AK128010_AK128835 DC2215\ DC2216 Intra\ Intra 13 CNV_ID_622 Merged both chr7 57376181 57770231 √ PF AK128010_AK128835 DC2218\ DC2220\ DC2217\ DC2219 Both\ Both\ Both\ Both 78 CNV_ID_623 Variation_1150\ Variation_0375\ DC2226\ DC2222\ DC2223\ DC2224\ DC2225\ Variation_1725\ Merged CENTq_AK128835\ DC2227\ DC2228\ DC2229\ DC2230\ DC2231\ Inter\ Both\ Both\ Both\ Both\ Inter\ Inter\ Intra\ both chr7 60893982 62556415 Variation_1426\ √ PF 226 CNV_ID_624 AK128010_AK128835 DC2232\ DC2233\ DC2234\ DC2235\ DC2236\ Intra\ Inter\ Inter\ Both\ Intra\ Both\ Intra\ Both Variation_2100\ DC2237 Variation_0104\ Variation_0721 DC2265\ DC2264\ DC2266\ DC2268\ DC2270\ Merged Variation_0722\ ZNF92|NM_007139\VKORC1L1|NM_173517\LOC441242|NM_001013464\ZNF Inter\ Inter\ Inter\ Intra\ Both\ Intra\ Both\ Both\ both chr7 63995424 64818001 QPCR √ PVEF DC2272\ DC2263\ DC2267\ DC2269\ DC2271\ 419 CNV_ID_625 Variation_2101 92|NM_152626\FLJ25037|NM_182596 Both\ Intra\ Both DC2262 Merged DC2300\ DC2301\ DC2302\ DC2304\ DC2306\ Intra\ Intra\ Intra\ Intra\ Intra\ Inter\ Intra\ Both\ WGTP chr7 65845580 66303403 √ F FLJ10099|NM_017994\RSAFD1|NM_018264\SBDS|NM_016038 607444 AK023257_BC064693 82 CNV_ID_626 DC2307\ DC2299\ DC2305\ DC2303 Intra Merged WGTP chr7 68857155 69038812 AUTS2|NM_015570 118 CNV_ID_627

LOC441257|NM_001023562\TRIM50A|NM_178125\LOC441257|NM_0010235 62_copy_2\TRIM50C|NM_198853\LOC442578|NM_001013739\NSUN5|NM_01 DC2331\ DC2319\ DC2322\ DC2324\ DC2325\ Merged 8044\WBSCR20C|NM_149379\BAZ1B|NM_032408\FKBP6|NM_003602\POM1 Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr7 71356121 72320549 Variation_2103 √ PVF 21|NM_172020\WBSCR20C|NM_148980\LOC441251|NM_001034844\LOC54 DC2326\ DC2329\ DC2330\ DC2332\ DC2320\ 233 CNV_ID_628 Intra\ Intra\ Intra\ Intra\ Both\ Both 1473|NM_001013748\LOC389517|NM_001032389\LOC442582|NM_00102520 DC2321\ DC2323\ DC2327\ DC2328 2\BAZ1B|NM_023005\WBSCR20C|NM_032158\WBSCR20C|NM_148936\FZD 9|NM_003508\NSUN5|NM_148956 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_1728\ Variation_1153\ Merged Variation_1151\ 500K EA chr7 78446039 78532576 √ F MAGI2|NM_012301 24 CNV_ID_630 Variation_1152\ Variation_1154\ Variation_1155 Merged WGTP chr7 78906115 79072297 AB014605_AF055013 40 CNV_ID_631 Merged WGTP chr7 82945157 83104763 Variation_0105 V 40 CNV_ID_632 Merged WGTP chr7 84797973 84962693 AY358937_BC041407 27 CNV_ID_633 Merged both chr7 87731680 87974020 P 103 CNV_ID_634 Merged 500K EA chr7 88201486 88268110 FLJ32110|NM_181646 7 CNV_ID_635 Merged 500K EA chr7 89331811 89501295 Variation_1729 V STEAP1|NM_012449\STEAP2|NM_152999 AK056672_AK098759 DC2360\ DC2362\ DC2361 Intra\ Intra\ Both 77 CNV_ID_636 Merged ASNS|NM_001673\LOC441268|NM_001013725\ASNS|NM_183356\ASNS|NM WGTP chr7 97120935 97292680 DC2370\ DC2371\ DC2372\ DC2374\ DC2373 Inter\ Inter\ Inter\ Intra\ Both 54 CNV_ID_637 _133436\OCM|NM_006188 ZAN|NM_173058\ZAN|NM_003386\LOC402682|NM_001015072\ACHE|NM_01 Variation_0616\ Merged 5831\TRIP6|NM_003302\ZAN|NM_173059\MUC17|NM_001004430\ZAN|NM_1 WGTP chr7 100000141 100342681 Variation_0617\ √ VF 73057\SLC12A9|NM_020246\ACHE|NM_000665\ARS2|NM_015908\ZAN|NM_ 100740\ 100740 71 CNV_ID_638 Variation_1431 173055\ARS2|NM_182800\TRIM56|NM_030961\EPHB4|NM_004444\ZAN|NM _173056 Merged PRKRIP1|NM_024653\CUTL1|NM_181500\CUTL1|NM_001913\APS|NM_0209 WGTP chr7 101494175 101666167 Variation_0899 √ F DC2394 Both 55 CNV_ID_639 79 Merged SRPK2|NM_182692\SRPK2|NM_182691\RINT- both chr7 104352201 104802443 √ PF 72 CNV_ID_640 1|NM_021930\FLJ20485|NM_019042 Merged 500K EA chr7 105179617 105181392 √ F CNV_ID_641 Merged 500K EA chr7 108189596 108254349 AK090417_AF359563 58 CNV_ID_642 Variation_0619\ Variation_1161\ Merged WGTP chr7 109003931 109201570 Variation_1735\ √ VF AK090417_AF359563 53 CNV_ID_643 Variation_1160\ Variation_1162 Merged WGTP chr7 109357547 109506183 AK090417_AF359563 42 CNV_ID_644 Merged WGTP chr7 110117249 110381800 Variation_0620 V LRRN3|NM_018334\IMMP2L|NM_032549 216 CNV_ID_645 Variation_1432\ Merged both chr7 110394862 110898776 Variation_1737\ √ PVF IMMP2L|NM_032549 277 CNV_ID_646 Variation_1163 Merged WGTP chr7 112086078 112362579 Variation_0108 V FLJ31818|NM_152556\GPR85|NM_018970 AF250237_X78578 DC2407 Intra 99 CNV_ID_647 Merged 500K EA chr7 115112000 115149266 AF054589_BC029891 24 CNV_ID_648 Merged FLJ21986|NM_024913\FAM3C|NM_014888\WNT16|NM_057168\WNT16|NM_ 500K EA chr7 120502410 120587277 44 CNV_ID_649 016087 Merged 500K EA chr7 120653822 120683906 7 CNV_ID_650 Merged 500K EA chr7 122392587 122483286 MassSpec E SLC13A1|NM_022444 35 CNV_ID_651 Merged WGTP chr7 125254760 125488816 √ F AK090675_U92459 48 CNV_ID_652 Merged WGTP chr7 126088740 126271794 GRM8|NM_000845 DC2412 Intra 183 CNV_ID_653 Merged WGTP chr7 130179011 130328113 √ F 95 CNV_ID_654 Merged WGTP chr7 131778945 132001738 √ F PLXNA4B|NM_181775\CHCHD3|NM_017812\FLJ40288|NM_173682 182 CNV_ID_655 Variation_1168\ Merged WGTP chr7 133094440 133281052 Variation_1167\ QPCR √ VEF EXOC4|NM_021807\FLJ32786|NM_144648 123 CNV_ID_656 Variation_1743 Merged 500K EA chr7 133517421 133525343 5 CNV_ID_657 Merged WGTP chr7 138190952 138384594 ZC3HAV1|NM_020119\FLJ12571|NM_024926\ZC3HAV1|NM_024625 66 CNV_ID_658 Merged WGTP chr7 141163595 141382145 Variation_1744 √ VF MGAM|NM_004668 DC2421\ DC2422 Intra\ Intra 160 CNV_ID_659 Variation_1746\ Merged Variation_1748\ TRPV6|NM_018646\PRSS2|NM_002770\OR9A2|NM_001001658\PRSS1|NM_ DC2425\ DC2426\ DC2428\ DC2429\ DC2430\ both chr7 141610138 142240984 √ PF 002769\TRPV5|NM_019841\KEL|NM_000420\EPHB6|NM_004445\C7orf34|N 276000\ 110900 Intra\ Intra\ Inter\ Inter\ Both\ Intra 271 CNV_ID_660 Variation_1747\ M_178829 DC2427 Variation_0623 Variation_1171\ Variation_0293\ Variation_2108\ LOC441294|NM_001008747\OR2A14|NM_001001659\OR2A12|NM_00100413 Variation_2107\ 5\FLJ40722|NM_173678\FLJ43692|NM_001003702\OR2A7|NM_001005328\O Merged Variation_0110\ R2A2|NM_001005480\OR6B1|NM_001005281\OR2A25|NM_001004488\ARH DC2433\ DC2434\ DC2436\ DC2437\ DC2431\ Intra\ Intra\ Both\ Intra\ Both\ Both\ Both\ Intra\ WGTP chr7 142664612 143806286 QPCR √ VEF GEF5|NM_001002861\OR2F1|NM_012369\OR2A5|NM_012365\OR2F2|NM_0 464 CNV_ID_661 Variation_0936\ 01004685\TAS2R41|NM_176883\KIAA0738|NM_014719\OR2A42|NM_001001 DC2432\ DC2438\ DC2439\ DC2435 Intra Variation_0726\ 802_copy_2\OR2A1|NM_001005287\OR2A1|NM_001005287_copy_2\TPK1|N Variation_2110\ M_022445\OR2A42|NM_001001802\ARHGEF5|NM_005435 Variation_0725\ Variation_2109 Merged Variation_0727\ both chr7 148879238 149394063 √ PVF LOC401431|NM_001008745\ATP6V0E2L|NM_145230\ZNF467|NM_207336 DC2445\ DC2446 Intra\ Both 266 CNV_ID_662 Variation_0728 Merged Variation_1437\ 500K EA chr7 149671475 149684632 V 1 CNV_ID_663 Variation_1749 Merged GIMAP1|NM_130759\GIMAP6|NM_001007224\GIMAP6|NM_024711\GIMAP5| WGTP chr7 149689597 149901452 35 CNV_ID_664 NM_018384\GIMAP4|NM_018326\GIMAP2|NM_015660 Merged KCNH2|NM_172057\ABP1|NM_001091\KCNH2|NM_172056\KCNH2|NM_000 WGTP chr7 149976469 150101345 152427\ 152427\ 152427 33 CNV_ID_665 238 Merged 500K EA chr7 152281712 152287772 AF023453_AK124285 3 CNV_ID_666 Merged AF023453_AK124285\ both chr7 152438821 152736427 Variation_1172 √ PVF FLJ42291|NM_207367 46 CNV_ID_667 AK124285_BC035912 Variation_0730\ Merged both chr7 152831155 153249486 Variation_0729\ √ PVF DPP6|NM_130797 AK124285_BC035912 DC2453\ DC2454 Intra\ Intra 97 CNV_ID_668 Variation_2111 Merged 500K EA chr7 154322472 154327193 CNV_ID_669 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged both chr7 155658864 155925343 √ PF AK124321_AF439977 107 CNV_ID_670 Merged hsa-mir-153- WGTP chr7 156849831 157112954 Variation_0112 √ VF PTPRN2|NM_130843\PTPRN2|NM_130842\PTPRN2|NM_002847 98 CNV_ID_671 2/7/156866503/156866590/100.000000 Merged FBXO25|NM_012173\OR4F21|NM_001005504\ZNF596|NM_173539\FBXO25| both chr8 59932 484890 √ PF NM_183421\C8orf42|NM_175075\OR4F29|NM_001005221_copy_4\FBXO25|N DC2498\ DC2499\ DC2500\ DC2497 Inter\ Inter\ Inter\ Inter 43 CNV_ID_672 M_183420 Variation_1175\ Variation_1178\ Variation_1177\ Variation_1752\ Merged both chr8 2105020 2411266 Variation_1176\ √ PVF X69089_AF333704 DC2501\ DC2502 Intra\ Intra 31 CNV_ID_673 Variation_0294\ Variation_0731\ Variation_2113 Variation_0732 Merged 500K EA chr8 2684771 2697799 X69089_AF333704 1 CNV_ID_674 Merged 500K EA chr8 3551652 3554023 CSMD1|NM_033225 2 CNV_ID_675 Variation_0969\ Variation_1754\ Variation_1753\ Variation_1439\ Variation_1755\ Variation_1756\ Variation_1179\ Variation_1757\ Merged both chr8 3586932 5942813 Variation_1180\ QPCR √ PVEF CSMD1|NM_033225 AF333704_BC030702 469 CNV_ID_676 Variation_1758\ Variation_1759\ Variation_1760\ Variation_1440\ Variation_1761\ Variation_1762\ Variation_0115\ Variation_0295 Merged Variation_1181\ 500K EA chr8 6023403 6069687 √ VF AF333704_BC030702 14 CNV_ID_677 Variation_1763 Merged Variation_1441\ 500K EA chr8 6092385 6147262 V AF333704_BC030702 9 CNV_ID_678 Variation_1764 Merged 500K EA chr8 6160762 6236366 √ F AF333704_BC030702 21 CNV_ID_679 Variation_1765\ Variation_1182\ Variation_0629\ Variation_0835\ Variation_0630\ Variation_1442\ Variation_0736\ Variation_2119\ Variation_0631\ Variation_0338\ SPAG11|NM_058203_copy_2\DEFA6|NM_001926\DEFB4|NM_004942\DEFB1 Variation_1766\ 04A|NM_080389\LOC349196|NM_001025473_copy_4\DEFB106A|NM_152251 Variation_0940\ \DEFA3|NM_005217\DEFB1|NM_005218\SPAG11|NM_058207\LOC349196|N Variation_0733\ M_001025473_copy_2\SPAG11|NM_058201_copy_2\DEFB106A|NM_152251_ Merged copy_2\DEFA1|NM_004084_copy_2\DEFB103A|NM_018661_copy_2\DEFB10 DC2503\ DC2504\ DC2505\ DC2507\ DC2506\ both chr8 6719130 8344153 Variation_0734\ √ PVF Intra\ Intra\ Both\ Both\ Both\ Both 344 CNV_ID_680 3A|NM_018661\DEFB105A|NM_152250\DEFA1|NM_004084\SPAG11|NM_05 DC2508 Variation_2115\ 8201\DEFB105A|NM_152250_copy_2\DEFA5|NM_021010\LOC349196|NM_00 Variation_0735\ 1025473\SPAG11|NM_058200\SPAG11|NM_058202\DEFB104A|NM_080389_ Variation_0296\ copy_2\LOC349196|NM_001025473_copy_3\SPAG11|NM_058203\DEFA4|NM _001925\SPAG11|NM_058206\SPAG11|NM_016512 Variation_0906\ Variation_0908\ Variation_0907\ Variation_2114\ Variation_0737\ Variation_2117\ Variation_0738\ Variation_2118\ Variation_0739\ Variation_2116 Merged 500K EA chr8 8375229 8448555 47 CNV_ID_681 Merged 500K EA chr8 8745049 8785304 MFHAS1|NM_004225 605352 23 CNV_ID_682 Merged 500K EA chr8 9091324 9108239 Variation_1443 V 5 CNV_ID_683 Variation_1183\ Variation_1768\ Variation_1444\ Variation_1767\ Merged DEFB134|NM_001033019\DEFB136|NM_001033017\DUB3|NM_201402_copy DC2510\ DC2514\ DC2512\ DC2513\ DC2515\ both chr8 11778967 12646342 Variation_1445\ QPCR √ PEF _9\DEFB137|NM_001033018\LONRF1|NM_152271\FAM86B1|NM_032916_co Both\ Both\ Both\ Both\ Both\ Both 207 CNV_ID_684 DC2511 Variation_0297\ py_2\FAM86B1|NM_032916 Variation_0740\ Variation_2102\ Variation_2121 Merged 500K EA chr8 12883370 12926648 KIAA1456|NM_020844\FLJ36980|NM_182598 7 CNV_ID_685 Variation_1769\ Variation_1188\ Merged Variation_1186\ both chr8 13581607 13896999 PCR √ PVEF AK058156_AY028700 91 CNV_ID_686 Variation_1185\ Variation_1184\ Variation_1187 Merged 500K EA chr8 14300858 14321648 √ F SGCZ|NM_139167 4 CNV_ID_687 Merged 500K EA chr8 14549778 14559616 AY502063_BC010370 CNV_ID_688 Variation_1447\ Variation_1449\ Variation_1452\ Variation_1446\ Variation_2122\ Merged both chr8 14670571 15809077 Variation_1448\ √ PVF TUSC3|NM_178234\TUSC3|NM_006765 601385\ 601385 AY502063_BC010370 324 CNV_ID_689 Variation_1451\ Variation_1453\ Variation_1772\ Variation_1771\ Variation_1450 Variation_1774\ Variation_1454\ Merged Variation_1455\ both chr8 16231929 17010633 QPCR √ PEF FGF20|NM_019851\EFHA2|NM_181723 D90187_AB044277 DC2516 Inter 250 CNV_ID_690 Variation_1773\ Variation_1189\ Variation_0116 Merged MTUS1|NM_001001927\MTUS1|NM_001001924\SLC7A2|NM_001008539\PD both chr8 17335551 17685810 Variation_0970 √ PVF GFRL|NM_006207\MTUS1|NM_001001925\MTUS1|NM_001001931\SLC7A2| 604584 131 CNV_ID_691 NM_003046\MTUS1|NM_020749 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged 500K EA chr8 18893788 18924134 √ F PSD3|NM_015310 22 CNV_ID_692 Merged 500K EA chr8 20030851 20073883 Variation_1775 V SLC18A1|NM_003053 7 CNV_ID_693 Merged WGTP chr8 20273229 20559087 AF123659_U97145 186 CNV_ID_694

Variation_1191\ Variation_1456\ Merged Variation_1776\ 500K EA chr8 25026436 25049622 √ F 4 CNV_ID_696 Variation_1192\ Variation_1193\ Variation_1457 Variation_1194\ Merged CDCA2|NM_152562\KCTD9|NM_017634\GNRH1|NM_000825\DOCK5|NM_02 WGTP chr8 25324942 25478051 Variation_1777\ V 152760 70 CNV_ID_697 4940 Variation_1458 Merged 500K EA chr8 25737239 25763131 25 CNV_ID_698 Variation_1199\ Variation_1200\ Variation_1461\ Variation_1465\ Variation_1464\ Merged both chr8 39293436 39716796 Variation_1779\ PCR √ PEF ADAM18|NM_014237 20 CNV_ID_699 Variation_1462\ Variation_1463\ Variation_1197\ Variation_1198\ Variation_1460 Merged 500K EA chr8 47534345 47684445 Variation_0860 √ VF AF015251_D63480 DC2529\ DC2528\ DC2527 Inter\ Inter\ Both 39 CNV_ID_700 Merged WGTP chr8 48343375 48554996 DC2534\ DC2535 Inter\ Inter 10 CNV_ID_701 Merged MCM4|NM_005914\MCM4|NM_182746\UBE2V2|NM_003350\PRKDC|NM_006 WGTP chr8 48950846 49170567 √ F 600899 AF049140_AK128232 30 CNV_ID_702 904 Merged both chr8 50577786 50819905 √ PF BC017981_AL161971 4 CNV_ID_703 Variation_1201\ Merged both chr8 51035846 51300548 Variation_1781\ QPCR √ PVEF SNTG1|NM_018967 20 CNV_ID_704 Variation_0633 Merged 500K EA chr8 51912593 52045960 √ F 6 CNV_ID_705 Merged both chr8 53823346 54163645 Variation_1202 √ PVF GPR7|NM_005285 46 CNV_ID_706 Merged WGTP chr8 54637142 54900026 √ F ATP6V1H|NM_015941\ATP6V1H|NM_213620\ATP6V1H|NM_213619 50 CNV_ID_707 Merged TCEA1|NM_201437\RGS20|NM_003702\TCEA1|NM_006756\LYPLA1|NM_00 WGTP chr8 54995543 55179518 49 CNV_ID_708 6330\RGS20|NM_170587 Variation_0634\ Merged Variation_0635\ WGTP chr8 58092946 58637003 √ VF AL080200_AB111913 110 CNV_ID_709 Variation_1203\ Variation_1785 Merged 500K EA chr8 59467844 59504885 Variation_1786 V DC2536 Inter 18 CNV_ID_710 Merged 500K EA chr8 61146767 61184397 Variation_1787 √ F AB018351_AY075022 16 CNV_ID_711 Merged 500K EA chr8 63318677 63422736 QPCR √ EF FAM77D|NM_173688 BC015518_AK096949 33 CNV_ID_712 Merged WGTP chr8 79784789 79950902 C8orf70|NM_016010\IL7|NM_000880 BC047698_D50375 49 CNV_ID_713 Merged 500K EA chr8 79962967 79977663 √ F BC047698_D50375 5 CNV_ID_714 Variation_0636\ Variation_0642\ Variation_0643\ Variation_0637\ Merged REXO1L1|NM_172239_copy_3\REXO1L1|NM_172239\REXO1L1|NM_172239 WGTP chr8 86592730 87124169 Variation_0639\ QPCR √ VEF DC2548\ DC2549 Both\ Intra 179 CNV_ID_715 _copy_2 Variation_0915\ Variation_0121\ Variation_0640\ Variation_0914 Merged WGTP chr8 89032945 89202820 MMP16|NM_005941\MMP16|NM_022564 88 CNV_ID_716 Merged 500K EA chr8 90162190 90164239 QPCR E D83646_AY358814 CNV_ID_717 Merged Variation_1205\ 500K EA chr8 90390763 90407394 √ VF D83646_AY358814 2 CNV_ID_718 Variation_1795 Merged both chr8 91069962 91398845 Variation_1796 √ PVF DECR1|NM_001359\CALB1|NM_004929 222745 X06661_AL834364 134 CNV_ID_719 Merged SLC26A7|NM_134266\OTUD6B|NM_016023\TMEM55A|NM_018710\SLC26A7 both chr8 92043675 92342900 P 137 CNV_ID_720 |NM_052832 Merged WGTP chr8 93612869 93782102 Variation_1797 QPCR VE BT009871_AF130048 152 CNV_ID_721 Merged 500K EA chr8 96892887 96916149 AK055162_BC043222 7 CNV_ID_722 Merged VPS13B|NM_181661\VPS13B|NM_152564\VPS13B|NM_015243\VPS13B|NM 607817\ 607817\ 607817\ WGTP chr8 100098024 100265857 Variation_0299 √ F 24 CNV_ID_723 _017890\VPS13B|NM_184042 607817 Merged WGTP chr8 100473327 100907800 √ F VPS13B|NM_152564\VPS13B|NM_017890\VPS13B|NM_184042 607817\ 607817 231 CNV_ID_724 Merged 500K EA chr8 102462222 102471681 CNV_ID_725 Merged 500K EA chr8 102678650 102718857 √ F GRHL2|NM_024915 608576 12 CNV_ID_726 Merged Variation_1802\ both chr8 114644879 115391133 √ PVF AB114604_AF183810 112 CNV_ID_727 Variation_0947 Merged both chr8 116948684 117250765 P AF183810_BC000386 232 CNV_ID_728 Merged 500K EA chr8 117692900 117714868 √ F AF183810_BC000386 9 CNV_ID_729 Merged WGTP chr8 120012490 120344931 Variation_1207 √ VF COLEC10|NM_006438\TNFRSF11B|NM_002546\MAL2|NM_052886 602643 178 CNV_ID_730 Merged 500K EA chr8 121834882 121898100 SNTB1|NM_021021 AF028828_U54804 43 CNV_ID_731 Merged WGTP chr8 129633607 129784954 AF336886_BC026098 70 CNV_ID_732 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged WGTP chr8 133470532 133754071 √ F LRRC6|NM_012472\KCNQ3|NM_004519 602232 99 CNV_ID_733 Merged 500K EA chr8 134236863 134249655 3 CNV_ID_734 Merged 500K EA chr8 135130463 135131756 √ F BC018357_BC012989 CNV_ID_735 Merged 500K EA chr8 135212786 135244049 √ F BC018357_BC012989 20 CNV_ID_736 Variation_1469\ Merged both chr8 137585971 138040412 Variation_1805\ √ PVF BC068536_AK127771 86 CNV_ID_737 Variation_0337 Merged 500K EA chr8 139050457 139114328 QPCR E 7 CNV_ID_738 Merged 500K EA chr8 140327110 140328379 AF406780_AF248241 CNV_ID_739 Merged 500K EA chr8 141036810 141046387 NIBP|NM_031466 1 CNV_ID_740 Merged 500K EA chr8 143460347 143679430 BAI1|NM_001702\TSNARE1|NM_145003 99 CNV_ID_741

VPS28|NM_016208\DGAT1|NM_012079\GPR172A|NM_024531\CYHR1|NM_0 Merged 32687\SLC39A4|NM_017767\FBXL6|NM_024555\FBXL6|NM_012162\ADCK5| WGTP chr8 145494501 145668486 √ F NM_174922\SCRT1|NM_031309_copy_2\NFKBIL2|NM_013432\CPSF1|NM_0 607059\ 607059 DC2570 Inter 77 CNV_ID_743 13291\KIFC2|NM_145754\HSF1|NM_005526\SLC39A4|NM_130849\VPS28|N M_183057 Merged 500K EA chr8 146120191 146264218 ZNF16|NM_001029976\ZNF16|NM_006958\C8orf33|NM_023080 51 CNV_ID_744 Merged C9orf66|NM_152569\FOXD4|NM_207305\DOCK8|NM_203447\CBWD1|NM_0 both chr9 21994 373816 Variation_1807\ √ PVF DC2749 Both 135 CNV_ID_745 18491 Variation_1208\ Variation_1210\ Merged Variation_1808\ both chr9 514413 843033 PCR √ PVEF ANKRD15|NM_153186\DMRT1|NM_021951\ANKRD15|NM_015158 602424 135 CNV_ID_746 Variation_1209\ Variation_1809\ Variation_0126 Merged Variation_1211\ both chr9 1045347 1519128 PV DMRT2|NM_006557\DMRT2|NM_181872 AF284225_AY499150 299 CNV_ID_747 Variation_1810 Merged 500K EA chr9 2955090 2975743 9 CNV_ID_748 Merged 500K EA chr9 3998954 4012297 Variation_1811 V GLIS3|NM_152629 9 CNV_ID_749 Merged 500K EA chr9 4517262 4518816 √ F SLC1A1|NM_004170 133550 CNV_ID_750 Merged RLN1|NM_006911\RLN2|NM_134441\RLN2|NM_005059\C9orf46|NM_018465\ both chr9 5278908 5444512 √ PF DC2751\ DC2752\ DC2753\ DC2754 Intra\ Intra\ Intra\ Intra 22 CNV_ID_751 CD274|NM_014143 Merged both chr9 6566991 6835561 Variation_0649 PV JMJD2C|NM_015061\GLDC|NM_000170 238300 98 CNV_ID_752 Merged both chr9 7165387 7472982 P JMJD2C|NM_015061 AB037901_AL137489 141 CNV_ID_753 Merged 500K EA chr9 7514075 7551271 √ F AB037901_AL137489 18 CNV_ID_754 Merged Variation_1470\ 500K EA chr9 9786608 9804116 √ VF L38929_X51420 3 CNV_ID_755 Variation_1813 Merged 500K EA chr9 9952603 9964221 L38929_X51420 CNV_ID_756 Merged WGTP chr9 10178450 10360398 L38929_X51420 63 CNV_ID_757 Variation_1471\ Merged 500K EA chr9 10502307 10576527 Variation_1814\ √ VF L38929_X51420 31 CNV_ID_758 Variation_1472 Merged 500K EA chr9 10629445 10670025 L38929_X51420 10 CNV_ID_759 Merged 500K EA chr9 11637401 11701989 L38929_X51420 18 CNV_ID_760 Variation_1815\ Merged Variation_1212\ both chr9 11783343 12187607 √ PVF L38929_X51420 65 CNV_ID_761 Variation_1816\ Variation_1213 Merged both chr9 12225048 12774092 P TYRP1|NM_000550\C9orf150|NM_203403 115501 L38929_X51420 213 CNV_ID_762 Merged 500K EA chr9 16053191 16072467 16 CNV_ID_763 Merged WGTP chr9 16631966 16799203 BNC2|NM_017637 uc.252 238 CNV_ID_764 Merged 500K EA chr9 16893850 16908196 5 CNV_ID_765 Merged 500K EA chr9 17801584 17818437 BX538074_BC030262 8 CNV_ID_766 Merged 500K EA chr9 19116476 19151145 MassSpec E ADFP|NM_001122 6 CNV_ID_767 Merged 500K EA chr9 20746547 20753840 KIAA1797|NM_017794 2 CNV_ID_768 Merged 500K EA chr9 21171454 21186515 Variation_1817 V IFNA4|NM_021068 DC2759 Intra CNV_ID_769 Merged 500K EA chr9 21271544 21293689 Variation_1818 √ VF CNV_ID_770 Merged 500K EA chr9 21489624 21516526 hsa-mir-31/9/21502113/21502184/100.000000 16 CNV_ID_771 Merged 500K EA chr9 22618931 22686345 AK096011_BC030692 42 CNV_ID_772 Merged 500K EA chr9 24457996 24518103 Variation_1820 V U12431_BC028316 47 CNV_ID_773 Merged 500K EA chr9 25211244 25374959 QPCR E U12431_BC028316 42 CNV_ID_774 Merged both chr9 28462018 28840774 √ PF LRRN6C|NM_152570 AK056372_AF091236 150 CNV_ID_775 Merged WGTP chr9 29125948 29299828 AK056372_AF091236 75 CNV_ID_776 Variation_1473\ Merged both chr9 29784954 30063518 Variation_1821\ √ PF AK056372_AF091236 44 CNV_ID_777 Variation_1474 Merged both chr9 30199650 30421507 √ PF AK056372_AF091236 26 CNV_ID_778 Merged WGTP chr9 30854032 31028881 AK056372_AF091236 46 CNV_ID_779 Merged 500K EA chr9 32085083 32107175 AF091236_AF261088 11 CNV_ID_780 Merged 500K EA chr9 33794006 33809555 UBE2R2|NM_017811 DC2772 Inter 14 CNV_ID_781 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_1824\ Variation_1475\ Variation_0747\ Variation_2136\ Variation_1825\ Variation_2128\ Variation_0743\ Variation_2132\ Variation_2129\ Variation_0742\ Variation_2131\ Variation_0744\ Variation_2133\ ZNF658B|NM_001032297_copy_2\LOC441425|NM_001012419_copy_2\FLJ45 DC2787\ DC2796\ DC2798\ DC2800\ DC2802\ 202|NM_207507\LOC441425|NM_001012419\ZNF658B|NM_001032297\LOC4 Variation_0750\ 01507|NM_001012278\NM_001013726\C9orf36|NM_015667\C9orf36|NM_015 AL110217_BC032596\ DC2804\ DC2779\ DC2780\ DC2782\ DC2783\ Both\ Intra\ Both\ Both\ Both\ Inter\ Intra\ Both\ Variation_0752\ BC032596_AK124538\ DC2784\ DC2785\ DC2786\ DC2788\ DC2790\ Both\ Intra\ Both\ Both\ Both\ Both\ Both\ Both\ Merged 667_copy_2\MGC21881|NM_203448\FLJ35740|NM_147195\ZNF658|NM_0331 both chr9 38493875 45935928 Variation_2140\ QPCR √ PVEF 60\CNTNAP3|NM_033655\ANKRD20A1|NM_032250_copy_2\LOC389832|NM BC006438_AL136793\ DC2792\ DC2793\ DC2794\ DC2797\ DC2799\ Both\ Both\ Intra\ Both\ Both\ Both\ Both\ Both\ 1475 CNV_ID_782 Variation_0746\ _001013654\ANKRD20A1|NM_032250\LOC441426|NM_001013727\LOC1583 AK054645_BX538190\ DC2801\ DC2803\ DC2805\ DC2806\ DC2807\ Both\ Both\ Both\ Both\ Both\ Both\ Both\ Both\ 18|NM_001024608\LOC401507|NM_001012278_copy_3\LOC401507|NM_001 Variation_2135\ 012278_copy_2\ANKRD20A2|NM_001012421_copy_2\ANKRD20A2|NM_0010 AK094938_AK130933 DC2808\ DC2810\ DC2811\ DC2812\ DC2813\ Both\ Intra\ Both Variation_0754\ 12421 DC2781\ DC2789\ DC2791\ DC2795\ DC2809 Variation_2142\ Variation_0748\ Variation_2137\ Variation_0749\ Variation_2138\ Variation_0753\ Variation_2141\ Variation_0751\ Variation_2139\ Variation_0937\ Variation_0302\ Variation_0301 Variation_1826\ Variation_0303\ Variation_0756\ Variation_0757\ Variation_2145\ Variation_0759\ MGC42630|NM_175923\RP11- BC019880_AF523265\ DC2814\ DC2816\ DC2829\ DC2815\ DC2817\ Inter\ Both\ Both\ Both\ Both\ Both\ Both\ Both\ Merged Variation_2147\ 561O23.3|NM_199135\FOXD4L4|NM_199244\KGFLP1|NM_174950\CBWD3|N AL136793_AK127288\ DC2818\ DC2820\ DC2821\ DC2822\ DC2824\ both chr9 64135929 68383081 √ PF M_201453\ANKRD20A1|NM_032250_copy_3\CBWD5|NM_001024916\PGM5| Both\ Both\ Both\ Both\ Both\ Both\ Both\ Both\ 1116 CNV_ID_783 Variation_2148\ AK094938_AK130933\ DC2825\ DC2826\ DC2827\ DC2828\ DC2830\ NM_021965\FOXD4L3|NM_199358\CBWD3|NM_201453_copy_2\LOC441425| Both\ Both\ Both Variation_2149\ NM_001012419_copy_3\C9orf71|NM_153237\LOC504188|NM_001013404 CENTq_AK130933 DC2832\ DC2819\ DC2823\ DC2831 Variation_2150\ Variation_2151\ Variation_0755\ Variation_2143\ Variation_2146 Merged 500K EA chr9 68520661 68583297 PIP5K1B|NM_003558 41 CNV_ID_784 Merged 500K EA chr9 69247800 69277652 APBA1|NM_001163 13 CNV_ID_785 Merged 500K EA chr9 69330123 69363930 Variation_1827 √ F APBA1|NM_001163 14 CNV_ID_786 Merged 500K EA chr9 71486407 71491754 CNV_ID_787 Merged WGTP chr9 76595419 76903461 √ F C9orf65|NM_138818\RP11-159H20.4|NM_001013735 uc.259 169 CNV_ID_788 Merged 500K EA chr9 76999952 77020098 √ F 8 CNV_ID_789 Merged 500K EA chr9 78658863 78703638 QPCR √ EF uc.260 BC004863_BC059405 23 CNV_ID_790 Merged Variation_0305\ WGTP chr9 80822890 80931674 V AF068197_BC010100 41 CNV_ID_791 Variation_0939 Merged HNRPK|NM_031263\C9orf76|NM_024945\HNRPK|NM_031262\KIF27|NM_017 WGTP chr9 83643578 83833156 Variation_1828 V uc.264\uc.263 DC2840\ DC2842\ DC2841 Intra\ Intra\ Intra hsa-mir-7-1/9/83814216/83814326/100.000000 50 CNV_ID_792 576\HNRPK|NM_002140\C9orf64|NM_032307\GKAP1|NM_025211 Merged WGTP chr9 85353708 85507991 AGTPBP1|NM_015239 14 CNV_ID_793

Merged HCTSL- WGTP chr9 87248281 87654534 Variation_0129 V 105 CNV_ID_794 s|NM_001023564\CTSL|NM_001912\CTSL|NM_145918\DAPK1|NM_004938 Merged both chr9 101717505 101905114 Variation_0306 PCR √ PEF AF416558_BC058038 79 CNV_ID_795 Merged 500K EA chr9 101918912 101963391 Variation_1830 V AF416558_BC058038 9 CNV_ID_796 Merged 500K EA chr9 103893020 103919961 Z46788_BC055081 7 CNV_ID_797 Merged 500K EA chr9 104439357 104463949 Variation_0130 √ F OR13C2|NM_001004481\OR13C9|NM_001001956\OR13C5|NM_001004482 AF092563_BC005935 10 CNV_ID_798 Merged both chr9 106230185 106435633 P AK130032_AK023447 142 CNV_ID_799 Merged WGTP chr9 109264965 109454331 PTPN3|NM_002829 93 CNV_ID_800 Merged SLC31A2|NM_001860\KIAA1958|NM_133465\C9orf80|NM_021218\ZFP37|NM both chr9 112320009 113082505 Variation_0131 √ PF DC2877\ DC2878 Intra\ Intra 298 CNV_ID_801 _003408\TSCOT|NM_033051\SLC31A1|NM_001859 Merged 500K EA chr9 116604215 116620188 ASTN2|NM_198187\ASTN2|NM_198186\ASTN2|NM_014010 14 CNV_ID_802 Merged 500K EA chr9 119368741 119383168 BC021560_AF448860 12 CNV_ID_803 Merged WGTP chr9 120727751 120922549 TRAF1|NM_005658\C5|NM_001735 120900 33 CNV_ID_804 Merged 500K EA chr9 125822418 125845443 13 CNV_ID_805 Merged WGTP chr9 125955511 126116512 Variation_1215 V 57 CNV_ID_806 Merged 500K EA chr9 129679522 129702320 USP20|NM_006676\USP20|NM_001008563 2 CNV_ID_807 Merged ABL1|NM_005157\LAMC3|NM_006059\C9orf58|NM_001002260\NUP214|NM_ WGTP chr9 130767120 131058115 Variation_0954 QPCR VE 005085\P518|NM_198180\ABL1|NM_007313\C9orf58|NM_031426\FIBCD1|NM 189980\ 189980\ 114350 146 CNV_ID_808 _032843 Merged Variation_1833\ POMT1|NM_007171\RAPGEF1|NM_198679\UCK1|NM_031432\RAPGEF1|NM U62B/9/131395426/131395512/100.000000, both chr9 131300676 131508504 PV 607423 65 CNV_ID_809 Variation_0954 _005312 U62A/9/131390605/131390691/100.000000 Merged WGTP chr9 133461155 133485243 √ F ADAMTSL2|NM_014694 DC2890 Inter 15 CNV_ID_810

Merged WGTP chr9 137473621 137617588 Variation_0654 √ VF NOXA1|NM_006647\FLJ20433|NM_017820\ENTPD8|NM_198585 54 CNV_ID_812 Merged Variation_1835\ WGTP chr9 138161400 138429268 √ F CACNA1B|NM_000718 DC2895 Inter 83 CNV_ID_813 Variation_1836 Merged WGTP chr10 50001 214405 √ F ZMYND11|NM_212479\TUBB8|NM_177987\ZMYND11|NM_006624 DC2949 Inter 25 CNV_ID_814 Merged 500K EA chr10 1432709 1453158 ADARB2|NM_018702 13 CNV_ID_815 Merged 500K EA chr10 1842791 1913557 √ F AF034837_BC029138 21 CNV_ID_816 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged both chr10 2650802 3188773 Variation_1477 MassSpec PVE PITRM1|NM_014889\PFKP|NM_002627 AF034837_BC029138 162 CNV_ID_817 Merged 500K EA chr10 3297225 3300298 BC005025_BC004301 CNV_ID_818 Merged 500K EA chr10 4276880 4313493 BC004301_AY423624 13 CNV_ID_819 Merged both chr10 5547024 5844786 √ PF ASB13|NM_024701\CALML3|NM_005185 66 CNV_ID_820 Merged Variation_1478\ 500K EA chr10 6690997 6705355 QPCR √ VEF AK093639_AB046837 5 CNV_ID_821 Variation_1871 Merged 500K EA chr10 7136154 7179524 AK093639_AB046837 14 CNV_ID_822 Merged ITIH5|NM_032817\ITIH5|NM_030569\ITIH5|NM_001001851\SFMBT2|NM_0010 both chr10 7463502 7777745 P 89 CNV_ID_823 29880 Merged 500K EA chr10 13089087 13104413 √ F 7 CNV_ID_824 Merged 500K EA chr10 13718676 13726648 FRMD4A|NM_018027 CNV_ID_825 Merged 500K EA chr10 16741412 16752674 RSU1|NM_012425\RSU1|NM_152724 7 CNV_ID_826 Merged 500K EA chr10 18875331 18946513 NSUN6|NM_182543 CNV_ID_827 Merged both chr10 19734150 20065000 P BC024163_AY358486 94 CNV_ID_828 Merged Variation_1479\ 500K EA chr10 20324355 20366013 √ VF PLXDC2|NM_032812 10 CNV_ID_829 Variation_1873 Variation_1480\ Merged Variation_1874\ both chr10 20726725 20949210 √ PVF AK027529_Y16241 78 CNV_ID_830 Variation_1219\ Variation_1481 Merged 500K EA chr10 27200938 27269999 √ F DC2981\ DC2982\ DC2983\ DC2984 Intra\ Intra\ Intra\ Intra 14 CNV_ID_831 Merged 500K EA chr10 32991417 33000799 C10orf68|NM_024688 CNV_ID_832 Merged DC3030\ DC3031\ DC3032\ DC3034\ DC3028\ WGTP chr10 37325769 37665705 √ F ANKRD30A|NM_052997 AB043703_AF269087 Inter\ Inter\ Both\ Both\ Inter\ Inter\ Both 66 CNV_ID_833 DC3029\ DC3033 Merged 500K EA chr10 37971818 37998918 √ F DC3043 Intra 1 CNV_ID_834 Merged both chr10 38717029 39194941 √ PF LOC399744|NM_001013665 AY026352_BC007394 DC3057\ DC3059\ DC3058 Inter\ Both\ Both 127 CNV_ID_835 Merged DC3060\ DC3063\ DC3064\ DC3065\ DC3062\ both chr10 41753546 42249122 Variation_0763 PV AY026352_BC007394 Both\ Inter\ Intra\ Intra\ Both\ Both 102 CNV_ID_836 DC3061 DC3067\ DC3068\ DC3070\ DC3071\ DC3072\ Merged Variation_0763 Intra\ Intra\ Intra\ Intra\ Intra\ Inter\ Inter\ Inter\ both chr10 42285137 42830197 √ PF BMS1L|NM_014753\MGC16291|NM_032770\ZNF11B|NM_006955 AY026352_BC007394 DC3073\ DC3075\ DC3076\ DC3077\ DC3079\ 139 CNV_ID_837 Variation_2152 Inter\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra DC3080\ DC3066\ DC3069\ DC3074\ DC3078 Variation_1223\ Variation_1879\ Variation_1224\ Variation_1878\ GDF2|NM_016204\MARCH8|NM_001002265\ANUBL1|NM_174890\MARCH8| Variation_1880\ DC3097\ DC3098\ DC3099\ DC3100\ DC3101\ Merged NM_001002266\SYT15|NM_181519\PPYR1|NM_005972\RP11- Both\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Both\ both chr10 45341719 48101925 Variation_0136\ QPCR √ PVEF 142I17.1|NM_015605\GDF10|NM_004962\KIAA0514|NM_014696\RBP3|NM_0 BC008813_BC031882 DC3102\ DC3091\ DC3092\ DC3094\ DC3095\ 1114 CNV_ID_838 Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra Variation_0764\ 02900\SYT15|NM_031912\CTGLF1|NM_133446\ANXA8|NM_001630\FAM21C DC3103\ DC3104\ DC3105\ DC3093\ DC3096 |NM_015262\ZNF488|NM_153034\MARCH8|NM_145021 Variation_2153\ Variation_1483\ Variation_0307\ Variation_0845 Variation_1225\ Merged Variation_2154\ FRMPD2|NM_001017929\RP11- WGTP chr10 48213402 49121538 √ VF DC3106\ DC3107\ DC3108 Intra\ Intra\ Intra 391 CNV_ID_839 Variation_2155\ 142I17.1|NM_015605_copy_2\FRMPD2|NM_001018071\FRMPD2|NM_152428 Variation_0845 Merged PARG|NM_003631\PARG|NM_003631_copy_2\TIMM23|NM_006327\MSMB|N DC3111\ DC3112\ DC3114\ DC3109\ DC3113\ WGTP chr10 50641980 51595172 √ F M_002443\PARG|NM_003631_copy_3\NCOA4|NM_005437\RP11- 601984 Intra\ Intra\ Intra\ Both\ Both\ Intra\ Both 494 CNV_ID_840 56A21.1|NM_001005751\MSMB|NM_138634 DC3115\ DC3110 Merged 500K EA chr10 52665980 52685589 V PRKG1|NM_006258 12 CNV_ID_841 Merged 500K EA chr10 52967781 52992342 V PRKG1|NM_006258 9 CNV_ID_842 Merged 500K EA chr10 54778135 54807367 √ F X15422_AY388963 CNV_ID_843 Variation_1226\ Merged both chr10 55027142 55256936 Variation_1227\ √ PVF PCDH15|NM_033056 605514 X15422_AY388963 55 CNV_ID_844 Variation_1881\ Merged both chr10 56078033 56236143 QPCR √ PVEF PCDH15|NM_033056 605514 AY029205_BC020979 DC3124 Intra 23 CNV_ID_845 Merged WGTP chr10 56503549 56781399 QPCR E AY029205_BC020979 DC3125 Inter 27 CNV_ID_846 Merged 500K EA chr10 56849158 56853483 √ VF AY029205_BC020979 CNV_ID_847 Merged 500K EA chr10 56872041 56988850 V AY029205_BC020979 16 CNV_ID_848 Variation_1484\ Merged both chr10 58160636 58359959 Variation_1882\ PV BC020979_BC065709 12 CNV_ID_849 Variation_1228\ Merged 500K EA chr10 58492250 58618213 PCR √ VEF BC020979_BC065709 7 CNV_ID_850 Merged both chr10 59214388 59489499 PCR PVE BC020979_BC065709 55 CNV_ID_851 Merged both chr10 60388039 60641367 √ PF PHYHIPL|NM_032439 144 CNV_ID_852 Merged 500K EA chr10 60994141 61003145 V CNV_ID_853 Merged both chr10 67987416 68162396 P CTNNA3|NM_013266 74 CNV_ID_854 Merged WGTP chr10 70127725 70301318 Variation_1230 √ F CCAR1|NM_018237\STOX1|NM_152709 189,800,609,397 uc.285 HBII-419/10/70184934/70185001/100.000000 37 CNV_ID_855 Merged 500K EA chr10 70708723 70722894 HK1|NM_033500\HK1|NM_033497\HK1|NM_033498 142600\ 142600\ 142600 3 CNV_ID_856 Merged 500K EA chr10 72907909 72956161 CDH23|NM_052836\CDH23|NM_022124 605516\ 605516 41 CNV_ID_857 Merged WGTP chr10 74105644 74277126 C10orf42|NM_138357 101 CNV_ID_858 Merged both chr10 76904943 77440455 QPCR √ PEF C10orf11|NM_032024 uc.288\uc.287 619 CNV_ID_859 Merged both chr10 78781397 79263477 P DLG5|NM_004747\KCNMA1|NM_001014797\KCNMA1|NM_002247 600150\ 604090\ 600150 265 CNV_ID_860 Merged Variation_0765 SFTPA2|NM_006926\SFTPA1|NM_005411_copy_2\SFTPD|NM_003019\SFTP both chr10 80945468 81810835 √ PF 178630 DC3143\ DC3144\ DC3145\ DC3142\ DC3141 Intra\ Intra\ Intra\ Both\ Both 241 CNV_ID_861 Variation_2159 A1|NM_005411\SFTPA2|NM_006926_copy_2 Merged 500K EA chr10 84034612 84048907 NRG3|NM_001010848 AK123885_BC030098 6 CNV_ID_862 Merged 500K EA chr10 84390694 84427173 √ F NRG3|NM_001010848 AK123885_BC030098 10 CNV_ID_863 Merged 500K EA chr10 84561902 84608631 NRG3|NM_001010848 AK123885_BC030098 14 CNV_ID_864 Merged SNCG|NM_003087\MINPP1|NM_004897\FAM35A|NM_019054\MMRN2|NM_0 DC3152\ DC3153\ DC3154\ DC3156\ DC3157\ both chr10 88505038 89299742 Variation_0404 QPCR √ PVEF 24756\C10orf116|NM_006829\BMPR1A|NM_004329\GLUD1|NM_005271\NM_ 605391\ 601299\ 138130 Both\ Intra\ Intra\ Both\ Intra\ Both 318 CNV_ID_865 001009610 DC3155 Merged WGTP chr10 90825044 91007466 Variation_1488 V CH25H|NM_003956\LIPA|NM_000235 278000 15 CNV_ID_866 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged 500K EA chr10 92891080 92922917 23 CNV_ID_867 Merged WGTP chr10 98779953 98952462 SLIT1|NM_003061 108 CNV_ID_868 Merged 500K EA chr10 99824786 99883943 √ F 52 CNV_ID_869 uc.293\uc.295\uc.296\uc.2 Merged PAX2|NM_003989\PAX2|NM_003987\PAX2|NM_000278\PAX2|NM_003988\W 167409\ 167409\ 167409\ both chr10 102141840 102555726 QPCR √ PEF NT8B|NM_003393\NDUFB8|NM_005004\PAX2|NM_003990\HIF1AN|NM_0179 97\uc.299\uc.300\uc.294\u 426 CNV_ID_870 167409\ 167409 02\SEC31L2|NM_015490\SEC31L2|NM_198138 c.298 Merged both chr10 107519652 107743529 Variation_1886 √ PVF BC045754_AF284756 120 CNV_ID_871 Merged 500K EA chr10 109121712 109123622 AY099453_BC007579 CNV_ID_872 Merged WGTP chr10 110448977 110633486 QPCR E AY099453_BC007579 37 CNV_ID_873 Merged 500K EA chr10 117404858 117461605 ATRNL1|NM_207303 16 CNV_ID_874 Merged WGTP chr10 122625702 122891863 Variation_1234 √ VF FGFR2|NM_022971\BRWD2|NM_018117 606417 AB037772_M87770 157 CNV_ID_875 Merged 500K EA chr10 123426455 123451644 15 CNV_ID_876 Merged Variation_0405\ DMBT1|NM_017579\DMBT1|NM_007329\HTRA1|NM_002775\DMBT1|NM_00 WGTP chr10 124253065 124444805 √ VF 601969\ 601969\ 601969 DC3163\ DC3164 Intra\ Intra 35 CNV_ID_877 Variation_0406 4406 Merged WGTP chr10 125047207 125259149 QPCR √ EF 173 CNV_ID_878 Merged ADAM12|NM_003474\BCCIP|NM_078468\BCCIP|NM_078469\BCCIP|NM_016 WGTP chr10 127443890 127776692 QPCR √ EF 567\ADAM12|NM_021641\DHX32|NM_018180\MMP21|NM_147191\FANK1|N 606938 DC3165 Inter 131 CNV_ID_879 M_145235\UROS|NM_000375 Merged both chr10 128798515 129129012 P DOCK1|NM_001380 206 CNV_ID_880 Merged 500K EA chr10 133485668 133634871 √ F PPP2R2D|NM_001003656\PPP2R2D|NM_018461\BNIP3|NM_004052 18 CNV_ID_881 Merged WGTP chr10 134076220 134277057 √ F INPP5A|NM_005539\PWWP2|NM_138499\C10orf91|NM_173541 68 CNV_ID_882 Merged both chr10 134515692 134683302 P C10orf93|NM_173572\C10orf92|NM_017609 55 CNV_ID_883

Merged 500K EA chr11 5373198 5448609 OR51I2|NM_001004754\OR51I1|NM_001005288\OR51Q1|NM_001004757 17 CNV_ID_891

Merged 500K EA chr11 7376191 7402481 SYT9|NM_175733 15 CNV_ID_893 Merged NRIP3|NM_020645\C11orf16|NM_020643\ST5|NM_005418\C11orf17|NM_020 WGTP chr11 8741389 8966149 642\ST5|NM_139157\TMEM9B|NM_020644\C11orf17|NM_182901_copy_2\AS 153 CNV_ID_894 CL3|NM_020646\ST5|NM_213618 Merged 500K EA chr11 11250242 11269413 GALNTL4|NM_198516 16 CNV_ID_895 Merged 500K EA chr11 16871867 16890706 PLEKHA7|NM_175058 16 CNV_ID_896 Merged Variation_0415 both chr11 18775305 19038644 PCR √ PEF MRGPRX2|NM_054030\MRGPRX1|NM_147199 DC3389 Intra 55 CNV_ID_897 Variation_0416 Merged 500K EA chr11 19439936 19450983 8 CNV_ID_898 Merged Variation_1236\ 500K EA chr11 21112669 21194273 √ VF NELL1|NM_006157 47 CNV_ID_899 Variation_1237 Merged 500K EA chr11 21740206 21805311 √ F AK093338_AB032435 11 CNV_ID_900 Merged Variation_1888\ both chr11 25045288 25322096 √ PVF LUZP2|NM_001009909 AY358386_BC058160 28 CNV_ID_901 Variation_1239 Variation_1241\ Merged AY358386_BC058160\ both chr11 25520766 25799242 Variation_1240\ √ PVF 24 CNV_ID_902 BC058160_AJ300461 Variation_1242 Merged WGTP chr11 28881069 29029074 AK091298_M55514 48 CNV_ID_903 Merged 500K EA chr11 30121848 30136966 Variation_1243 √ VF 7 CNV_ID_904 Merged WGTP chr11 30936338 31020588 FLJ46154|NM_198462 46 CNV_ID_905 Merged both chr11 32671219 33006516 P LOC91614|NM_139160\PRRG4|NM_024081\FLJ21924|NM_024774 119 CNV_ID_906 Merged 500K EA chr11 34177080 34326812 √ F ABTB2|NM_145804 142 CNV_ID_907 Merged 500K EA chr11 34869891 34920304 √ F APIP|NM_015957\PDHX|NM_003477 608769 20 CNV_ID_908 Merged CD44|NM_001001389\CD44|NM_001001392\CD44|NM_001001391\CD44|NM 107269\ 107269\ 107269\ both chr11 34986509 35195154 P 146 CNV_ID_909 _000610\CD44|NM_001001390 107269\ 107269 Merged SLC1A2|NM_004171\DKFZP586H2123|NM_015430\DKFZP586H2123|NM_00 WGTP chr11 35275896 35437098 100 CNV_ID_910 1001991 Merged 500K EA chr11 37079701 37100001 QPCR E BC009561_AK127441 12 CNV_ID_911 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged 500K EA chr11 38401344 38437928 √ F BC009561_AK127441 4 CNV_ID_912 Merged WGTP chr11 40879434 41039419 AB046800_U83857 60 CNV_ID_913 Merged both chr11 41075935 41290487 P AB046800_U83857 86 CNV_ID_914 DC3395\ DC3399\ DC3400\ DC3401\ DC3403\ Merged OR4C3|NM_001004702\FOLH1|NM_001014986\FOLH1|NM_004476\OR4A47| Intra\ Inter\ Both\ Both\ Inter\ Intra\ Intra\ Intra\ both chr11 48260247 49141766 √ PF U10886_BC025672 DC3396\ DC3397\ DC3398\ DC3404\ DC3405\ 157 CNV_ID_915 NM_001005512\OR4S1|NM_001004725 Intra\ Intra\ Both DC3402 Merged both chr11 49168813 49425542 √ PF FOLH1|NM_001014986\FOLH1|NM_004476 M99487_BC067889 DC3405 Intra 81 CNV_ID_916 Merged DC3407\ DC3409\ DC3410\ DC3411\ DC3412\ 500K EA chr11 49538501 49820388 Variation_1889 QPCR √ VEF M99487_BC067889 Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Both 56 CNV_ID_917 DC3406\ DC3408\ DC3413 BC067889_CENTp\ DC3426\ DC3429\ DC3431\ DC3421\ DC3422\ Merged Inter\ Inter\ Inter\ Inter\ Both\ Inter\ Inter\ Inter\ both chr11 50013000 50405768 Variation_0904 √ PF BC067889_AF521869\ DC3424\ DC3425\ DC3427\ DC3428\ DC3430\ 104 CNV_ID_918 Inter\ Both\ Inter M99487_BC067889 DC3423 Variation_1890\ Variation_0419\ OR4S2|NM_001004059\OR5D14|NM_001004735\OR4C16|NM_001004701\O Merged R5D18|NM_001001952\OR4P4|NM_001004124\OR5L2|NM_001004739\OR4C both chr11 54978996 55394688 Variation_2167\ PCR √ PVEF BC001862_X64990 DC3437\ DC3438 Intra\ Both 82 CNV_ID_919 6|NM_001004704\OR4C11|NM_001004700\OR5D13|NM_001001967\OR5L1| Variation_1244\ NM_001004738\OR5D16|NM_001005496\OR4C15|NM_001001920 Variation_0308 Merged Variation_1245\ OR5AS1|NM_001001921\OR5F1|NM_003697\OR5I1|NM_006637\OR10AG1|N 500K EA chr11 55446439 55605732 √ VF AK055955_AK127591 20 CNV_ID_920 Variation_0308 M_001005491 Variation_0768\ Merged GLYATL1|NM_080661\FLJ22794|NM_198847\CANP|NM_198947\FLJ22794|N DC3452\ DC3447\ DC3448\ DC3449\ DC3451\ both chr11 58456668 58765249 Variation_2168\ √ PF Intra\ Intra\ Intra\ Intra\ Intra\ Intra 57 CNV_ID_921 M_022074 DC3450 Variation_0149 Merged DDB1|NM_001923\VPS37C|NM_017966\FLJ32009|NM_152718\PGA5|NM_01 WGTP chr11 60671936 60837233 Variation_0420 QPCR √ VEF 600045 DC3458\ DC3459\ DC3457\ DC3460 Intra\ Intra\ Intra\ Intra 35 CNV_ID_922 4224 Merged 500K EA chr11 61505378 61650609 QPCR E 17 CNV_ID_923 Merged 500K EA chr11 62801568 62883430 6 CNV_ID_924 FIBP|NM_198897\TSGA10IP|NM_152762\FLJ30934|NM_152760\CTSW|NM_0 Merged 01335\DIPA|NM_006848\OVOL1|NM_004561\MUS81|NM_025128\CFL1|NM_ WGTP chr11 65316469 65478939 √ F 82 CNV_ID_925 005507\FOSL1|NM_005438\EFEMP2|NM_016938\FIBP|NM_004214\Bles03|N M_031450\DRAP1|NM_006442 Merged ALDH3B1|NM_000694\CHKA|NM_212469\UNC93B1|NM_030930\TCIRG1|NM both chr11 67229481 67647865 Variation_2169 √ PVF _006019\NDUFS8|NM_002496\TCIRG1|NM_006053\CHKA|NM_001277\ALDH 604592\ 602141\ 604592 DC3461\ DC3462\ DC3463 Both\ Both\ Both 161 CNV_ID_926 3B1|NM_001030010 Merged DEFB108B|NM_001002035\FLJ10661|NM_152563\RNF121|NM_194452\RNF WGTP chr11 71041287 71335224 √ F DC3473\ DC3474\ DC3472\ DC3475 Both\ Both\ Both\ Both 101 CNV_ID_927 121|NM_018320\RNF121|NM_194453\FLJ10661|NM_018172 Merged P4HA3|NM_182904\PGM2L1|NM_173582\POLD3|NM_006591\DKFZP586P01 both chr11 73520257 74235245 P 23|NM_015531\KCNE3|NM_005472\PPME1|NM_016147\MGC12965|NM_198 604433 304 CNV_ID_928 519\CHRDL2|NM_015424 Merged 500K EA chr11 74875928 74878739 GDPD5|NM_030792 1 CNV_ID_929 Merged 500K EA chr11 79645152 79693784 PCR √ EF AF009227_AK095054 13 CNV_ID_930 Merged 500K EA chr11 80076875 80080035 AF009227_AK095054 DC3483 Inter 3 CNV_ID_931 Merged 500K EA chr11 80553027 80556842 AF009227_AK095054 CNV_ID_932 Merged 500K EA chr11 80665959 80695621 √ F AF009227_AK095054 23 CNV_ID_933 Merged both chr11 80996713 81508270 Variation_1492 √ PVF AF009227_AK095054 100 CNV_ID_934 Merged 500K EA chr11 84234326 84271303 Variation_0152 V DLG2|NM_001364 21 CNV_ID_935

Merged 500K EA chr11 85547592 85583161 31 CNV_ID_937 Merged 500K EA chr11 87287865 87304787 AK025757_BC015808 3 CNV_ID_938 Merged WGTP chr11 88083993 88339832 √ F GRM5|NM_000842 DC3488\ DC3489 Intra\ Intra 52 CNV_ID_939 Merged both chr11 89082686 89569836 √ PF TRIM49|NM_020358\NAALAD2|NM_005467 DC3497\ DC3495\ DC3496\ DC3494 Inter\ Both\ Both\ Intra 180 CNV_ID_940 Merged WGTP chr11 90247849 90559703 √ F AF123249_BC016722 DC3498 Inter 48 CNV_ID_941 Merged 500K EA chr11 90605720 90702192 AF123249_BC016722 28 CNV_ID_942 Merged 500K EA chr11 91456251 91464123 AF123249_BC016722 6 CNV_ID_943 Merged 500K EA chr11 92537990 92573785 SLC36A4|NM_152313 DC3500 Inter 5 CNV_ID_944 Merged 500K EA chr11 93315872 93354598 √ F 5 CNV_ID_945 Merged both chr11 96355736 96698006 P AF004715_AB013802 81 CNV_ID_946 Merged 500K EA chr11 97120050 97249540 QPCR E AF004715_AB013802 30 CNV_ID_947 Merged 500K EA chr11 97309468 97384974 AF004715_AB013802 2 CNV_ID_948 Merged 500K EA chr11 98266953 98310378 AF004715_AB013802 4 CNV_ID_949 Merged both chr11 98575697 98717492 √ PF CNTN5|NM_014361\CNTN5|NM_175566 AF004715_AB013802 41 CNV_ID_950 Merged 500K EA chr11 99309814 99358487 √ F CNTN5|NM_014361\CNTN5|NM_175566 15 CNV_ID_951 Merged 500K EA chr11 102541001 102720677 QPCR E 80 CNV_ID_952 Merged 500K EA chr11 104224803 104303755 BC030645_AY358222 22 CNV_ID_953 Merged CASP1|NM_001223\INCA|NM_001007232\CASP1|NM_033292\CASP1|NM_0 500K EA chr11 104401086 104484927 PCR √ EF 33295\CASP1|NM_033294\CASP1|NM_033293\COP1|NM_052889\COP1|NM DC3504\ DC3505\ DC3506 Intra\ Intra\ Intra 12 CNV_ID_954 _001017534 Merged 500K EA chr11 106829486 106849778 √ F CWF19L2|NM_152434 1 CNV_ID_955 Merged WGTP chr11 113877495 114024335 FAM55A|NM_152315\FAM55D|NM_017678 17 CNV_ID_956 Merged 500K EA chr11 120978808 121045852 SORL1|NM_003105 49 CNV_ID_957 Merged 500K EA chr11 122339246 122372360 28 CNV_ID_958 Merged WGTP chr11 122784405 123050005 SCN3B|NM_018400 176 CNV_ID_959 Merged 500K EA chr11 124580498 124605648 20 CNV_ID_960 Merged 500K EA chr11 126701966 126709174 AK097543_BX640634 1 CNV_ID_961 Merged BTBD15|NM_014155\APLP2|NM_001642\ST14|NM_021978\ADAMTS15|NM_ both chr11 129474432 129847927 √ PF 153 CNV_ID_962 139055\ADAMTS8|NM_007037 Merged 500K EA chr11 130484613 130489555 4 CNV_ID_963 Merged WGTP chr11 130938011 131254195 Variation_0160 √ VF C11orf39|NM_207432 262 CNV_ID_964 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged 500K EA chr11 134085801 134147144 √ F 12 CNV_ID_965

Merged DCAL1|NM_172004\CD69|NM_001781\CLEC2D|NM_013269\CLEC2D|NM_00 both chr12 9262862 9814796 QPCR √ PEF DC3670\ DC3672\ DC3671\ DC3673 Intra\ Intra\ Intra\ Intra 257 CNV_ID_969 1004420\CLEC2D|NM_001004419\KLRB1|NM_002258 Variation_1247\ Variation_1498\ TAS2R14|NM_023922\PRB3|NM_006249\PRH2|NM_005042\TAS2R49|NM_1 Variation_1248\ 76889\PRB1|NM_199354\TAS2R46|NM_176887\PRB1|NM_199353\TAS2R13| Merged NM_023920\PRB1|NM_005039\PRH1|NM_006250\PRR4|NM_007244\NM_00 DC3674\ DC3676\ DC3677\ DC3678\ DC3679\ both chr12 10860887 11606188 Variation_1496\ √ PVF Both\ Intra\ Intra\ Intra\ Inter\ Intra\ Both\ Intra 62 CNV_ID_970 1013697\TAS2R44|NM_176885\TAS2R43|NM_176884\TAS2R48|NM_176888\ DC3681\ DC3675\ DC3680 Variation_1497\ T2R55|NM_181429\PRB2|NM_006248\PRB4|NM_002723\TAS2R50|NM_1768 Variation_1894\ 90\TAS2R10|NM_023921 Variation_1495 Merged WGTP chr12 12511921 12674391 √ F CREBL2|NM_001310\DUSP16|NM_030640 99 CNV_ID_971 Merged WGTP chr12 16156359 16337645 116 CNV_ID_972 Merged WGTP chr12 20833482 21009087 Variation_0162 √ VF LST3|NM_001009562\SLCO1B3|NM_019844 5 CNV_ID_973 Variation_1898\ Merged Variation_1251\ WGTP chr12 22032101 22628174 √ VF KIAA0528|NM_014802\CMAS|NM_018686\ST8SIA1|NM_003034 DC3684\ DC3685 Intra\ Intra 171 CNV_ID_974 Variation_1899\ Variation_0163 Merged 500K EA chr12 25125048 25143445 LRMP|NM_006152 3 CNV_ID_975 Merged 500K EA chr12 25540624 25545712 FLJ36004|NM_152590 CNV_ID_976 Merged WGTP chr12 25883598 26052383 RASSF8|NM_007211 65 CNV_ID_977 Variation_1254\ Merged Variation_1253\ 500K EA chr12 27539678 27542418 PCR √ EF 7 CNV_ID_978 Variation_1252\ Variation_1901 Merged WGTP chr12 29002049 29181116 56 CNV_ID_979 Merged WGTP chr12 29914434 30066499 √ F BC042083_U77494 58 CNV_ID_980 Merged DDX11|NM_004399\FAM60A|NM_021238\DDX11|NM_030653\DDX11|NM_03 both chr12 31016734 31382371 √ PF DC3699\ DC3698 Intra\ Both 109 CNV_ID_981 0655 Merged 500K EA chr12 31882773 31963864 √ F 15 CNV_ID_982 Variation_1500\ Variation_1904\ DC3702\ DC3706\ DC3709\ DC3710\ DC3703\ Merged AY198413_AJ312278\ Intra\ Both\ Both\ Intra\ Intra\ Inter\ Both\ Both\ both chr12 33333291 34727104 Variation_1256\ √ PVF ALG10|NM_032834\SYT10|NM_198992 DC3704\ DC3707\ DC3708\ DC3701\ DC3705\ 146 CNV_ID_983 AK027657_BC046366 Intra\ Inter\ Intra Variation_1905\ DC3700 Variation_2170 DC3717\ DC3723\ DC3712\ DC3713\ DC3714\ Merged Variation_1257\ AK027657_BC046366\ Both\ Intra\ Inter\ Intra\ Intra\ Inter\ Inter\ Both\ both chr12 36142962 37321303 √ PF KCR1|NM_001013620 DC3715\ DC3718\ DC3719\ DC3721\ DC3724\ 133 CNV_ID_984 Variation_1906 CENTq_BC046366 Intra\ Intra\ Inter\ Both\ Intra\ Intra DC3711\ DC3716\ DC3720\ DC3722 Merged AK027657_BC046366\ 500K EA chr12 37328102 37332250 1 CNV_ID_985 CENTq_BC046366 Merged 500K EA chr12 38586180 38618120 √ F FLJ40126|NM_173599\SLC2A13|NM_052885 7 CNV_ID_986 Merged 500K EA chr12 40067025 40102269 41 CNV_ID_987 Merged WGTP chr12 44435605 44636158 ARID2|NM_152641\SFRS2IP|NM_004719 37 CNV_ID_988

Merged AY395526_AY358295\ both chr12 57308996 57609312 Variation_1915 PV LRIG3|NM_153377 152 CNV_ID_993 AY358288_AK124203 Merged 500K EA chr12 59797263 59898818 QPCR √ EF AF058056_AL834160 16 CNV_ID_994 Merged 500K EA chr12 60060452 60082655 AF058056_AL834160 7 CNV_ID_995 Merged both chr12 62188068 62538439 √ PF TMEM5|NM_014254\SRGAP1|NM_020762\DPY19L2|NM_173812 DC3738\ DC3740\ DC3742\ DC3739\ DC3741 Intra\ Inter\ Intra\ Inter\ Inter 73 CNV_ID_996 Merged 500K EA chr12 65191672 65266447 AJ133439_AL136810 33 CNV_ID_997 Merged both chr12 70388731 70594440 P RAB21|NM_014999\TBC1D15|NM_022771 61 CNV_ID_998 Merged both chr12 71276974 71537376 P TRHDE|NM_013381 AF126372_BC009111 DC3746 Intra 84 CNV_ID_999 Merged 500K EA chr12 71660953 71703530 AF126372_BC009111 10 CNV_ID_1000 Merged 500K EA chr12 73396068 73500176 19 CNV_ID_1001 Merged both chr12 81603513 81860089 Variation_1265 PV TMTC2|NM_152588 157 CNV_ID_1002 Merged WGTP chr12 90649382 90813144 NM_001920_X61123 104 CNV_ID_1003 Merged 500K EA chr12 92175967 92188663 1 CNV_ID_1004 Merged WGTP chr12 96672954 96848094 BC027605_BC053675 118 CNV_ID_1005 Merged 500K EA chr12 114691670 114713454 BC025258_AL137644 18 CNV_ID_1006 Merged 500K EA chr12 117692414 117757043 BC030252_AB058756 38 CNV_ID_1007 Merged OASL|NM_198213\TCF1|NM_000545\P2RX7|NM_177427\FLJ12448|NM_0228 602566\ 142410,222100\ WGTP chr12 119878565 120047533 DC3769\ DC3770 Intra\ Intra 37 CNV_ID_1008 95\P2RX7|NM_002562\OASL|NM_003733 602566 Merged 500K EA chr12 122635002 122720736 √ F FLJ12975|NM_024809\GTF2H3|NM_001516\EIF2B1|NM_001414 606686 5 CNV_ID_1009 Merged 500K EA chr12 125324021 125362245 Variation_1268 √ VF AB067493_AY070435 8 CNV_ID_1010 Merged WGTP chr12 127597185 127906190 √ F SLC15A4|NM_145648\FLJ31978|NM_144669 BC032019_AL831921 35 CNV_ID_1011 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged FZD10|NM_007197\PIWIL1|NM_004764\KIAA0318|NM_015347\KIAA1944|NM both chr12 128471344 129640456 √ PF 295 CNV_ID_1012 _133448 Variation_1509\ Variation_1272\ Variation_1939\ Variation_1508\ DC3775\ DC3774\ DC3777\ DC3778\ DC3780\ Merged Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr12 130248171 130935124 Variation_1938\ √ PVF SFRS8|NM_004592\SFRS8|NM_152235\LOC338797|NM_001025466 AK126039_BC024041 DC3781\ DC3782\ DC3783\ DC3784\ DC3785\ 83 CNV_ID_1013 Intra\ Intra\ Intra\ Intra Variation_0769\ DC3776\ DC3779 Variation_2172\ Variation_1273\ Variation_1940 Merged ZNF10|NM_015394\ZNF84|NM_003428\ZNF26|NM_019591\ZNF605|NM_1832 both chr12 132095571 132344463 Variation_1941 PV 26 CNV_ID_1014 38\ZNF140|NM_003440 Merged both chr13 17918001 18358616 Variation_1510 √ PVF DC3957\ DC3961\ DC3959\ DC3960\ DC3958 Inter\ Inter\ Inter\ Both\ Inter 114 CNV_ID_1015 Merged both chr13 19870722 20122478 P IFT88|NM_175605\CRYL1|NM_015974\IFT88|NM_006531 51 CNV_ID_1016 Merged 500K EA chr13 20717264 20796168 DC3990\ DC3991\ DC3992\ DC3993\ DC3994 Inter\ Inter\ Both\ Intra\ Inter 50 CNV_ID_1017 Merged 500K EA chr13 23927295 23948923 PARP4|NM_006437 DC4008 Both 1 CNV_ID_1018 Merged WGTP chr13 25898592 26065378 WASF3|NM_006646 34 CNV_ID_1019 Merged 500K EA chr13 30423174 30476563 MGC40178|NM_152325 BC042083_U77494 7 CNV_ID_1020 Merged WGTP chr13 33768946 33934202 √ F BC000149_AF467288 80 CNV_ID_1021 Merged 500K EA chr13 36209331 36273415 √ F 25 CNV_ID_1022 Merged 500K EA chr13 36968044 37011260 4 CNV_ID_1023 Merged 500K EA chr13 38938036 38988742 √ F LHFP|NM_005780 35 CNV_ID_1024 Merged 500K EA chr13 41649707 41674117 DGKH|NM_152910\DGKH|NM_178009 14 CNV_ID_1025 Merged 500K EA chr13 42098764 42130996 Variation_1276 √ F 21 CNV_ID_1026 Merged WGTP chr13 48181984 48370518 Variation_0168 V 71 CNV_ID_1027 Merged 500K EA chr13 53231210 53319335 BC047740_AK097615 53 CNV_ID_1028 Merged 500K EA chr13 53590033 53609237 BC047740_AK097615 9 CNV_ID_1029 Variation_1945\ Variation_1278\ Variation_1946\ Merged FLJ40296|NM_198441_copy_4\FLJ40296|NM_198441\FLJ40296|NM_198441_ both chr13 56523625 56824435 Variation_1513\ √ PVF BC047740_AK097615 77 CNV_ID_1030 copy_2\FLJ40296|NM_198441_copy_5\FLJ40296|NM_198441_copy_3 Variation_1280\ Variation_0169\ Variation_1279 Merged both chr13 62097238 62619249 √ PF AL833830_AL137719 DC4051\ DC4053\ DC4052 Inter\ Inter\ Inter 104 CNV_ID_1031 Merged 500K EA chr13 63201508 63285508 AL833830_AL137719 DC4055\ DC4056\ DC4057 Intra\ Intra\ Intra 23 CNV_ID_1032 Merged both chr13 65062295 65292451 Variation_0312 √ PVF AK098560_AL834258 97 CNV_ID_1033 Merged 500K EA chr13 65903813 66017201 QPCR √ EF PCDH9|NM_020403\PCDH9|NM_203487 78 CNV_ID_1034 Merged 500K EA chr13 66129506 66217983 PCDH9|NM_020403\PCDH9|NM_203487 70 CNV_ID_1035 Merged 500K EA chr13 68253637 68290580 AF169692_AB040923 5 CNV_ID_1036 Merged 500K EA chr13 69634065 69687992 QPCR √ EF AB040923_AF356492 11 CNV_ID_1037 Merged WGTP chr13 71226326 71383406 √ F DACH1|NM_080759\DACH1|NM_004392\DACH1|NM_080760 AF356492_BC025367 190 CNV_ID_1038 Merged 500K EA chr13 72712442 72713960 AF132818_BC019680 CNV_ID_1039 Merged WGTP chr13 74102052 74275589 AK093158_AB011175 74 CNV_ID_1040 Merged WGTP chr13 75219611 75440004 √ F LMO7|NM_005358 AK092698_AF359381 125 CNV_ID_1041 Merged WGTP chr13 76523033 76666465 MYCBP2|NM_015057 37 CNV_ID_1042 Merged WGTP chr13 82035430 82280653 AF039843_BC016673 29 CNV_ID_1043 Merged WGTP chr13 82592802 82779067 Variation_1516 V BC016673_AB067497 33 CNV_ID_1044 Merged both chr13 82956558 83175698 √ PF BC016673_AB067497 51 CNV_ID_1045 Merged 500K EA chr13 84446595 84452592 Variation_0313 √ VF AB067497_AL137517 1 CNV_ID_1046 Merged WGTP chr13 86954602 87112550 AK026427_AB020725 27 CNV_ID_1047 Merged both chr13 88209082 88673975 Variation_0314 √ PVF AB020725_BC039730 89 CNV_ID_1048 Merged WGTP chr13 92972655 93146180 Variation_0173 V GPC6|NM_005708 120 CNV_ID_1049 Merged 500K EA chr13 97712694 97753390 FARP1|NM_005766 20 CNV_ID_1050 Merged 500K EA chr13 101459508 101483261 FGF14|NM_175929 601515 11 CNV_ID_1051 Merged 500K EA chr13 103073528 103079107 √ F U10417_AY138548 7 CNV_ID_1052 Merged 500K EA chr13 103201047 103222979 U10417_AY138548 7 CNV_ID_1053 Merged 500K EA chr13 103783832 103787454 U10417_AY138548 2 CNV_ID_1054 Merged both chr13 104418323 104585016 P U10417_AY138548 60 CNV_ID_1055 Merged both chr13 107090320 107274703 QPCR √ PEF AF144054_BC037491 30 CNV_ID_1056 Merged WGTP chr13 108719614 109007551 Variation_0361 √ VF AB020672_AF073310 90 CNV_ID_1057 Merged both chr13 110460034 110604912 P ARHGEF7|NM_003899\ARHGEF7|NM_145735 14 CNV_ID_1058 Merged WGTP chr13 110872855 111151995 BC029889_NM_005986 107 CNV_ID_1059 Merged WGTP chr13 112424858 112739202 √ F ATP11A|NM_015205\ATP11A|NM_032189\MCF2L|NM_024979 39 CNV_ID_1060

Merged DKFZp451A211|NM_001003399\DCUN1D2|NM_018185\TMCO3|NM_017905\ WGTP chr13 113086430 113259065 QPCR E 37 CNV_ID_1061 ADPRHL1|NM_199162\DCUN1D2|NM_001014283\ADPRHL1|NM_138430 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_0812\ Variation_2256\ Variation_0316\ OR4K13|NM_001004714\OR4K2|NM_001005501\OR4M1|NM_001005500\OR Merged Variation_0376\ 4L1|NM_001004717\OR4Q3|NM_172194\ACTBL1|NM_001004053_copy_2\OR DC4095\ DC4093\ DC4094\ DC4096\ DC4097\ both chr14 18732531 19626027 QPCR √ PEF AY466021_BX640732 Inter\ Inter\ Inter\ Inter\ Inter\ Both\ Both 298 CNV_ID_1062 Variation_2175\ 4K1|NM_001004063\OR4N2|NM_001004723\OR4K14|NM_001004712\LOC44 DC4091\ DC4092 Variation_0853\ 0157|NM_001013701\OR4K5|NM_001005483\OR4K15|NM_001005486 Variation_0854\ Variation_0935

Merged 500K EA chr14 21462543 21466983 2 CNV_ID_1064 Merged 500K EA chr14 22011989 22057862 Variation_0333 V 96 CNV_ID_1065 Merged WGTP chr14 25297720 25474958 √ F uc.358 AL834346_U04840 139 CNV_ID_1066 Merged 500K EA chr14 25833467 25854753 AL834346_U04840 5 CNV_ID_1067 Merged WGTP chr14 27134939 27513082 √ F U04840_BC050072 DC4100\ DC4101 Inter\ Inter 94 CNV_ID_1068 Merged WGTP chr14 31928231 32086193 QPCR √ EF AKAP6|NM_004274 92 CNV_ID_1069 Merged 500K EA chr14 37858356 37874184 BX248017_BC036649 7 CNV_ID_1070 Merged 500K EA chr14 40541848 40562301 √ F BX248273_BC043165 1 CNV_ID_1071 Merged 500K EA chr14 40646835 40769154 PCR √ EF BX248273_BC043165 10 CNV_ID_1072 Merged 500K EA chr14 40836311 40950477 BX248273_BC043165 25 CNV_ID_1073 Merged WGTP chr14 41115623 41329261 LRFN5|NM_152447 BX248273_BC043165 59 CNV_ID_1074 Merged both chr14 41920404 42078579 √ PF BC043165_AL136775 20 CNV_ID_1075 Merged both chr14 43468955 43714231 PCR √ PEF BC043165_AL136775 58 CNV_ID_1076 Merged both chr14 44127583 44383416 P 170 CNV_ID_1077 Merged both chr14 44775832 45052160 √ PF C14orf106|NM_018353 BC065544_BC014310 98 CNV_ID_1078 Merged 500K EA chr14 45120624 45190488 BC065544_BC014310 37 CNV_ID_1079 Merged WGTP chr14 45863402 46018276 BC065544_BC014310 36 CNV_ID_1080 Merged WGTP chr14 47329907 47516073 QPCR E AY369208_L31610 29 CNV_ID_1081 Merged 500K EA chr14 52872802 52890807 QPCR E AB051492_M22490 10 CNV_ID_1082 Merged 500K EA chr14 53759574 53803592 33 CNV_ID_1083 Merged both chr14 59477247 59652794 P C14orf135|NM_022495\FLJ46156|NM_198499 52 CNV_ID_1084 Merged 500K EA chr14 64324218 64341533 SPTB|NM_000347\SPTB|NM_001024858 182870\ 182870 16 CNV_ID_1085 Merged 500K EA chr14 71872489 71889437 √ F RGS6|NM_004296 10 CNV_ID_1086 Merged ACOT2|NM_006821\C14orf168|NM_031427\MGC48595|NM_203309\ACOT4| WGTP chr14 73030050 73196823 QPCR √ EF 65 CNV_ID_1087 NM_152331 Merged 500K EA chr14 73620134 73676171 C14orf46|NM_001024674\ALDH6A1|NM_005589 603178 37 CNV_ID_1088 Merged C14orf156|NM_031210\FLJ25976|NM_174943\SPTLC2|NM_004863\SNW1|N both chr14 77143933 77332325 MassSpec PE 68 CNV_ID_1089 M_012245\ALKBH|NM_006020 Merged 500K EA chr14 77448909 77571772 ADCK1|NM_020421 63 CNV_ID_1090 Merged both chr14 77945360 78243281 P NRXN3|NM_004796 275 CNV_ID_1091 Merged 500K EA chr14 78728484 78735438 NRXN3|NM_004796 10 CNV_ID_1092 Merged WGTP chr14 82105460 82216550 AY358651_BX248253 47 CNV_ID_1093 Merged WGTP chr14 83206211 83363593 AY358651_BX248253 36 CNV_ID_1094 Merged 500K EA chr14 84633513 84635740 AY358651_BX248253 0 CNV_ID_1095 Merged both chr14 85228067 85495155 P AB007865_BC034577 106 CNV_ID_1096 Merged 500K EA chr14 85520078 85568590 √ F AB007865_BC034577 12 CNV_ID_1097 Merged WGTP chr14 86259051 86411966 √ F AB007865_BC034577 37 CNV_ID_1098 Merged 500K EA chr14 87460869 87500047 √ F GALC|NM_000153 606890\ 606890 BC034577_D25283 19 CNV_ID_1099 Merged 500K EA chr14 93382087 93414055 √ F 8 CNV_ID_1100 Merged 500K EA chr14 94007639 94015670 SERPINA9|NM_175739 1 CNV_ID_1101 Merged 500K EA chr14 97199755 97224576 √ F 5 CNV_ID_1102 Merged 500K EA chr14 98604476 98636221 15 CNV_ID_1103 Merged KNS2|NM_005552\ZFYVE21|NM_024071\XRCC3|NM_005432\C14orf2|NM_0 WGTP chr14 103217278 103482566 Variation_0181 V 600675 94 CNV_ID_1104 04894\KNS2|NM_182923\PPP1R13B|NM_015316 Merged NUDT14|NM_177533\BTBD6|NM_033271\PACS2|NM_015197\CRIP2|NM_00 WGTP chr14 104584391 105020471 1312\JAG2|NM_002226\BRF1|NM_145685\JAG2|NM_145159\GPR132|NM_01 127 CNV_ID_1105 3345\MTA1|NM_004689\BRF1|NM_001519\BRF1|NM_145696 Merged Variation_0774\ 500K EA chr14 106210547 106295344 √ VF 45 CNV_ID_1106 Variation_2179 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_0442\ Variation_2123\ Variation_0913\ Variation_0877\ Variation_0909\ Variation_0776\ Variation_2181\ Variation_0849\ Variation_0848\ Variation_0775\ Variation_2180\ Variation_2182\ Variation_2183\ DC3795\ DC3786\ DC3787\ DC3792\ DC3794\ Variation_1281\ DC3796\ DC3798\ DC3799\ DC3801\ DC3802\ MKRN3|NM_005664\NIPA2|NM_001008894\NIPA1|NM_144599\NIPA2|NM_00 Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Variation_0874\ DC3806\ DC3808\ DC3810\ DC3811\ DC3812\ 1008892\NIPA2|NM_001008860\NIPA2|NM_030922\OR4N4|NM_001005241\F Inter\ Intra\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Merged Variation_0948\ LJ36144|NM_182561\NM_001024681\POTE15|NM_207355\LOC283755|NM_0 DC3813\ DC3815\ DC3816\ DC3820\ DC3821\ both chr15 18263733 21365850 QPCR √ PEF 608145 AK127783_AK097517 Inter\ Inter\ Both\ Inter\ Inter\ Both\ Both\ Both\ 962 CNV_ID_1107 Variation_0912\ 01024682\LOC400968|NM_001013678\GOLGA8E|NM_001012423\CYFIP1|N DC3788\ DC3789\ DC3790\ DC3791\ DC3797\ Inter\ Inter\ Both\ Both\ Both\ Inter\ Both\ Both\ Variation_0938\ M_001033028\CYFIP1|NM_014608\OR4M2|NM_001004719\TUBGCP5|NM_0 DC3800\ DC3803\ DC3804\ DC3805\ DC3807\ 52903\NM_173613 Both\ Both\ Both\ Inter Variation_0875\ DC3814\ DC3817\ DC3819\ DC3793\ DC3818\ Variation_0876\ DC3809 Variation_0873\ Variation_0318\ Variation_0910\ Variation_0928\ Variation_0864\ Variation_0903\ Variation_0949\ Variation_0850\ Variation_0851\ Variation_0852\ Variation_0917\ Variation_0901\ Merged 500K EA chr15 21606530 21610088 BC008750_NM_018958 CNV_ID_1108 DC3823\ DC3824\ DC3826\ DC3827\ DC3829\ Merged Variation_1958\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr15 21805431 22452007 √ PVF BC008750_NM_018958 DC3830\ DC3832\ DC3833\ DC3835\ DC3822\ 9 CNV_ID_1109 Variation_0900 Intra\ Intra\ Intra\ Intra\ Intra\ Intra DC3828\ DC3831\ DC3834\ DC3825 176270,182279\ Merged SNRPN|NM_022805\SNRPN|NM_022806\SNRPN|NM_022807\SNRPN|NM_0 176270,182279\ 500K EA chr15 22606371 22689056 √ F CNV_ID_1110 22808 176270,182279\ 176270,182279 Merged WGTP chr15 25060215 25335769 GABRG3|NM_033223 20 CNV_ID_1111 Merged HERC2|NM_004667\LOC440248|NM_199045\FLJ32679|NM_001012452_copy DC3842\ DC3843\ DC3844\ DC3845\ DC3846\ WGTP chr15 26086062 26763830 Variation_0868 √ VF _2\FLJ32679|NM_001012452\GOLGA8G|NM_001012420\GOLGA8G|NM_001 Intra\ Both\ Both\ Both\ Both\ Both 319 CNV_ID_1112 012420_copy_2 DC3847 Variation_0447\ Variation_0448\ Variation_0449\ Variation_0450\ Variation_0451\ Variation_0452\ Merged Variation_0453\ DC3849\ DC3850\ DC3852\ DC3854\ DC3848\ both chr15 28080236 28964768 √ PF CHRFAM7A|NM_148911\CHRFAM7A|NM_139320 Both\ Inter\ Intra\ Intra\ Both\ Intra\ Both 437 CNV_ID_1113 Variation_0446\ DC3851\ DC3853 Variation_0454\ Variation_0319\ Variation_0779\ Variation_2185\ Variation_2186\ Variation_0925 Variation_2187\ Variation_2188\ Variation_0780\ Variation_2189\ Merged Variation_0782\ C15orf45|NM_001035530\ARHGAP11A|NM_014783\ARHGAP11A|NM_19935 both chr15 29553592 30773871 √ PVF 118511 DC3855\ DC3857\ DC3856\ DC3858 Intra\ Intra\ Intra\ Both 473 CNV_ID_1114 Variation_2190\ 7\SGNE1|NM_003020\CHRNA7|NM_000746\OTUD7|NM_130901 Variation_0321\ Variation_0185\ Variation_0925\ Variation_0320 Variation_1960\ Variation_2192\ Variation_0187\ Merged Variation_0783\ SLC12A6|NM_005135\GOLGA8A|NM_181077\NUT|NM_175741\GOLGA8A|N both chr15 32330313 32775539 PCR √ PVEF M_181076\NOLA3|NM_018648\AGPAT7|NM_153613\GOLGA8A|NM_015003\ 604878 DC3860\ DC3863\ DC3859\ DC3861\ DC3862 Both\ Inter\ Both\ Both\ Inter 229 CNV_ID_1115 Variation_0455\ GOLGA8B|NM_001023567 Variation_0322\ Variation_0784\ Variation_2193 Merged WGTP chr15 35618861 35759779 AK001298_AK093126 86 CNV_ID_1116 Merged CCDC32|NM_052849\CASC5|NM_170589\RPUSD2|NM_152260\RAD51|NM_ WGTP chr15 38619837 38782403 179617\ 179617 37 CNV_ID_1117 002875\RAD51|NM_133487\CASC5|NM_144508 Merged 500K EA chr15 39834465 39909909 MAPKBP1|NM_014994\PLA2G4B|NM_005090 64 CNV_ID_1118 CATSPER2|NM_172097\CKMT1B|NM_020990\STRC|NM_153700\PDIA3|NM_ 005313\CKMT1A|NM_001015001\ELL3|NM_025165\HISPPD2A|NM_0010244 Merged 63\WDR76|NM_024908\SERF2|NM_001018108\CATSPER2|NM_172095\MFA both chr15 41610450 41935933 Variation_1282 √ PF 606440 DC3867\ DC3868 Intra\ Intra 245 CNV_ID_1119 P1|NM_005926\CATSPER2|NM_172096\HISPPD2A|NM_014659\SERINC4|N M_001033517\HYPK|NM_016400\CATSPER2|NM_054020\MAP1A|NM_00237 3 DC3874\ DC3869\ DC3871\ DC3872\ DC3873\ Merged DUOX2|NM_014080\NM_182985\DUOX1|NM_175940\LOC405753|NM_20758 Intra\ Inter\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr15 42756160 43210134 √ PF 1\NIP|NM_144565\B2M|NM_004048\MGC33951|NM_152448\NM_080745\SO 606759\ 182500\ 109700 DC3876\ DC3877\ DC3878\ DC3879\ DC3880\ 169 CNV_ID_1120 Intra\ Intra\ Intra\ Intra\ Intra RD|NM_003104\DUOX1|NM_017434 DC3881\ DC3870\ DC3875 Merged DUT|NM_001025248\DUT|NM_001025249\SLC12A1|NM_000338\DUT|NM_00 WGTP chr15 46296330 46451070 600839 86 CNV_ID_1121 1948 Merged TNFAIP8L3|NM_207381\DMXL2|NM_015263\CYP19A1|NM_031226\CYP19A1 both chr15 49069549 49617631 P 107910\ 107910 DC3886 Both 192 CNV_ID_1122 |NM_000103\GLDN|NM_181789\AP4E1|NM_007347 Merged 500K EA chr15 51557013 51572775 U96173_BX537884 12 CNV_ID_1123 Merged 500K EA chr15 54523770 54577372 MNS1|NM_018365\TEX9|NM_198524 17 CNV_ID_1124 Merged 500K EA chr15 59467652 59487950 BC008831_AK000143 15 CNV_ID_1125 Merged WGTP chr15 63967839 64137439 Variation_0786 V MEGF11|NM_032445\RAB11A|NM_004663 169 CNV_ID_1126 Merged WGTP chr15 66325126 66601717 ITGA11|NM_001004439\FEM1B|NM_015322\ITGA11|NM_012211 123 CNV_ID_1127 Merged RPLP1|NM_213725\RPLP1|NM_001003\KIF23|NM_004856\PAQR5|NM_0177 WGTP chr15 67421806 67579253 √ F 47 CNV_ID_1128 05\KIF23|NM_138555 Merged 500K EA chr15 68815452 68834724 UACA|NM_018003 4 CNV_ID_1129 Merged Variation_2195\ ARIH1|NM_005744\BBS4|NM_033028\GOLGA|NM_018652\ADPGK|NM_0312 WGTP chr15 70606839 70907613 √ VF 600374 DC3894\ DC3895 Intra\ Both 137 CNV_ID_1130 Variation_0189 84 PML|NM_033249\PML|NM_033245\PML|NM_002675\PML|NM_033244\PML|N 102578\ 102578\ 102578\ Merged Variation_0356\ M_033250\PML|NM_033247\PML|NM_033240\PML|NM_033246\STOML1|NM 102578\ 102578\ 102578\ WGTP chr15 72002167 72251969 √ F DC3896\ DC3897 Intra\ Both 137 CNV_ID_1131 Variation_2196 _004809\KIAA1465|NM_020851\PML|NM_033239\LOXL1|NM_005576\PML|N 102578\ 102578\ 102578\ M_033242\PML|NM_033238 102578\ 102578 Merged TSPAN3|NM_198902\ZNF291|NM_020843\RCN2|NM_002902\PSTPIP1|NM_0 WGTP chr15 74957605 75160503 604,416,606,347 74 CNV_ID_1132 03978\TSPAN3|NM_005724 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged WGTP chr15 77142292 77305824 QPCR E RASGRF1|NM_002891 hsa-mir-184/15/77289184/77289268/100.000000 63 CNV_ID_1133 Merged 500K EA chr15 77337962 77340626 CNV_ID_1134 Merged 500K EA chr15 77737577 77850372 DC3920 Inter 78 CNV_ID_1135 Merged both chr15 79728575 80011124 P BX640632_AB095929 DC3924\ DC3923 Intra\ Intra 115 CNV_ID_1136 Merged RPS17|NM_001021\FLJ22795|NM_025084_copy_2\CPEB1|NM_030594\FLJ2 WGTP chr15 80676701 81107580 Variation_0190 √ F DC3929 Both 456 CNV_ID_1137 2795|NM_025084_copy_3 Merged 500K EA chr15 82330480 82359162 ADAMTSL3|NM_207517 13 CNV_ID_1138 Variation_2198\ Merged Variation_2199\ both chr15 82506626 82904075 QPCR √ PVEF LOC388152|NM_203426\FLJ43276|NM_207382\KIAA1920|NM_052919 DC3932\ DC3933\ DC3934\ DC3935 Intra\ Intra\ Both\ Both 271 CNV_ID_1139 Variation_0790\ Variation_0791 Merged WGTP chr15 83063933 83217534 ZNF592|NM_014630\ALPK3|NM_020778 99 CNV_ID_1140 Merged Variation_0792\ PDE8A|NM_173455\PDE8A|NM_173457\PDE8A|NM_173456\PDE8A|NM_173 WGTP chr15 83451942 83685716 √ VF DC3938\ DC3940\ DC3941\ DC3939 Both\ Intra\ Inter\ Both 159 CNV_ID_1141 Variation_2200 454\FLJ40113|NM_198079_copy_2\PDE8A|NM_002605 Merged 500K EA chr15 84140970 84162590 √ F 6 CNV_ID_1142 Merged 500K EA chr15 84946745 84954786 AK056872_AK056023 5 CNV_ID_1143 Merged 500K EA chr15 85706849 85711119 √ F AK056872_AK056023 9 CNV_ID_1144 Merged SEMA4B|NM_020210\LOC390637|NM_001013657\NGRN|NM_001033088\CIB both chr15 88366960 88610637 √ PF 1|NM_006384\FLJ46079|NM_001029964\ZNF710|NM_198526\IDH2|NM_0021 154 CNV_ID_1145 68\NGRN|NM_016645\SEMA4B|NM_198925 Merged WGTP chr15 89632854 89841316 QPCR E SV2B|NM_014848 AK124722_AF205074 85 CNV_ID_1146 Merged 500K EA chr15 90382555 90416250 √ F SLCO3A1|NM_013272 15 CNV_ID_1147 Merged 500K EA chr15 91597772 91620597 √ F AY358254_BC021741 10 CNV_ID_1148 Merged WGTP chr15 93267980 93447142 AL360258_AK128633 96 CNV_ID_1149 Merged WGTP chr15 94219335 94439704 AL360258_AK128633 261 CNV_ID_1150 Merged both chr15 95508704 95833748 Variation_0192 PV AY489187_BC028704 173 CNV_ID_1151 Merged LOC400464|NM_001013670\ADAMTS17|NM_139057\DKFZp434I1020|NM_19 DC3948\ DC3949\ DC3950\ DC3952\ DC3953\ both chr15 98091816 98574562 MassSpec PE Inter\ Both\ Both\ Inter\ Inter\ Both 169 CNV_ID_1152 4295 DC3951 Merged WGTP chr15 99298613 99478425 LRRK1|NM_024652 64 CNV_ID_1153 PCSK6|NM_138323\SELS|NM_018445\PCSK6|NM_138324\PCSK6|NM_1383 Merged 20\CHSY1|NM_014918\PCSK6|NM_138322\PCSK6|NM_138321\SNRPA1|NM both chr15 99537666 99872978 √ PF 607918\ 607918 153 CNV_ID_1154 _003090\PCSK6|NM_002570\SELS|NM_203472\PCSK6|NM_138319\PCSK6| NM_138325 Merged Variation_0475\ WGTP chr15 100089153 100248597 V OR4F15|NM_001001674\OR4F6|NM_001005326 DC3955\ DC3956 Both\ Inter 120 CNV_ID_1155 Variation_2202

PRSS21|NM_144956\NM_152340\PRSS21|NM_006799\PDPK1|NM_002613\ Merged PRSS33|NM_152891\TESSP1|NM_183379\CGI- DC3526\ DC3522\ DC3523\ DC3524\ DC3525\ WGTP chr16 2476826 2810537 √ F 14|NM_015944\SRRM2|NM_016333\LOC283874|NM_001012731\PRSS21|NM Intra\ Intra\ Intra\ Intra\ Inter\ Intra 103 CNV_ID_1158 _144957\TCEB2|NM_207013\PRSS27|NM_031948\ATP6V0C|NM_001694\KC DC3527 TD5|NM_018992\TCEB2|NM_007108\PDPK1|NM_031268 Merged 500K EA chr16 4149842 4198092 √ F 15 CNV_ID_1159 Merged PPL|NM_002705\FAM86A|NM_201598\MGC45438|NM_152459\ALG1|NM_01 both chr16 4912851 5364830 Variation_0476 MassSpec √ PVEF 605907 AY037162_AF107203 DC3529\ DC3531\ DC3532\ DC3528\ DC3530 Inter\ Inter\ Inter\ Inter\ Inter 119 CNV_ID_1160 9109\FAM86A|NM_201400\NAGPA|NM_016256 Merged 500K EA chr16 5542095 5551122 AY037162_AF107203 2 CNV_ID_1161 Merged 500K EA chr16 6448405 6449672 A2BP1|NM_018723 1 CNV_ID_1162 Merged both chr16 6588011 6878909 Variation_1283 √ PVF A2BP1|NM_018723 186 CNV_ID_1163 Merged 500K EA chr16 6973749 7021963 A2BP1|NM_018723 22 CNV_ID_1164 Merged 500K EA chr16 7855056 7915358 AF109106_BC001908 33 CNV_ID_1165 Merged 500K EA chr16 9721050 9729949 AF090898_U09002 2 CNV_ID_1166 Merged WGTP chr16 9968477 10165051 √ F GRIN2A|NM_000833 96 CNV_ID_1167 Merged 500K EA chr16 12554682 12561909 √ F CNV_ID_1168 Merged 500K EA chr16 12584246 12619700 √ F CNV_ID_1169 Merged PARN|NM_002582\NTAN1|NM_173474\KIAA0251|NM_015027\NM_00103168 DC3539\ DC3540\ DC3543\ DC3545\ DC3541\ WGTP chr16 14529556 15274051 Variation_0358 √ F 8\NOMO1|NM_014287\BFAR|NM_016561\PLA2G10|NM_003561\NPIP|NM_00 Intra\ Both\ Intra\ Intra\ Both\ Both\ Both\ Intra 258 CNV_ID_1170 6985\RRN3|NM_018427 DC3544\ DC3546\ DC3542 Merged Variation_2204\ ABCC1|NM_019900\ABCC1|NM_004996\ABCC6|NM_001171\NOMO3|NM_00 both chr16 16092718 16831289 √ PVF 1004067\ABCC1|NM_019899\ABCC1|NM_019902\ABCC1|NM_019862\ABCC 603234 BC008178_AJ539163 DC3547\ DC3548 Both\ Intra 392 CNV_ID_1171 Variation_2205 1|NM_019898\ABCC1|NM_019901 NOMO2|NM_173614\NOMO2|NM_001004060\COQ7|NM_016138\TMC7|NM_ Merged 024847\LOC162073|NM_001034841\RPS15A|NM_001030009\XYLT1|NM_022 both chr16 17441601 19066807 √ PF AJ539163_AK131085 DC3553\ DC3549\ DC3550\ DC3551\ DC3552 Intra\ Both\ Intra\ Intra\ Intra 840 CNV_ID_1172 166\SMG1|NM_015092\ARL6IP|NM_015161\RPS15A|NM_001019\NOMO3|N M_001004067_copy_2 Merged 500K EA chr16 20352824 20506848 Variation_1285 √ F ACSM2|NM_182617\FLJ20581|NM_017888\LOC123876|NM_001010845 DC3555\ DC3556 Intra\ Intra 7 CNV_ID_1173 Merged LOC94431|NM_145237\CRYM|NM_001014444\NM_001031629\OTOA|NM_17 both chr16 21212772 21856623 Variation_2206 QPCR √ PVEF 0664\IGSF6|NM_005849\DREV1|NM_016025\OTOA|NM_144672\LOC400509| 123740\ 607038\ 607038 DC3558\ DC3559\ DC3560 Both\ Intra\ Both 252 CNV_ID_1174 NM_001012391\NM_199182 Variation_0793\ Merged both chr16 22201625 22679810 Variation_0323\ QPCR √ PVEF POLR3E|NM_018119\EEF2K|NM_013302\CDR2|NM_001802 DC3561\ DC3562\ DC3563 Intra\ Intra\ Both 248 CNV_ID_1175 Variation_2207 Merged LCMT1|NM_016309\ARHGAP17|NM_018054\LCMT1|NM_001032391\ARHGA both chr16 24850896 25094479 √ PF 127 CNV_ID_1176 P17|NM_001006634 Merged WGTP chr16 25532212 25718755 HS3ST4|NM_006040 130 CNV_ID_1177 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Variation_0483\ Variation_0084\ Variation_2213\ Variation_0794\ Variation_2211\ Variation_0896\ Variation_0795\ DC3581\ DC3599\ DC3602\ DC3604\ DC3582\ Variation_2214\ DC3583\ DC3584\ DC3587\ DC3589\ DC3590\ Intra\ Inter\ Inter\ Both\ Intra\ Intra\ Intra\ Inter\ Variation_0195\ Merged TP53TG3|NM_016212\TP53TG3|NM_015369_copy_3\FLJ43855|NM_198857\L DC3594\ DC3595\ DC3596\ DC3597\ DC3601\ Inter\ Inter\ Inter\ Inter\ Both\ Inter\ Inter\ Inter\ both chr16 31658070 34900436 Variation_2212\ QPCR √ PVEF OC124411|NM_001004300\TP53TG3|NM_015369\TP53TG3|NM_015369_cop BC029861_AK125968 1172 CNV_ID_1181 DC3603\ DC3606\ DC3585\ DC3588\ DC3592\ Intra\ Both\ Inter\ Both\ Both\ Both\ Both\ Inter\ Variation_0796\ y_2\ZNF267|NM_003414 DC3593\ DC3598\ DC3600\ DC3605\ DC3586\ Both\ Both Variation_2215\ DC3591 Variation_0484\ Variation_0485\ Variation_0486\ Variation_0196\ Variation_0197\ Variation_2210\ Variation_0324 Merged both chr16 45819013 46163788 Variation_0761 PV PHKB|NM_001031835\CDA08|NM_030790\PHKB|NM_000293 172490\ 172490 71 CNV_ID_1182 Merged WGTP chr16 46886938 47037255 SIAH1|NM_003031\LONPL|NM_031490\SIAH1|NM_001006610 41 CNV_ID_1183 Merged 500K EA chr16 52965305 52987359 √ F AY335943_AY335945 28 CNV_ID_1184 Merged WGTP chr16 53121783 53309710 AY335943_AY335945 199 CNV_ID_1185 Merged 500K EA chr16 53310669 53336408 QPCR E AY335943_AY335945 14 CNV_ID_1186 Merged CES4|NM_016280\CES1|NM_001025195\SLC6A2|NM_001043\CES1|NM_001 114835\ 114835\ 114835\ DC3615\ DC3616\ DC3617\ DC3618\ DC3620\ WGTP chr16 54226897 54541091 √ F Intra\ Intra\ Intra\ Intra\ Inter\ Intra 89 CNV_ID_1187 025194\CES1|NM_001266\CES7|NM_145024 163970 DC3619 Merged CNOT1|NM_206999\FLJ10815|NM_018231\CNOT1|NM_016284\GOT2|NM_00 ACA46/16/57139903/57140038/100.000000, WGTP chr16 57136506 57433538 √ F 76 CNV_ID_1188 2080 ACA50/16/57151200/57151336/100.000000 Merged 500K EA chr16 62639947 62714192 √ F AB035305_D21255 19 CNV_ID_1189 Variation_0357\ Merged AARS|NM_001605\WWP2|NM_199423\WWP2|NM_199424\MGC34761|NM_1 DC3626\ DC3627\ DC3628\ DC3629\ DC3625\ both chr16 68412623 68870723 Variation_0797\ √ PVF 73619\PDPR|NM_017990\LOC348174|NM_182619\WWP2|NM_007014\EXOS Intra\ Intra\ Intra\ Intra\ Both\ Intra hsa-mir-140/16/68524484/68524584/100.000000 138 CNV_ID_1190 DC3630 Variation_2216 C6|NM_058219 Merged both chr16 69364623 69874484 Variation_0678 √ PF VAC14|NM_018052\HYDIN|NM_017558\FLJ11171|NM_018348 245 CNV_ID_1191 Merged PKD1L3|NM_181536\DHODH|NM_001361\DHODH|NM_001025193\HP|NM_0 WGTP chr16 70533845 70831848 √ F 05143\HPR|NM_020995\TXNL4B|NM_017853\PMFBP1|NM_031293\DHX38|N 140100 AK093285_L32832 DC3631\ DC3632 Intra\ Intra 160 CNV_ID_1192 M_014003 Merged 500K EA chr16 72330599 72332356 AK129695_BC000338 1 CNV_ID_1193 Merged GLG1|NM_012201\LOC497190|NM_001011880\LOC348174|NM_182619_cop WGTP chr16 72892281 73144686 √ F DC3633\ DC3635\ DC3634 Intra\ Intra\ Both 80 CNV_ID_1194 y_2\PSMD7|NM_002811 Merged CHST5|NM_012126\CHST6|NM_021615\CHST5|NM_024533\CFDP1|NM_006 WGTP chr16 73977115 74134472 √ F 605294 DC3636\ DC3637 Intra\ Intra 47 CNV_ID_1195 324\LOC124491|NM_145254 Merged 500K EA chr16 74567282 74579010 BC022428_AB051550 4 CNV_ID_1196 Merged 500K EA chr16 74819177 74829497 BC022428_AB051550 10 CNV_ID_1197 Merged WWOX|NM_016373\WWOX|NM_130788\WWOX|NM_018560\WWOX|NM_13 both chr16 76811430 76974815 Variation_0490 √ PVF 605131\ 605131 135 CNV_ID_1198 0790\WWOX|NM_130791\WWOX|NM_130792 Merged WWOX|NM_016373\WWOX|NM_130788\WWOX|NM_130790\WWOX|NM_13 500K EA chr16 77607617 77626238 √ F 605131 10 CNV_ID_1199 0792 Merged 500K EA chr16 78452465 78480811 AF055376_AF125108 17 CNV_ID_1200 Merged 500K EA chr16 79529780 79584643 Variation_1286 PCR √ VEF DC13|NM_020188 13 CNV_ID_1201 Merged 500K EA chr16 82340616 82351735 CDH13|NM_001257 1 CNV_ID_1202 Merged 500K EA chr16 84834231 84849716 7 CNV_ID_1203 Merged 500K EA chr16 85079026 85094533 √ F 7 CNV_ID_1204 Merged both chr16 85399263 85564336 √ PF NM_005250_AL136762 99 CNV_ID_1205 Merged WGTP chr16 86476851 86671233 BANP|NM_079837\BANP|NM_017869\CA5A|NM_001739 DC3643\ DC3642\ DC3644\ DC3645\ DC3641 Intra\ Intra\ Intra\ Intra\ Intra 32 CNV_ID_1206 Merged WGTP chr16 86986673 87137417 √ F ZFPM1|NM_153813 161 CNV_ID_1207 Merged SPG7|NM_003119\CPNE7|NM_014427\RPL13|NM_000977\RPL13|NM_03325 WGTP chr16 87970408 88179649 √ F 602783\ 602783 HBII-202/16/88155338/88155410/100.000000 33 CNV_ID_1208 1\CPNE7|NM_153636\ANKRD11|NM_013275\SPG7|NM_199367 Merged FANCA|NM_001018112\SPIRE2|NM_032451\FANCA|NM_000135\NULP1|NM WGTP chr16 88398233 88495450 √ F 607139\ 607139 39 CNV_ID_1209 _014972 Merged WGTP chr17 343377 440727 VPS53|NM_018289 57 CNV_ID_1210 Merged ABR|NM_021962\FAM57A|NM_024792\TIMM22|NM_013337\NXN|NM_02246 both chr17 568336 1008155 QPCR √ PEF 3\C17orf25|NM_016080\ABR|NM_001092\GEMIN4|NM_015721\RNMTL1|NM_ 282 CNV_ID_1211 018146 Merged 500K EA chr17 6034605 6087870 √ F 12 CNV_ID_1212 Merged both chr17 13821966 14069281 Variation_0897 PV COX10|NM_001303 602125 DC3184\ DC3185 Intra\ Intra 163 CNV_ID_1213 Merged both chr17 16467781 16758162 √ PF ZNF624|NM_020787 DC3198\ DC3201\ DC3199\ DC3200 Intra\ Intra\ Intra\ Intra 110 CNV_ID_1214 Merged Variation_0496\ FLJ36492|NM_182568\SHMT1|NM_004169\LOC220594|NM_145809\SHMT1| WGTP chr17 18175250 18387109 √ F DC3203\ DC3204 Intra\ Both 127 CNV_ID_1215 Variation_2219 NM_148918\FLJ35934|NM_207453\FLJ11800|NM_024974 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

U3-2/17/18905949/18906166/100.000000, U3- 2/17/18907957/18908174/100.000000, U3- Merged EPN2|NM_148921\EPN2|NM_014964\PRPSAP2|NM_002767\GRAP|NM_0066 WGTP chr17 18771341 19132640 QPCR √ EF DC3210 Intra 4/17/18956457/18956674/100.000000, 162 CNV_ID_1216 13\SLC5A10|NM_152351 U3/17/19031921/19032138/100.000000, U3- 3/17/19033934/19034151/100.000000 Merged 500K EA chr17 19426327 19504358 Variation_1288 √ VF ALDH3A2|NM_000382\ALDH3A2|NM_001031806 609523\ 609523 76 CNV_ID_1217 Merged WGTP chr17 20227887 20640432 √ F FLJ35934|NM_207453_copy_2 DC3214\ DC3211\ DC3212\ DC3213 Intra\ Both\ Intra\ Both 271 CNV_ID_1218 DC3220\ DC3223\ DC3224\ DC3225\ DC3227\ Intra\ Intra\ Intra\ Both\ Inter\ Intra\ Intra\ Intra\ Merged Variation_0497\ DC3228\ DC3229\ DC3230\ DC3232\ DC3233\ both chr17 21191534 22014559 QPCR √ PVEF KCNJ12|NM_021012\FAM27L|NM_203392 AK093319_AL110269 Inter\ Intra\ Intra\ Both\ Intra\ Intra\ Inter\ Inter\ 304 CNV_ID_1219 Variation_0498 DC3235\ DC3236\ DC3221\ DC3222\ DC3226\ Intra\ Both DC3231\ DC3234\ DC3237 Merged DC3239\ DC3245\ DC3238\ DC3240\ DC3242\ Inter\ Intra\ Inter\ Both\ Intra\ Inter\ Inter\ Inter\ WGTP chr17 22045526 22465691 √ F AK093319_AL110269 77 CNV_ID_1220 DC3243\ DC3244\ DC3246\ DC3247\ DC3241 Inter\ Inter Merged NOS2A|NM_153292\LGALS9|NM_009587\NOS2A|NM_000625\KSR1|NM_014 163730,248310\ WGTP chr17 22902614 23201246 √ F DC3254\ DC3255\ DC3256\ DC3253 Intra\ Intra\ Intra\ Intra 102 CNV_ID_1221 238\LGALS9|NM_002308 163730,248310 Merged RHOT1|NM_018307\RHOT1|NM_001033566\C17orf40|NM_018428\LRRC37B| WGTP chr17 27245834 27562095 NM_052888\RHOT1|NM_001033568\RHOT1|NM_001033567\SUZ12|NM_015 606245 DC3274\ DC3275\ DC3273\ DC3276 Intra\ Both\ Intra\ Both 119 CNV_ID_1222 355

Merged YPEL2|NM_001005404\GDPD1|NM_182569\TRIM37|NM_001005207\FAM33A WGTP chr17 54437361 54780416 605073\ 605073 DC3322 Inter hsa-mir-301/17/54583278/54583364/100.000000 108 CNV_ID_1237 |NM_182620\PRR11|NM_018304\C17orf71|NM_018149\TRIM37|NM_015294 Merged WGTP chr17 55350429 55513944 Variation_0805 √ VF ABC1|NM_022070\LOC51136|NM_016125\RPS6KB1|NM_003161 DC3325\ DC3324 Both\ Both 84 CNV_ID_1238 Merged WGTP chr17 57650339 57826573 Variation_2230 √ F LOC440452|NM_001024654\FLJ25818|NM_173503 DC3330\ DC3329 Intra\ Both 83 CNV_ID_1239 Merged WGTP chr17 65403530 65490775 U39657_AF153816 65 CNV_ID_1240 Merged 500K EA chr17 69252400 69258719 C17orf54|NM_182564 12 CNV_ID_1241 Merged WGTP chr17 72638503 72807003 SEC14L1|NM_003003 43 CNV_ID_1242 Merged 500K EA chr17 74743681 74774728 √ F LOC146713|NM_001025448 19 CNV_ID_1243 Merged 500K EA chr17 75752791 75790078 Variation_2235 V CARD14|NM_052819\CARD14|NM_024110 1 CNV_ID_1244

Merged MGC15523|NM_138570\AZI1|NM_014984\AZI1|NM_001009811\C17orf55|NM WGTP chr17 76741026 76933757 √ F 79 CNV_ID_1245 _178519\TMEM105|NM_178520\FLJ44861|NM_207389\C17orf56|NM_144679 Merged 500K EA chr18 277648 306558 Variation_1289 √ VF 9 CNV_ID_1246 Merged 500K EA chr18 667302 695598 ENOSF1|NM_017512 5 CNV_ID_1247 Merged both chr18 3667422 4160252 Variation_1966 √ PF DLGAP1|NM_004746\DLGAP1|NM_001003809 AB000277_BC010538 203 CNV_ID_1248 Merged WGTP chr18 6752909 6933645 LAMA1|NM_005559\ARHGAP28|NM_030672\ARHGAP28|NM_001010000 39 CNV_ID_1249 Merged 500K EA chr18 9733326 9743992 Variation_2236 V RAB31|NM_006868 3 CNV_ID_1250 Merged WGTP chr18 11887023 12066102 √ F IMPA2|NM_014214\MPPE1|NM_138608\MPPE1|NM_023075 DC2908\ DC2909 Intra\ Intra 60 CNV_ID_1251 Merged CIDEA|NM_198289\SPIRE1|NM_020148\AFG3L2|NM_006796\TUBB6|NM_03 WGTP chr18 12230681 12489525 46 CNV_ID_1252 2525\CIDEA|NM_001279\C18orf43|NM_006553 DC2922\ DC2919\ DC2921\ DC2923\ DC2925\ Merged BC024227_AF269088\ DC2926\ DC2928\ DC2931\ DC2916\ DC2917\ Inter\ Both\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ both chr18 13988748 15367893 Variation_1292 √ PVF MGC26718|NM_001029999\ANKRD30B|NM_001029862\ZNF519|NM_145287 346 CNV_ID_1253 AK126828_U43195 DC2918\ DC2920\ DC2927\ DC2929\ DC2930\ Both\ Inter\ Inter\ Both\ Inter\ Inter\ Inter\ Inter DC2924 Merged WGTP chr18 19024430 19181612 CABLES1|NM_138375\C18orf45|NM_032933 37 CNV_ID_1254 Merged 500K EA chr18 24413258 24450849 √ F BC036470_AF083130 14 CNV_ID_1255 Merged 500K EA chr18 26068546 26073661 √ F BC036470_AF083130 2 CNV_ID_1256 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged 500K EA chr18 27886747 27928990 RNF138|NM_198128\RNF125|NM_017831\RNF138|NM_016271 15 CNV_ID_1257 Merged WGTP chr18 28637325 28828735 C18orf34|NM_198995 116 CNV_ID_1258 Merged 500K EA chr18 32241210 32272575 FHOD3|NM_025135 14 CNV_ID_1259 Variation_1293\ Merged Variation_1971\ both chr18 32304033 32735865 QPCR PE KIAA1328|NM_020776\FHOD3|NM_025135\C18orf10|NM_015476 uc.429 182 CNV_ID_1260 Variation_1972\ Variation_1970 Merged WGTP chr18 35736115 35903305 BC001946_Z46973 91 CNV_ID_1261 Merged 500K EA chr18 37638408 37686676 √ F BC001946_Z46973 43 CNV_ID_1262 Merged 500K EA chr18 38183758 38194401 √ F CNV_ID_1263 Merged 500K EA chr18 49503791 49532928 X76132_AF039701 7 CNV_ID_1264 Merged 500K EA chr18 54081842 54095115 √ F NEDD4L|NM_015277 5 CNV_ID_1265 Merged 500K EA chr18 55803729 55838153 √ F 9 CNV_ID_1266 Merged 500K EA chr18 56251349 56278547 NM_005912_AF217289 1 CNV_ID_1267 Merged 500K EA chr18 59700021 59742065 √ F SERPINB2|NM_002575\SERPINB10|NM_005024 12 CNV_ID_1268 Merged 500K EA chr18 60558805 60600790 BC029565_AK098573 10 CNV_ID_1269 Merged WGTP chr18 61863327 62021348 Variation_1983 QPCR √ VEF AB035301_AJ007607 32 CNV_ID_1270 Merged 500K EA chr18 62053230 62087598 QPCR √ EF AB035301_AJ007607 5 CNV_ID_1271 Merged WGTP chr18 62157007 62341492 √ F CDH19|NM_021153 AB035301_AJ007607 21 CNV_ID_1272 Merged 500K EA chr18 63098485 63123732 BC015877_AL831865 1 CNV_ID_1273 Variation_1297\ Merged Variation_1985\ both chr18 64126718 64543942 √ PVF TXNDC10|NM_019022 AK021849_AB058733 50 CNV_ID_1274 Variation_1984\ Variation_1296 Merged 500K EA chr18 64888576 64912007 Variation_1986 PCR √ EF AK027247_AK057795 4 CNV_ID_1275 Merged both chr18 67700021 68125877 P AY262164_BC035789 92 CNV_ID_1276 Merged 500K EA chr18 68579533 68585381 NETO1|NM_153181\NETO1|NM_138966 1 CNV_ID_1277 Merged WGTP chr18 73047414 73306926 √ F GALR1|NM_001480 U53511_NM_171999 DC2948 Inter 35 CNV_ID_1278 Merged WGTP chr18 74125373 74378820 √ F U53511_NM_171999 112 CNV_ID_1279 Merged Variation_0931\ THEG|NM_199202\PPAP2C|NM_003712\PPAP2C|NM_177543\THEG|NM_01 WGTP chr19 183069 327646 V DC2572\ DC2571 Both\ Inter 39 CNV_ID_1280 Variation_0959 6585\PPAP2C|NM_177526\KIAA1193|NM_017550 ATP5D|NM_001001975\HMHA1|NM_012292\WDR18|NM_024100\C19orf24|N M_017914\MIDN|NM_177401\APC2|NM_005883\THSD6|NM_213604\CNN2|N Variation_0931\ M_201277\CNN2|NM_004368\C19orf6|NM_033420\PCSK4|NM_017573\DAZA Variation_0959\ P1|NM_018959\POLR2E|NM_002695\GAMT|NM_138924\C19orf6|NM_001033 Merged 026\MUM1|NM_032853\NDUFS7|NM_024407\GRIN3B|NM_138690\GPX4|NM 602216\ 601825\ 601240\ WGTP chr19 902641 1495933 Variation_0866\ √ F 294 CNV_ID_1281 _002085\C19orf26|NM_152769\C19orf32|NM_138393\C19orf25|NM_152482\D 601240 Variation_2237\ AZAP1|NM_170711\RPS15|NM_001018\ABCA7|NM_033308\EFNA2|NM_001 Variation_0858 405\ARID3A|NM_005224\ATP5D|NM_001687\C19orf23|NM_152480\ABCA7|N M_019112\CIRBP|NM_001280\STK11|NM_000455\GAMT|NM_000156\KIAA09 63|NM_014963 Variation_0509\ Variation_0862\ Variation_0871\ Variation_0943\ Variation_0941\ Merged Variation_0945\ WGTP chr19 8758670 8832847 √ VF ZNF558|NM_144693\MBD3L1|NM_145208 DC2579 Intra 13 CNV_ID_1282 Variation_0958\ Variation_0882\ Variation_0220\ Variation_0944\ Variation_0956\ Variation_0957 Merged 500K EA chr19 12350726 12410655 MGC71805|NM_203381\ZNF443|NM_005815 DC2589\ DC2590 Intra\ Intra 13 CNV_ID_1283 Merged ILVBL|NM_006844\CASP14|NM_012114\SYDE1|NM_033025\FLJ40365|NM_1 WGTP chr19 14957950 15120179 30 CNV_ID_1284 73482\ILVBL|NM_176826\OR1I1|NM_001004713 Merged 500K EA chr19 15641041 15712261 √ F CYP4F12|NM_023944\OR10H2|NM_013939 DC2595 Intra 9 CNV_ID_1285 Merged both chr19 20028401 20290544 P DC2601\ DC2602\ DC2603 Intra\ Intra\ Intra 70 CNV_ID_1286 Merged both chr19 20321226 20637787 Variation_1520 PCR √ PEF ZNF626|NM_145297 DC2607\ DC2604\ DC2605\ DC2606 Intra\ Intra\ Intra\ Intra 64 CNV_ID_1287 DC2627\ DC2631\ DC2646\ DC2622\ DC2623\ DC2624\ DC2625\ DC2626\ DC2628\ DC2629\ Intra\ Intra\ Intra\ Inter\ Intra\ Intra\ Intra\ Intra\ Merged ZNF91|NM_003430\ZNF676|NM_001001411\ZNF675|NM_138330\ZNF257|NM DC2630\ DC2632\ DC2633\ DC2634\ DC2635\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr19 21777328 23732307 Variation_2241 √ PVF 496 CNV_ID_1288 _033468\ZNF681|NM_138286\ZNF208|NM_007153\ZNF43|NM_003423 DC2636\ DC2637\ DC2638\ DC2639\ DC2640\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ DC2641\ DC2642\ DC2643\ DC2644\ DC2645\ Intra\ Intra DC2647 Merged Variation_0329\ both chr19 24131560 24349203 PV BC043147_AY371041 33 CNV_ID_1289 Variation_2242 Merged U87593_BC068609\ WGTP chr19 32658593 32953337 Variation_0863 √ F 15 CNV_ID_1290 BC043147_AY371041 Merged WGTP chr19 34038496 34356975 108 CNV_ID_1291 Merged 500K EA chr19 34447521 34456548 2 CNV_ID_1292 Merged CHST8|NM_022467\KCTD15|NM_024076\PEPD|NM_000285\CEBPG|NM_00 both chr19 38468914 39273401 √ PF 116897\ 170100 520 CNV_ID_1293 1806\CEBPA|NM_004364 Merged ZNF181|NM_001029997\ZNF302|NM_001012320\ZNF599|NM_001007248\ZN WGTP chr19 39817858 39984175 DC2655\ DC2656 Intra\ Intra 34 CNV_ID_1294 F599|NM_001007247\ZNF302|NM_018443 Merged 500K EA chr19 40345482 40365173 √ F FXYD5|NM_144779\FXYD5|NM_014164 1 CNV_ID_1295 GPR40|NM_005303\USF2|NM_003367\GPR41|NM_005304\LSR|NM_015925\ Merged FLJ25660|NM_152481\HAMP|NM_021175\MAG|NM_080600\LSR|NM_205835 WGTP chr19 40402918 40578953 Variation_0511 √ F 606464 62 CNV_ID_1296 \GPR42|NM_005305\CD22|NM_001771\LSR|NM_205834\MAG|NM_002361\U SF2|NM_207291 Merged ZNF570|NM_144694\HKR1|NM_181786\ZNF569|NM_152484\ZNF540|NM_15 500K EA chr19 42486690 42743446 DC2661\ DC2662 Both\ Intra 16 CNV_ID_1297 2606\LOC390927|NM_001013659 Merged Variation_0514\ CLC|NM_001828\PSMC4|NM_006503\FCGBP|NM_003890\DYRK1B|NM_006 WGTP chr19 44919744 45212970 √ VF 484\DYRK1B|NM_004714\FBL|NM_001436\PSMC4|NM_153001\ZNF546|NM_ DC2667\ DC2668 Intra\ Intra 38 CNV_ID_1298 Variation_0515 178544\DYRK1B|NM_006483 Merged MAP3K10|NM_002446\FLJ36888|NM_178830\AKT2|NM_001626\TTC9B|NM_ WGTP chr19 45304260 45531360 164731 54 CNV_ID_1299 152479\FLJ13265|NM_024877 Merged Variation_1990\ EGLN2|NM_053046\RAB4B|NM_016154\CYP2A6|NM_000762\CYP2B6|NM_0 DC2672\ DC2677\ DC2669\ DC2670\ DC2671\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ both chr19 45983467 46237908 QPCR √ PVEF 00767\EGLN2|NM_017555\CYP2A7|NM_000764\EGLN2|NM_080732\CYP2A7 122720 65 CNV_ID_1300 Variation_1299 |NM_030589 DC2673\ DC2675\ DC2674\ DC2676 Intra Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged EPS8L1|NM_017729\TNNT1|NM_003283\GP6|NM_016363\RDH13|NM_13841 500K EA chr19 60229274 60342499 191041 28 CNV_ID_1310 2\EPS8L1|NM_133180\EPS8L1|NM_139204\PPP1R12C|NM_017607 Merged 500K EA chr19 60927349 61018118 √ F NALP11|NM_145007\NALP9|NM_176820 DC2736\ DC2737 Intra\ Intra 5 CNV_ID_1311 Merged 500K EA chr19 62684998 62694776 ZNF419|NM_024691 DC2741 Intra CNV_ID_1312 Merged 500K EA chr19 63590775 63596527 QPCR √ EF RPS5|NM_001009 CNV_ID_1313 Merged WGTP chr20 8001 11943 1 CNV_ID_1314 Variation_1522\ Merged SIRPB2|NM_018556\SIRPB1|NM_006065\SIRPB2|NM_080816\PTPNS1L2|N WGTP chr20 1424781 1627256 Variation_1992\ √ VF DC2456\ DC2457 Intra\ Intra 18 CNV_ID_1315 M_178460 Variation_0536 Merged TGM6|NM_198994\SNRPB|NM_003091\SNRPB|NM_198216\TGM3|NM_0032 both chr20 2078560 2423469 Variation_0222 PV 87 CNV_ID_1316 45\ZNF343|NM_024325 Merged both chr20 8002182 8595665 P PLCB1|NM_182734\PLCB1|NM_015192 337 CNV_ID_1317 Merged WGTP chr20 8898291 9227700 PLCB4|NM_182797\PLCB4|NM_000933 182 CNV_ID_1318 Merged WGTP chr20 10840138 11064725 √ F AF003837_AB023169 182 CNV_ID_1319 Merged AF003837_AB023169\ both chr20 11638021 12381393 √ PF BTBD3|NM_181443\BTBD3|NM_014962 401 CNV_ID_1320 AL137756_AK001974 Merged 500K EA chr20 12581827 12609944 √ F AL137756_AK001974 10 CNV_ID_1321 Variation_1523\ Merged both chr20 14653888 14803457 Variation_1993\ QPCR √ PVEF C20orf133|NM_001033086 AK074883_AK125594 115 CNV_ID_1322 Variation_0537 Merged 500K EA chr20 14825886 14863051 Variation_0537 V C20orf133|NM_001033086 AK074883_AK125594 40 CNV_ID_1323 Merged 500K EA chr20 15230448 15279007 PCR √ EF C20orf133|NM_001033086\C20orf133|NM_001033087 AK074883_AK125594 34 CNV_ID_1324 Merged 500K EA chr20 17305806 17338095 √ F PCSK2|NM_002594 22 CNV_ID_1325 Merged 500K EA chr20 18197877 18221632 ZNF133|NM_003434 6 CNV_ID_1326 Merged both chr20 22977404 23127604 √ PF THBD|NM_000361\LOC200261|NM_182535\C1QR1|NM_012072 36 CNV_ID_1327 Merged DC2473\ DC2474\ DC2475\ DC2470\ DC2471\ WGTP chr20 25649992 26267569 Variation_0225 QPCR √ VEF C20orf91|NM_182583 AK095693_AK127732 Inter\ Inter\ Inter\ Both\ Both\ Both\ Both 98 CNV_ID_1328 DC2476\ DC2472 Merged AK095693_AK127732\ both chr20 28033231 28267569 √ PF FLJ45832|NM_207470\MGC72104|NM_207350 DC2478\ DC2480\ DC2481\ DC2477\ DC2479 Both\ Inter\ Inter\ Both\ Both 92 CNV_ID_1329 BC062743_AF347073 Merged SPAG4L|NM_080675\BPIL3|NM_174897\BPIL1|NM_025227\C20orf186|NM_1 WGTP chr20 30959468 31211827 √ F 107 CNV_ID_1330 82519\C20orf185|NM_182658 Merged 500K EA chr20 35736026 35759976 FLJ42133|NM_001001690\CTNNBL1|NM_030877 10 CNV_ID_1331 U71b/20/36487256/36487394/100.000000, U71a/20/36489362/36489500/100.000000, Merged BPI|NM_001725\KIAA1219|NM_020336\LOC128439|NM_139016\LBP|NM_00 U71c/20/36491723/36491861/100.000000, both chr20 36367793 36539571 MassSpec PE 55 CNV_ID_1332 4139 U71d/20/36495918/36496056/100.000000, ACA39/20/36510139/36510275/100.000000, ACA60/20/36511425/36511561/100.000000 Merged 500K EA chr20 40686319 40710511 √ F PTPRT|NM_007050\PTPRT|NM_133170 14 CNV_ID_1333 Merged NCOA5|NM_020967\CD40|NM_152854\CDH22|NM_021248\CD40|NM_00125 WGTP chr20 44126322 44398283 √ F 109535\ 109535 304 CNV_ID_1334 0 Merged 500K EA chr20 44681417 44722596 SLC13A3|NM_001011554\SLC13A3|NM_022829 12 CNV_ID_1335 Merged EYA2|NM_172112\EYA2|NM_172111\EYA2|NM_005244\EYA2|NM_172113\E 500K EA chr20 45195752 45227374 7 CNV_ID_1336 YA2|NM_172110 Variation_0539\ Merged NCOA3|NM_006534\SULF2|NM_018837\NCOA3|NM_181659\SULF2|NM_198 WGTP chr20 45701817 45957486 Variation_0538\ √ VF DC2486\ DC2484\ DC2487\ DC2485 Intra\ Inter\ Both\ Both 98 CNV_ID_1337 596 Variation_2251 Merged 500K EA chr20 49756024 49852802 SALL4|NM_020436\ATP9A|NM_006045 607343 34 CNV_ID_1338 Merged 500K EA chr20 52112544 52118615 BCAS1|NM_003657 2 CNV_ID_1339 Merged TMEPAI|NM_199169\TMEPAI|NM_199171\ZBP1|NM_030776\TMEPAI|NM_19 WGTP chr20 55604184 56121677 √ F 123 CNV_ID_1340 9170\TMEPAI|NM_020182 Merged 500K EA chr20 58995933 59023990 √ F AK128288_L34059 10 CNV_ID_1341 Merged WGTP chr20 59894657 60016638 √ F TAF4|NM_003185\CDH4|NM_001794 32 CNV_ID_1342 hsa-mir-1-1/20/60561957/60562028/100.000000, Merged GATA5|NM_080473\SLCO4A1|NM_016354\FLJ30313|NM_152757\C20orf166| WGTP chr20 60464834 60897084 √ F hsa-mir-133a- 86 CNV_ID_1343 NM_178463\NTSR1|NM_002531 2/20/60572563/60572665/100.000000 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

OPRL1|NM_182647\C20orf14|NM_012469\TCEA2|NM_003195\OPRL1|NM_0 Merged 00913\GPR8|NM_005286\TCEA2|NM_198723\RGS19|NM_005873\LOC19843 WGTP chr20 62108666 62435964 Variation_2252 √ VF 601618 DC2496 Inter 178 CNV_ID_1345 7|NM_001007125\LOC284739|NM_207349\SOX18|NM_018419\PCMTD2|NM_ 018257\MYT1|NM_004535 Variation_1305\ Variation_2253\ DC2062\ DC2055\ DC2056\ DC2058\ DC2059\ Merged Variation_0905\ TPTE|NM_199260\TPTE|NM_199259\BAGE5|NM_182484\TPTE|NM_013315\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ both chr21 9941889 10197104 QPCR √ PVEF BAGE4|NM_181704\BAGE2|NM_182482\TPTE|NM_199261\BAGE3|NM_1824 NM_001187_AF427490 DC2061\ DC2063\ DC2064\ DC2065\ DC2060\ 57 CNV_ID_1346 Variation_0893\ Inter\ Inter\ Inter\ Inter 81\BAGE|NM_001187 DC2066\ DC2057 Variation_1304\ Variation_1997 Variation_1998\ Variation_2000\ Variation_2001\ DC2069\ DC2070\ DC2072\ DC2073\ DC2075\ Merged Variation_1999\ Both\ Both\ Both\ Inter\ Inter\ Inter\ Both\ Both\ both chr21 13354570 14261623 √ PF LOC441956|NM_001013729\ANKRD21|NM_174981\C21orf81|NM_153750 AF427490_AY172978 DC2067\ DC2068\ DC2071\ DC2074\ DC2076\ 297 CNV_ID_1347 Variation_0810\ Inter\ Inter\ Both\ Inter DC2078\ DC2077 Variation_2254\ Variation_2255\ Variation_0811 Merged WGTP chr21 15834517 16018549 QPCR E AF130090_AF170562 52 CNV_ID_1348 Merged 500K EA chr21 19561892 19565214 U09860_U75330 2 CNV_ID_1349 Merged 500K EA chr21 19626353 19677375 U09860_U75330 17 CNV_ID_1350 Variation_1306\ Merged both chr21 20637992 20877335 Variation_1307\ √ PVF U09860_U75330 56 CNV_ID_1351 Variation_0918 Merged 500K EA chr21 22433789 22596775 PCR √ EF AY077696_AK124194 26 CNV_ID_1352 Merged Variation_2002\ 500K EA chr21 23320362 23512054 √ F AY077696_AK124194 50 CNV_ID_1353 Variation_1308 Merged 500K EA chr21 24483440 24515887 Variation_2003 V AY077696_AK124194 4 CNV_ID_1354 Merged WGTP chr21 27302101 27462314 AF142099_AF427489 75 CNV_ID_1355 Merged 500K EA chr21 29161064 29191388 C21orf127|NM_013240\C21orf127|NM_182749 10 CNV_ID_1356 Merged WGTP chr21 32151463 32438711 √ F HUNK|NM_014586 122 CNV_ID_1357 Merged 500K EA chr21 39779393 39888026 QPCR E SH3BGR|NM_007341\SH3BGR|NM_001001713 28 CNV_ID_1358 Merged 500K EA chr21 46067460 46144196 PCBP3|NM_020528 19 CNV_ID_1359 Merged HRMT1L1|NM_206962\HRMT1L1|NM_001535\DIP2A|NM_015151\S100B|NM_ 500K EA chr21 46811098 46902240 16 CNV_ID_1360 006272 Variation_0919\ Variation_0950\ Variation_0920\ DC1793\ DC1788\ DC1789\ DC1790\ DC1792\ Merged Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ both chr22 14461115 15652016 Variation_0951\ QPCR √ PVEF XKR3|NM_175878\OR11H1|NM_001005239\CESK1|NM_014406 BX248778_AY026350 DC1794\ DC1796\ DC1797\ DC1786\ DC1787\ 440 CNV_ID_1361 Both\ Both\ Both\ Both\ Inter Variation_0331\ DC1791\ DC1795\ DC1798 Variation_0813\ Variation_2257 Variation_0857\ Variation_0856\ Variation_2259\ Merged USP18|NM_017414\PRODH|NM_016335\DGCR2|NM_005137\GGT2|NM_002 DC1805\ DC1807\ DC1808\ DC1809\ DC1810\ both chr22 16926349 17436267 Variation_0815\ √ PF 058\PEX26|NM_017929\DGCR6|NM_005675\DKFZp434K191|NM_001029950\ 137181\ 606810\ 608666 Both\ Intra\ Intra\ Intra\ Intra\ Intra\ Both 179 CNV_ID_1362 DC1811\ DC1806 Variation_2260\ TUBA8|NM_018943 Variation_0814\ Variation_2258 Merged DGCR6L|NM_033257\RANBP1|NM_002882\HTF9C|NM_182984\HTF9C|NM_ WGTP chr22 18401047 18684001 Variation_2261 √ VF 022727\ZDHHC8|NM_013373\RTN4R|NM_023004\DGCR8|NM_022720\DKFZ 605566 DC1812\ DC1813\ DC1814 Intra\ Intra\ Intra 182 CNV_ID_1363 p761P1121|NM_152906 Variation_2010\ Merged WGTP chr22 20619657 20733158 Variation_2011\ √ VF TOP3B|NM_003935\PPM1F|NM_014634 9 CNV_ID_1364 Variation_2264 Variation_0548\ Variation_2036\ Merged HS322B1A|NM_015371\GSTT2|NM_000854_copy_2\DDT|NM_001355\GSTT2 500K EA chr22 22581891 22727762 Variation_2035\ √ F DC1861\ DC1862\ DC1863 Intra\ Intra\ Intra 64 CNV_ID_1365 |NM_000854\GSTT1|NM_000853 Variation_2032\ Variation_2033 Merged WGTP chr22 23382276 23422245 DC1868 Both 25 CNV_ID_1366 Variation_1528\ Variation_1531\ Variation_2023\ Variation_1312\ Variation_2021\ Variation_1529\ DC1882\ DC1869\ DC1871\ DC1872\ DC1873\ Variation_1530\ Merged CRYBB3|NM_004076\ADRBK2|NM_005160\CRYBB2|NM_000496\CTA- DC1874\ DC1875\ DC1876\ DC1877\ DC1878\ Intra\ Intra\ Intra\ Intra\ Intra\ Inter\ Inter\ Inter\ both chr22 23691355 24371067 Variation_2022\ √ PVF 123620\ 123630 171 CNV_ID_1367 246H3.1|NM_001013618\LRP5L|NM_182492 DC1879\ DC1880\ DC1881\ DC1883\ DC1884\ Inter\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra Variation_2269\ DC1870 Variation_2271\ Variation_0336\ Variation_0819\ Variation_2271\ Variation_2270\ Variation_2029 Merged 500K EA chr22 24460443 24475138 MYO18B|NM_032608 3 CNV_ID_1368 Merged TPST2|NM_003595\TFIP11|NM_012143\CRYBB1|NM_001887\CRYBA4|NM_0 WGTP chr22 25223053 25354450 600929 28 CNV_ID_1369 01886\TFIP11|NM_001008697\TPST2|NM_001008566 Merged WGTP chr22 32193499 32234100 √ F LARGE|NM_133642\LARGE|NM_004737 603590\ 603590 18 CNV_ID_1370 Merged WGTP chr22 32494349 32528033 LARGE|NM_133642\LARGE|NM_004737 603590\ 603590 9 CNV_ID_1371 Merged WGTP chr22 33068219 33107464 AJ007583_BC052624 10 CNV_ID_1372 Merged both chr22 33762965 33957507 P RAXLX|NM_001008494 AJ007583_BC052624 48 CNV_ID_1373 Merged WGTP chr22 35231063 35366534 EIF3S7|NM_003753\CACNG2|NM_006078 72 CNV_ID_1374 Merged NCF4|NM_013416\FLJ90680|NM_207475\CSF2RB|NM_000395\NCF4|NM_00 WGTP chr22 35499654 35685405 √ F 138981 55 CNV_ID_1375 0631\PVALB|NM_002854

Merged POLDIP3|NM_178136\NFAM1|NM_145912\CYB5R3|NM_007326\CYB5R3|NM both chr22 41091699 41407804 √ PF _000398\SERHL|NM_170694\SERHL2|NM_014509\CTA- 250800\ 250800 DC1918\ DC1920\ DC1919\ DC1921 Intra\ Intra\ Intra\ Intra 78 CNV_ID_1377 126B4.3|NM_015703\POLDIP3|NM_032311 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged 500K EA chr22 42695340 42716298 SAMM50|NM_015380 CNV_ID_1378 Merged WGTP chr22 42968722 43026202 Variation_2027 √ VF DC1924 Intra 35 CNV_ID_1379 Merged LOC553158|NM_181334\PRR5|NM_015366\PRR5|NM_001017528\PRR5|NM WGTP chr22 43347341 43531066 √ F _001017529\PRR5|NM_001017530\PRR5|NM_181333\ARHGAP8|NM_001017 50 CNV_ID_1380 526\ARHGAP8|NM_181335 C22orf9|NM_015264\FBLN1|NM_006485\RIBC2|NM_015653\SMC1L2|NM_14 Merged 8674\FBLN1|NM_001996\FBLN1|NM_006486\C22orf9|NM_001009880\C22orf 135820\ 135820\ 135820\ both chr22 43894761 44245703 P 71 CNV_ID_1381 8|NM_017911\UPK3A|NM_006953\NUP50|NM_153645\FBLN1|NM_006487\N 135820 M_153684\NUP50|NM_007172 Merged WGTP chr22 44975462 45018495 QPCR √ EF FLJ20699|NM_017931\GTSE1|NM_016426\PKDREJ|NM_006071 4 CNV_ID_1382 Merged WGTP chr22 45709833 45931039 √ F TBC1D22A|NM_014346 65 CNV_ID_1383 Merged 500K EA chr22 46758244 46775212 AK128136_AF131851 1 CNV_ID_1384 Merged WGTP chr22 46845829 46850201 √ F AK128136_AF131851 CNV_ID_1385 Merged WGTP chr22 47095130 47136752 √ F AK128136_AF131851 10 CNV_ID_1386 Merged WGTP chr22 47465793 47475686 √ F FAM19A5|NM_015381 7 CNV_ID_1387 Merged 500K EA chr22 47780805 47808278 AK124622_AK126356 9 CNV_ID_1388 Merged WGTP chr22 48248831 48252981 AK124622_AK126356 1 CNV_ID_1389 CPT1B|NM_152246\CPT1B|NM_152247\hCAP-H2|NM_152299\hCAP- Merged H2|NM_014551\BC002942|NM_033200\CHKB|NM_005198\CPT1B|NM_15224 WGTP chr22 49219663 49307552 131222\ 604272 24 CNV_ID_1390 5\ECGF1|NM_001953\CHKB|NM_152253\CPT1B|NM_004377\SCO2|NM_005 138\KLHDC7B|NM_138433\LOC440836|NM_001014440 Merged WGTP chr22 49392382 49495206 √ F MGC70863|NM_203477\ACR|NM_001097 102480 DC1927 Inter 55 CNV_ID_1391 Merged WGTP chrX 313529 532251 Variation_0821 √ F PPP2R3B|NM_013239 DC1323 Both 47 CNV_ID_1392 DC1333\ DC1336\ DC1339\ DC1329\ DC1330\ Merged CD99|NM_002414\GYG2|NM_003918\ZBED1|NM_004729\ARSF|NM_004042\ DC1332\ DC1334\ DC1335\ DC1337\ DC1338\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ Inter\ both chrX 1865728 3187726 √ PF XG|NM_175569\ARSE|NM_000047\ARSD|NM_009589\ARSH|NM_001011719 300180\ 314700 U11090_AB018328 52 CNV_ID_1393 \ARSD|NM_001669 DC1340\ DC1341\ DC1342\ DC1328\ DC1331\ Inter\ Inter\ Inter\ Inter\ Inter\ Both\ Inter\ Inter DC1327 Merged 500K EA chrX 4010786 4023267 √ F X85545_AF376803 CNV_ID_1394 Merged 500K EA chrX 6249179 6726074 Variation_0655 √ F VCX3A|NM_016379 AF167079_M86934 DC1368\ DC1369 Both\ Inter 32 CNV_ID_1395 Merged Variation_1839\ both chrX 7061134 7483618 PCR PVE STS|NM_000351 308100 DC1376\ DC1377\ DC1378 Inter\ Inter\ Inter 27 CNV_ID_1396 Variation_0362 Merged 500K EA chrX 7830174 7901660 2 CNV_ID_1397 Merged Variation_0656\ WGTP chrX 9138826 9310156 √ F TBL1X|NM_005647 108 CNV_ID_1398 Variation_2275 Merged WGTP chrX 9860872 10041747 KIAA1280|NM_015691\CLCN4|NM_001830 84 CNV_ID_1399 Merged 500K EA chrX 15418427 15483661 TMEM27|NM_020665 41 CNV_ID_1400 Merged 500K EA chrX 16946317 16971335 32 CNV_ID_1401 Merged 500K EA chrX 22628358 22749222 √ F AK098601_AY039237 43 CNV_ID_1402 DMD|NM_004018\DMD|NM_004014\DMD|NM_004007\DMD|NM_004016\DMD 300377\ 300377\ 300377\ |NM_004009\MAGEB3|NM_002365\TAB3|NM_152787\MAGEB4|NM_002367\ 300377\ 300474\ 300377\ MAGEB1|NM_002363\DMD|NM_004020\MAGEB1|NM_177415\DMD|NM_004 300473\ 300377\ 300377\ Merged Variation_1844\ 022\DMD|NM_004015\GK|NM_203391\DMD|NM_004017\WDR42B|NM_00101 300206\ 300377\ 300377\ both chrX 27751188 31356624 √ PVF 7930\DMD|NM_004023\MAGEB1|NM_177404\DMD|NM_004011\FTHL17|NM_ AK057527_AJ243874 2055 CNV_ID_1403 Variation_0241 031894\IL1RAPL1|NM_014271\DMD|NM_004021\TAB3|NM_198312\DMD|NM 300377\ 300377\ 300377\ _004006\NR0B1|NM_000475\GK|NM_000167\DMD|NM_004019\DMD|NM_00 300474\ 300377\ 300377\ 0109\DMD|NM_004012\MAGEB2|NM_002364\DMD|NM_004010\DMD|NM_00 300377\ 300377\ 300377\ 4013\CXorf21|NM_025159 300377 Variation_0962\ Variation_0822\ RP11- Merged Variation_2276\ 38O23.2|NM_205856\ZNF81|NM_007137\SSX5|NM_175723\SSX1|NM_00563 DC1429\ DC1430\ DC1431\ DC1433\ DC1434\ both chrX 47523164 47902964 PCR √ PEF 5\SSX6|NM_173357\RP11- 314998\ 312820 Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra 93 CNV_ID_1404 Variation_1847\ 38O23.2|NM_205856_copy_2\ZNF21|NM_006962\SSX5|NM_021015\ZNF21|N DC1432\ DC1435 Variation_0823\ M_001007088 Variation_2277 Merged WGTP chrX 56622090 56770769 Variation_0661 √ VF 15 CNV_ID_1405 Merged WGTP chrX 57515394 57773429 √ F 14 CNV_ID_1406 Variation_2279\ Merged CENTq_AF336876\ WGTP chrX 61984759 62329082 Variation_0363\ √ F DC1479\ DC1480 Intra\ Intra 16 CNV_ID_1407 BC059356_AF336876 Variation_0963 Merged both chrX 63292574 63919710 Variation_1851 PV MTMR8|NM_017677\KIAA1166|NM_018684 BC012399_AB032992 DC1483\ DC1482 Intra\ Inter 81 CNV_ID_1408 Merged both chrX 66282690 67102115 Variation_1852 PV AR|NM_000044\OPHN1|NM_002547\AR|NM_001011645 313700\ 313700\ 300127 BC034919_M23263 269 CNV_ID_1409 Merged DC1488\ DC1489\ DC1490\ DC1491\ DC1492\ WGTP chrX 70654274 71083437 √ F AF469635_AB082532 Intra\ Inter\ Intra\ Intra\ Intra\ Intra 265 CNV_ID_1410 DC1493 Merged 500K EA chrX 75852421 75934438 Variation_1853 PCR √ VEF AF490507_AB009391 hsa-mir-384/23/75922387/75922475/100.000000 18 CNV_ID_1411 Merged WGTP chrX 77031055 77115217 Variation_0245 V NM_001024459\PGAM4|NM_001029891_copy_2\ATP7A|NM_000052 300011 DC1517\ DC1516 Inter\ Inter 50 CNV_ID_1412 Merged 500K EA chrX 78897478 78910649 BC040437_AY035371 CNV_ID_1413 Merged BC027614_AF497480\ 500K EA chrX 88800734 89069512 TGIF2LX|NM_138960 DC1534\ DC1535 Inter\ Inter 17 CNV_ID_1414 AF497480_BC063113 Merged WGTP chrX 89260661 89673776 AF497480_BC063113 DC1537\ DC1538\ DC1539\ DC1540 Inter\ Inter\ Inter\ Inter 43 CNV_ID_1415 Merged both chrX 89957981 90252381 P AF497480_BC063113 DC1544\ DC1546\ DC1547\ DC1545 Inter\ Inter\ Inter\ Inter 7 CNV_ID_1416 Merged WGTP chrX 96741719 96861762 Variation_1861 √ VF L22650_AB037734 DC1562 Inter 103 CNV_ID_1417 Merged RAB9B|NM_016370\MGC39900|NM_194324\H2BFWT|NM_001002916\CXorf3 DC1574\ DC1571\ DC1572\ DC1573\ DC1575\ both chrX 102888546 103261206 √ PF Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra 102 CNV_ID_1418 9|NM_207318\MCART6|NM_001012755 DC1576\ DC1577 Merged WGTP chrX 104109151 104221182 IL1RAPL2|NM_017416 107 CNV_ID_1419 Merged WGTP chrX 105343681 105487922 DC1579 Intra 42 CNV_ID_1420 Merged NXT2|NM_018698\ACSL4|NM_004458\KCNE1L|NM_012282\ACSL4|NM_022 WGTP chrX 108585146 108787037 Variation_1862 √ VF 300157\ 300157 98 CNV_ID_1421 977 Merged WGTP chrX 109387916 109517626 Variation_1863 V RGAG1|NM_020769 151 CNV_ID_1422 Merged WGTP chrX 114768844 114795257 Variation_0666 V DC1583\ DC1582\ DC1584 Intra\ Intra\ Intra 9 CNV_ID_1423 Merged 500K EA chrX 115037017 115175870 AGTR2|NM_000686 300034 51 CNV_ID_1424 Merged both chrX 115553046 115883234 P AF151978_BC008729 81 CNV_ID_1425 RNF113A|NM_006978\AKAP14|NM_001008535\PEPP- Merged 2|NM_032498_copy_2\NDUFA1|NM_004541\UPF3B|NM_023010\UPF3B|NM_ WGTP chrX 118739321 119110866 √ F 080632\PEPP- DC1589\ DC1588 Intra\ Intra 48 CNV_ID_1426 2|NM_032498\OTEX|NM_139282\AKAP14|NM_178813\AKAP14|NM_0010085 34\NKAP|NM_024528 Merged Experimental Population All validation* P= both platforms, Plaform Chr Start End DGV_ID V= DGV overlap, E = RefSeq_ID OMIM_ID Ulraconserved_ID GeneDesert_ID LCR_ID LCR_Type ncRNA_ID CNC_Count CNV_ID validation freq > 1 experimental, F = freq > 1

Merged ATP1B4|NM_012069\FAM70A|NM_017938\LAMP2|NM_002294\LAMP2|NM_0 WGTP chrX 119183307 119364831 309060\ 309060 217 CNV_ID_1427 13995 Merged WGTP chrX 122690351 122888100 STAG2|NM_006603\BIRC4|NM_001167 112 CNV_ID_1428 Merged WGTP chrX 125340415 125399344 Variation_0253 V AF100772_BC035674 13 CNV_ID_1429 Merged BC035674_BC014597\ WGTP chrX 126868603 127019222 ACTRT1|NM_138289 19 CNV_ID_1430 BC014597_M88163

Merged WGTP chrX 141595220 141794235 √ F BC013318_BC040986 37 CNV_ID_1435

hsa-mir-514- 3/23/146071719/146071777/100.000000, hsa-mir- 514-2/23/146069021/146069079/100.000000, hsa- mir-514-1/23/146066330/146066388/100.000000, hsa-mir- 510/23/146059398/146059472/100.000000, hsa- mir-509/23/146047595/146047689/100.000000, Merged Variation_1867\ 500K EA chrX 145829455 146494249 V Y08902_S65791 hsa-mir- 120 CNV_ID_1436 Variation_0670 508/23/146023976/146024091/100.000000, hsa- mir-507/23/146018047/146018141/100.000000, hsa-mir- 506/23/146017783/146017907/100.000000, hsa- mir-513-2/23/146012889/146013016/100.000000, hsa-mir-513- 1/23/146000526/146000655/100.000000

RBMY1B|NM_001006121_copy_3\RBMY1E|NM_001006118\RBMY1J|NM_001 006117_copy_2\RBMY1A1|NM_001007526_copy_4\PRY2|NM_001002758\RB MY1D|NM_001006120_copy_2\RBMY1D|NM_001006120_copy_3\RBMY1F|N DC1151\ DC1152\ DC1153\ DC1134\ DC1135\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Variation_0831\ M_152585_copy_2\RBMY1A1|NM_001007526_copy_2\RBMY1D|NM_0010061 DC1136\ DC1137\ DC1139\ DC1140\ DC1142\ Merged 20\RBMY1B|NM_001006121_copy_4\RBMY1A1|NM_005058_copy_2\RBMY1 Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ WGTP chrY 21771803 22936103 Variation_0833\ √ F DC1144\ DC1145\ DC1146\ DC1148\ DC1154\ 326 CNV_ID_1446 E|NM_001006118_copy_2\RBMY1A1|NM_005058_copy_3\RBMY1F|NM_1525 Intra\ Intra\ Intra\ Intra\ Intra\ Intra\ Both\ Intra\ Variation_0832 DC1155\ DC1156\ DC1157\ DC1138\ DC1143\ 85\RBMY1A1|NM_001007526_copy_3\RBMY1A1|NM_005058\PRY|NM_00467 Both 6\RBMY1A1|NM_001007526\RBMY1D|NM_001006120_copy_4\RBMY1B|NM_ DC1147\ DC1149\ DC1150\ DC1141\ DC1158 001006121_copy_2\RBMY1E|NM_001006118_copy_3\RBMY1J|NM_00100611 7\RBMY1B|NM_001006121

Supplementary Table 12: * CNVRs were validated based on overlap between 500KEA and WGTP, locus specific assays (i.e. experimental validation), being found in more than one individual (population frequency > 1), or overlap with the literature, based on citations in the Database of Genomic Variants (http://projects.tcag.ca/variation/). Supplementary Table 13A: Summary of Genomic Features Analysis Total Overlapping Overlapping Percent Enrichment or Event Overlapping Overlapping Overlapping Overlapping Event Overlapping Overlapping Event Overlapping Overlapping Event Overlapping Overlapping CNV Set Data Type Feature Total CNVs p Value Event Type Features Features CNVs Overlap Impoverishment Type events Feature events Feature Type events Feature Type events Feature Type events Feature

Ends Recombination Hotspots 48628 1251 2406 842 35.00 0.0020 impoverishment CCDS 14815 980 980 308 31.43 0.0000 impoverishment Ensembl Exons 237787 11539 980 445 45.41 0.0000 impoverishment Ensembl Genes 21999 1576 980 518 52.86 0.0030 impoverishment miRNAs & snoRNAs 772 29 980 13 1.33 0.1360 CNCs 1220572 55937 980 925 94.39 0.0000 enrichment Database of Genomic Variants 2172 857 980 276 28.16 0.0000 enrichment tcagLCR 4139 929 980 202 20.61 0.0000 enrichment Telomere/Centromere 86 47 980 57 5.82 0.0001 enrichment UltraConserved 481 16 980 6 0.61 0.9929 impoverishment Fortna HLS (Gain/Loss) 263 53 980 26 2.65 0.0000 enrichment Regions Eichler ptrOnly Dup 202 61 980 47 4.80 0.0000 enrichment Eichler hsOnlyDup 515 189 980 71 7.24 0.0000 enrichment OMIM Genes 1961 112 980 87 8.88 0.9970 impoverishment RefSeq Genes 18333 1139 980 478 48.78 0.9996 impoverishment Gene Desert 765 286 980 393 40.10 0.0000 enrichment Cen/Telomere noLCR 778 16 778 17 2.19 N/A RefSeq noLCR 778 512 778 326 41.90 N/A DupPair (number is duplicated) 23489 9076 980 189 19.29 0.0000 enrichment 500K EA CNVs Unmapped sequence clones N/A N/A 980 45 4.59 N/A WSSD only 3109 341 980 101 10.31 0.0000 enrichment Voight_sel 752 69 980 53 5.41 CCDS 14816 1704 1203 591 49.13 0.0000 impoverishment dup 219 del 216 del/dup 63 complex 78 multiallelic 15 Ensembl Exons 237787 30083 1203 846 70.32 0.2090 dup 318 del 311 del/dup 84 complex 115 multiallelic 18 Ensembl Genes 21999 3301 1203 854 70.99 0.3450 dup 322 del 315 del/dup 84 complex 115 multiallelic 18 miRNAs & snoRNAs 772 58 1203 32 2.66 0.0400 dup 15 del 10 del/dup 2 complex 5 multiallelic 0 CNCs 1220572 76642 1203 1104 91.77 0.0000 enrichment dup 420 del 440 del/dup 97 complex 128 multiallelic 19 Fortna HLS (Gain/Loss) 263 53 1203 71 5.90 0.0000 enrichment dup 35 26 del 5 5 del/dup 8 25 complex 18 19 multiallelic 5 7 Eichler Hs Specific Dup 202 189 1203 154 12.80 0.0000 enrichment dup 66 94 del 29 48 del/dup 23 58 complex 26 51 multiallelic 10 23 Events Eichler Ptr Specific Dup 515 61 1203 70 5.82 0.0000 enrichment dup 30 30 del 16 20 del/dup 8 9 complex 13 9 multiallelic 3 3 UltraConserved 481 16 1203 6 0.50 0.9931 impoverishment dup 4 14 del 2 2 del/dup 0 0 complex 0 0 multiallelic 0 0 tcagLCR 4139 891 1203 328 27.27 0.0000 enrichment dup 140 404 del 101 307 del/dup 41 238 complex 35 150 multiallelic 11 74 WSSD only 3109 325 1203 161 13.38 0.0000 enrichment dup 73 196 del 36 68 del/dup 23 75 complex 21 68 multiallelic 8 25 OMIMgenes 1961 101 1203 98 8.15 0.8166 dup 39 47 del 39 43 del/dup 12 16 complex 8 8 multiallelic 0 0 OMIMdisease 2025 101 1203 98 8.15 N/A dup 39 47 del 39 43 del/dup 12 16 complex 8 8 multiallelic 0 0 RefSeq 18333 1085 1203 599 49.79 0.0000 enrichment dup 242 511 del 269 431 del/dup 43 183 complex 34 77 multiallelic 11 28 Voight_sel 752 66 1203 53 4.41 0.2596 Events + Ends* Gaps 345 82 1203 84 6.98 enrichment

Ends Recombination Hotspots 48628 3968 2232 1464 65.59 0.1210 CCDS 14815 1704 913 499 54.65 0.0950 Ensembl Exons 237787 29846 913 668 73.17 0.0490 enrichment Ensembl Genes 21999 3217 913 672 73.60 0.0920 miRNAs & snoRNAs 772 57 913 29 3.18 0.3570 CNCs 1220572 116678 913 903 98.90 0.0000 enrichment Database of Genomic Variants 2172 1083 913 331 36.25 0.0000 enrichment tcagLCR 4139 1519 913 308 33.73 0.0000 enrichment Telomere/Centromere 86 60 913 77 8.43 0.0000 enrichment UltraConserved 481 48 913 17 1.86 1.0000 impoverishment Fortna HLS (Gain/Loss) 263 94 913 40 4.38 0.0000 enrichment Regions Eichler Ptr Specific Dup 202 88 913 57 6.24 0.0000 enrichment Eichler Hs Specific Dup 515 317 913 118 12.92 0.0000 enrichment OMIM Genes 1961 251 913 184 20.15 0.1558 RefSeq Genes 18333 2561 913 626 68.57 0.2785 Gene Desert 765 303 913 363 39.76 0.0678 Cen/Telomere noLCR 605 16 605 17 2.81 N/A RefSeq noLCR 605 1091 605 371 61.32 N/A DupPair (number is duplicated) 23489 14529 913 293 32.09 0.0000 enrichment WTGP CNVs Unmapped sequence clones N/A N/A 913 91 9.97 N/A WSSD only 3109 649 913 196 21.47 0.0000 enrichment Voight_sel 752 96 913 72 7.89 0.5248 CCDS 14531 1640 1116 561 50.27 0.3930 dup 205 del 207 del/dup 60 complex 74 multiallelic 15 Ensembl Exons 237787 29117 1116 797 71.42 0.0010 enrichment dup 298 del 296 del/dup 79 complex 106 multiallelic 18 Ensembl Genes 21999 3152 1116 805 72.13 0.0010 enrichment dup 303 del 299 del/dup 79 complex 106 multiallelic 18 miRNAs & snoRNAs 772 58 1116 32 2.87 0.4210 dup 15 del 10 del/dup 2 complex 5 multiallelic 0 CNCs 1220572 133515 1116 1045 93.64 0.0000 enrichment dup 394 del 423 del/dup 91 complex 118 multiallelic 19 Fortna HLS (Gain/Loss) 263 94 1116 78 6.99 0.0000 enrichment dup 16 30 del 13 20 del/dup 18 38 complex 25 56 multiallelic 6 21 Eichler Hs Specific Dup 202 319 1116 197 17.65 0.0000 enrichment dup 58 87 del 36 57 del/dup 45 139 complex 45 101 multiallelic 13 19 Events Eichler Ptr Specific Dup 515 88 1116 79 7.08 0.0000 enrichment dup 32 46 del 11 15 del/dup 16 25 complex 18 19 multiallelic 2 2 UltraConserved 481 48 1116 17 1.52 0.9905 impoverishment dup 7 27 del 9 20 del/dup 1 1 complex 0 0 multiallelic 0 0 tcagLCR 4139 1519 1116 472 42.29 0.0000 enrichment dup 176 563 del 105 354 del/dup 80 396 complex 93 440 multiallelic 18 73 WSSD only 3109 649 1116 238 21.33 0.0000 enrichment dup 83 283 del 62 143 del/dup 41 134 complex 41 109 multiallelic 11 27 OMIMgenes 1961 252 1116 211 18.91 0.0007 enrichment dup 64 82 del 85 113 del/dup 33 43 complex 26 33 multiallelic 3 4 OMIMdisease 2025 252 1116 211 18.91 N/A dup 64 82 del 85 113 del/dup 33 43 complex 26 33 multiallelic 3 4 RefSeq 18333 2561 1116 776 69.53 0.0000 enrichment dup 284 968 del 294 936 del/dup 80 434 complex 100 429 multiallelic 18 101 Voight_sel 752 96 1116 73 6.54 0.4766 Events + Ends* Gaps 345 161 1116 146 13.08 enrichment

CCDS 14815 1785 1447 616 42.57 0.0630 Ensembl Exons 237787 32061 1447 825 57.01 0.0180 impoverishment Ensembl Genes 21999 3876 1447 901 62.27 0.1240 miRNAs & snoRNAs 772 67 1447 28 1.94 0.1510 CNCs 1220572 130353 1447 1393 96.27 0.0000 enrichment Database of Genomic Variants 2172 1251 1447 418 28.89 0.0000 enrichment tcagLCR 4139 1643 1447 343 23.70 0.0000 enrichment Telomere/Centromere 86 69 1447 89 6.15 0.0001 enrichment UltraConserved 481 50 1447 18 1.24 1.0000 impoverishment Fortna HLS (Gain/Loss) 263 96 1447 42 2.90 0.0000 enrichment Merged CNVs Regions Eichler Ptr Specific Dup 202 99 1447 64 4.42 0.0000 enrichment Eichler Hs Specific Dup 515 327 1447 120 8.29 0.0000 enrichment OMIM Genes 1961 285 1447 212 14.65 0.5985 RefSeq Genes 18333 2908 1447 836 57.77 0.9617 impoverishment Gene Desert 765 407 1447 587 40.57 0.0000 enrichment Cen/Telomere noLCR 1104 23 1104 23 2.08 N/A RefSeq noLCR 1104 1319 1104 557 50.45 N/A DupPair (number is duplicated) 23489 15287 1447 327 22.60 0.0000 enrichment Unmapped sequence clones N/A N/A 1447 95 6.57 N/A WSSD only 3109 704 1447 219 15.13 0.0000 enrichment Voight_sel 752 125 1447 95 6.57 0.4098

*Events and the corresponding ends for the WGTP and the 500K EA platforms, respectively, were searched for overlap with gaps. Unique records for events and gaps were counted. Supplementary Table 13B: Validation summary of UCE elements

merged freq in qPCR results # uce chr start end platform gain/loss uce locations tested CNPID population uc element CNV region elements uc3 loss confirmed uc.3 chr1 10685430 10685655 11 chr1 10676768 10989413 WGTP loss 12 CNV confirmed 8 uc9 no change uc.9 chr1 10859675 10859877 170 chr2 104052123 104218620 WGTP gain 1 uc67 no change CNV confirmed 1 uc.67 chr2 104195243 104195460 429 chr5 32281118 32774401 WGTP loss 1 uc151 no change CNV confirmed 1 uc.151 chr5 32415893 32416107 590 chr7 972336 1463188 WGTP loss 1 uc204 no change CNV confirmed 1 uc.204 chr7 1039144 1039346 764 chr9 16631966 16799203 WGTP loss 1 uc252 no change no change 1 uc.252 chr9 16700752 16700983 790 chr9 78664404 78703638 500K EA loss 3 uc260 no change CNV confirmed 1 uc.260 chr9 78701977 78702208 859 chr10 77090565 77440455 both gain 1 uc287 no change CNV confirmed 2 uc.287 chr10 77165948 77166205 870 chr10 102141840 102370625 both gain 3 uc293 gain confirmed CNV confirmed 3 uc.293 chr10 102362658 102362901 1224 chr17 32049873 32104672 both gain/loss 4 uc410 no change no change 1 uc.410 chr17 32086342 32086561 1232 chr17 43957672 44191836 both gain 3 uc415 no change CNV confirmed 3 uc.415 chr17 44018904 44019111 1260 chr18 32304033 32735865 both gain 1 uc429 no change CNV confirmed 1 uc.429 chr18 32734538 32734776

--See Supplementary Table 4 for details of qPCR Supplementary Table 13C: Data Sources for all Genomic Features Analyses Feature Type Data Source Data Description

UCSC track of recombination hotspots derived from HapMap release 16a data and data from Perlegen published in Hinds et Recombination Hotspots http://genome.ucsc.edu al. (2005). The recombination hotspots were ascertained by Simon Myers from the Mathematical Genetics Group at the University of Oxford. CCDS http://www.ncbi.nlm.nih.gov/CCDS/ Consensus CDS gene set, version Hs35.1.03032005 Ensembl Exons www.ensembl.org All exons from all protein coding Ensembl transcripts from release 37.35j Ensembl Genes www.ensembl.org Extents of known and novel protein coding genes from Ensembl release 37.35j UCSC track comprising miRNA database (release 8.1) and snoRNA-LBME-db (version 2) aligned to the NCBI35 verions of miRNAs & snoRNAs http://genome.ucsc.edu the genome using Blat. Generated using the method of Siepel et al (2005 Genome Res 15: 1034-1050) using the top 5% of the conserved genome CNCs as available at the UC Santa Cruz browser (http://genome.ucsc.edu) and filtered against the ensembl gene set to remove elements that overlapped transcript sequences. Database of Genomic Variants http://projects.tcag.ca/variation/ CNVs - Database of Genomic Variants – Previously identified CNVs tcagLCR http://projects.tcag.ca/humandup/ Segmental duplications from the Human Genome segmental Duplication Database Pericentromeric sequences were defined as regions within 1Mb of centromeric gaps in the NCBI assembly, while Telomere/Centromere genome.ucsc.edu subtelomeric regions encompassed 500Kb of sequence from annotated telomere ends (Bailey et al, 2001 Genome Research). UltraConserved http://www.cse.ucsc.edu/%7Ejill/ultra.html Regions as described in supplementary materials of Bejerano et al. (2004) Fortna HLS (Gain/Loss) Fortna A, et al. PLoS Biol. 2004 Jul;2(7):E207 Regions as described in supplementary material of Fortna et al. (2004) Eichler ptrOnly Dup Cheng Z, et al. Nature. 2005 Sep 1;437(7055):88-93 Regions described in Cheng et al. (2005). Coordinates were obtained directly from the authors. Eichler hsOnlyDup Cheng Z, et al. Nature. 2005 Sep 1;437(7055):88-93 Regions described in Cheng et al. (2005). Coordinates were obtained directly from the authors. OMIM Genes http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi Genes associated with a defined disease phenotype (OMIM morbid map) were downloaded from NCBI. RefSeq Genes http://genome.ucsc.edu RefSeq dataset downloaded from UCSC Genome Browser Gene Desert http://genome.ucsc.edu Regions > 500kb devoid of entries in the “Known genes” track at UCSC Cen/Telomere noLCR Non-LCR related CNVs compared to Telomere/Centromere dataset RefSeq noLCR Non-LCR related CNVs compared to the RefSeq gene dataset Information about related duplicon pairs was extracted from the Segmental duplications from the Human Genome segmental DupPair http://projects.tcag.ca/humandup/ Duplication Database Sequences were identified to have similarity to unmapped sequence clones based on overlap with LCRs having paralogous Unmapped sequence clones http://projects.tcag.ca/humandup/ sequences mapping to the random chromosomes. WSSD only http://genome.ucsc.edu UCSC track of WSSD regions were used, and those not overlapping tcagLCR entries were used for this analysis Voight_sel Voight BF, et al. PLoS Biol. 2006 Mar;4(3):e72 Regions as described in supplementary material of Voight et al. Gaps http://genome.ucsc.edu All types assembly gaps were used for this analysis. Supplementary Table 14: Homozygous deletions detected by 500K EA platform # without 500KEA Length McCaroll Refseq Genes # Homozyous # Heterozygous Location significant # duplicated3 event ID (Kbp)1 overlap 2 involved deleted 3 deleted3 change3 30 chr1:94846203-94863834 17.6 1 4 265 0 72 chr1:193555270-193618427 63.2 CFHL4 1 6 261 2 133 chr2:89740700-89951815 211.1 √ 3 33 228 6 268 chr4:34604640-34638958 34.3 10 46 214 0 329 chr5:17649730-17675214 25.5 1 11 258 0 390 chr6:29967224-30014028 46.8 13 62 195 0 418 chr6:77496587-77509523 12.9 9 46 214 1 419 chr6:79036117-79084209 48.1 5 60 205 0 542 chr8:13659506-13696428 36.9 1 26 243 0 557 chr8:39326152-39440685 114.5 √ 21 71 178 0 590 chr9:582757-597816 15.1 √ ANKRD15 1 7 262 0 641 chr9:101796515-101801974 5.5 3 67 197 3 694 chr10:58575853-58606498 30.6 1 8 261 0 696 chr10:59242689-59439185 196.5 1 0 269 0 OR52N5, 727 chr11:5743360-5765806 22.4 11 57 202 0 OR52N1 732 chr11:18905796-18915387 9.6 MRGPRX1 1 24 218 27 755 chr11:55130549-55176235 45.7 OR4P4, OR4S2 16 60 175 19 765 chr11:79650581-79660804 10.2 1 6 263 0 789 chr11:104428916-104436371 7.5 1 18 251 0 813 chr12:27539678-27542418 2.7 √ 1 1 268 0 901 chr14:40684540-40706033 21.5 7 41 222 0 904 chr14:43576461-43600178 23.7 1 10 259 0 972 chr15:32537861-32602617 64.8 √ 3 48 212 7 1034 chr16:79536934-79539177 2.2 1 30 238 1 1084 chr18:64897804-64903434 5.6 √ 2 27 241 0 1091 chr19:20424240-20490118 65.9 1 34 235 0 1120 chr19:59422014-59435029 13.0 LILRB3, LILRA6 2 25 216 27 KIR3DL1, 1122 chr19:59991881-60007809 15.9 KIR3DP1, 1 22 243 4 KIR2DL4 1134 chr20:15259431-15265978 6.5 C20ORF133 1 8 261 0 1153 chr21:22577771-22586139 8.4 22 40 208 0 X2-4 chr23:7211131-7355904 144.8 1 0 269 0 X2-6 chr23:47627524-47700051 72.5 1 0 266 3 X2-8 chr23:75918345-75923773 5.4 1 0 269 0 Supplementary Table 14: Homozygous deletions at 33 loci found using the 500K EA platform Immunoglobulin loci were removed. All homozygous deletions listed were validated by PCR, an additional 4 loci were identified by not be validated (see supplementary methods). 1 90% borders (minimal length) are listed 2 Regions overlapping with those described in a previous report by McCarroll et al. 3 These numbers are based on CNV calls using the 500KEA platform. Note that the precise evaluation of Hardy-Weinburg equilibrium requires robust genotypes and is confounded at these loci due to the presence of duplicated alleles at some loci and incomplete power to detect heterozygous samples. Supplementary Table 15 Gene ontology analysis of all genes overlapping CNVs as defined by the merged regions from the WGTP and 500K EA platforms Enriched GO terms Total Subtotal # of ref. # of test Expected # GO_Term_ID GO_Term reference gene in gene in the gene in the Enrichment P-value of gene gene dataset GO term GO term GO:0007155* cell adhesion 14742 2145 776 211 112.9 1.869 3.42E-21 GO:0007156 homophilic cell adhesion 14742 2145 134 65 19.5 3.334 7.30E-21 GO:0007606 sensory perception of chemical stimulus 14742 2145 351 116 51.1 2.271 7.81E-19 GO:0007608 sensory perception of smell 14742 2145 322 105 46.9 2.241 1.06E-16 GO:0050877 neurophysiological process 14742 2145 845 208 122.9 1.692 1.18E-15 GO:0016337 cell-cell adhesion 14742 2145 217 78 31.6 2.47 2.55E-15 GO:0004984 olfactory receptor activity 14742 2145 386 108 56.2 1.923 3.51E-12 GO:0016339 calcium-dependent cell-cell adhesion 14742 2145 20 17 2.9 5.842 4.08E-12 GO:0007600 sensory perception 14742 2145 622 151 90.5 1.668 3.83E-11 GO:0050808 synapse organization and biogenesis 14742 2145 21 15 3.1 4.909 6.03E-09 GO:0004930 G-protein coupled receptor activity 14742 2145 862 185 125.4 1.475 1.12E-08 GO:0005509 calcium ion binding 14742 2145 819 177 119.2 1.485 1.40E-08 GO:0007416 synaptogenesis 14742 2145 20 14 2.9 4.811 2.99E-08 GO:0001584 rhodopsin-like receptor activity 14742 2145 908 184 132.1 1.393 8.45E-07 GO:0007268* synaptic transmission 14742 2145 242 62 35.2 1.761 3.76E-06 GO:0019226* transmission of nerve impulse 14742 2145 236 60 34.3 1.747 6.95E-06 GO:0043062 extracellular structure organization and biogenesis 14742 2145 40 17 5.8 2.921 1.72E-05 GO:0030198 extracellular matrix organization and biogenesis 14742 2145 41 17 6 2.85 2.54E-05 GO:0009613 response to pest, pathogen or parasite 14742 2145 532 111 77.4 1.434 3.78E-05 GO:0019864 IgG binding 14742 2145 7 6 1 5.891 5.78E-05 GO:0001848 complement binding 14742 2145 5 5 0.7 6.873 6.50E-05 GO:0051707 response to other organism 14742 2145 565 114 82.2 1.387 0.000128926 GO:0016798* hydrolase activity, acting on glycosyl bonds 14742 2145 146 38 21.2 1.789 0.000189046 GO:0007267 cell-cell signaling 14742 2145 532 107 77.4 1.382 0.000233 GO:0042742 defense response to bacteria 14742 2145 75 23 10.9 2.108 0.000279192 GO:0009617 response to bacteria 14742 2145 90 26 13.1 1.985 0.000333663 GO:0008146 sulfotransferase activity 14742 2145 50 17 7.3 2.337 0.000450851 GO:0019865 immunoglobulin binding 14742 2145 15 8 2.2 3.665 0.000489299 GO:0006044* N-acetylglucosamine metabolism 14742 2145 22 10 3.2 3.124 0.0005023 GO:0006959 humoral immune response 14742 2145 158 39 23 1.696 0.000502355 GO:0006956 complement activation 14742 2145 39 14 5.7 2.467 0.000763462 GO:0006041* glucosamine metabolism 14742 2145 23 10 3.3 2.988 0.000773515 GO:0006955 immune response 14742 2145 873 160 127 1.26 0.000880225 GO:0050909 sensory perception of taste 14742 2145 28 11 4.1 2.7 0.001180919 GO:0007399* nervous system development 14742 2145 471 92 68.5 1.342 0.00161494 GO:0009607 response to biotic stimulus 14742 2145 966 173 140.6 1.231 0.001617443 GO:0016782 transferase activity, transferring sulfur-containing groups 14742 2145 51 16 7.4 2.156 0.001745346 GO:0007565 pregnancy 14742 2145 51 16 7.4 2.156 0.001745346 GO:0005275* amine transporter activity 14742 2145 70 20 10.2 1.964 0.001802584 GO:0009620 response to fungi 14742 2145 14 7 2 3.436 0.001829599

* Indicates that the GO term remains as one of the 40 most significant GO terms also after CNVs overlapping segmental duplications are removed.

Gene ontology analysis of all genes overlapping CNVs as defined by the merged regions from the WGTP and 500K EA platforms Impoverished GO terms Total Subtotal # of ref. # of test Expected # GO_Term_ID GO_Term reference gene in gene in the gene in the Enrichment P-value of gene gene dataset GO term GO term

GO:0016310 phosphorylation 14742 2145 640 62 93.1 0.666 7.11147E-05 GO:0006468 protein amino acid phosphorylation 14742 2145 546 52 79.4 0.655 0.000138954 GO:0044249 cellular biosynthesis 14742 2145 1011 110 147.1 0.748 0.000162556 GO:0008283 cell proliferation 14742 2145 554 54 80.6 0.67 0.000240185 GO:0005581 collagen 14742 2145 50 1 7.3 0.137 0.000379644 GO:0006796 phosphate metabolism 14742 2145 790 85 114.9 0.739 0.000536448 GO:0006793 phosphorus metabolism 14742 2145 787 85 114.5 0.742 0.000623394 GO:0004674 protein serine/threonine kinase activity 14742 2145 459 45 66.8 0.674 0.000846421 GO:0007200 G-protein signaling, coupled to IP3 second messenger (ph 14742 2145 59 2 8.6 0.233 0.001017116 GO:0005840 ribosome 14742 2145 285 25 41.5 0.603 0.001125856 GO:0006633 fatty acid biosynthesis 14742 2145 58 2 8.4 0.237 0.001172657 GO:0016772 transferase activity, transferring phosphorus-containing gro 14742 2145 898 101 130.7 0.773 0.001209492 GO:0005506 iron ion binding 14742 2145 239 20 34.8 0.575 0.001287002 GO:0016491 oxidoreductase activity 14742 2145 933 106 135.8 0.781 0.001418496 GO:0006457 protein folding 14742 2145 224 19 32.6 0.583 0.002081994 GO:0004672 protein kinase activity 14742 2145 585 63 85.1 0.74 0.00254539 GO:0016773 phosphotransferase activity, alcohol group as acceptor 14742 2145 648 71 94.3 0.753 0.002561391 GO:0019752 carboxylic acid metabolism 14742 2145 420 43 61.1 0.704 0.003259655 GO:0016301 kinase activity 14742 2145 882 102 128.3 0.795 0.003353211 GO:0006082 organic acid metabolism 14742 2145 418 43 60.8 0.707 0.003655734 GO:0009059 macromolecule biosynthesis 14742 2145 655 73 95.3 0.766 0.003863272 GO:0006690 icosanoid metabolism 14742 2145 35 1 5.1 0.196 0.004044692 GO:0004428 inositol or phosphatidylinositol kinase activity 14742 2145 34 1 4.9 0.202 0.004735281 GO:0008289 lipid binding 14742 2145 271 26 39.4 0.659 0.005547311 GO:0045934 negative regulation of nucleobase, nucleoside, nucleotide a 14742 2145 176 15 25.6 0.586 0.005557385 GO:0003735 structural constituent of ribosome 14742 2145 219 20 31.9 0.628 0.00591614 GO:0031324 negative regulation of cellular metabolism 14742 2145 201 18 29.2 0.615 0.006214695 GO:0045926 negative regulation of growth 14742 2145 32 1 4.7 0.215 0.006490097 GO:0051082 unfolded protein binding 14742 2145 156 13 22.7 0.573 0.006572283 GO:0016327 apicolateral plasma membrane 14742 2145 57 3 8.3 0.362 0.007219349 GO:0051276 chromosome organization and biogenesis 14742 2145 300 30 43.7 0.687 0.007312764 GO:0007001 chromosome organization and biogenesis (sensu Eukaryot 14742 2145 349 36 50.8 0.709 0.007349526 GO:0006366 transcription from RNA polymerase II promoter 14742 2145 469 51 68.2 0.747 0.007371314 GO:0015267 channel or pore class transporter activity 14742 2145 373 39 54.3 0.719 0.007465253 GO:0000785 chromatin 14742 2145 172 15 25 0.599 0.007641712 GO:0042127 regulation of cell proliferation 14742 2145 291 29 42.3 0.685 0.007658785 GO:0006412 protein biosynthesis 14742 2145 668 77 97.2 0.792 0.008569552 GO:0007049 cell cycle 14742 2145 933 112 135.8 0.825 0.008779777 GO:0048511 rhythmic process 14742 2145 30 1 4.4 0.229 0.008894804 GO:0015268 alpha-type channel activity 14742 2145 353 37 51.4 0.72 0.009272144

Supplementary Table 15: The gene ontology analysis was performed using the GOTree Machine as previously described Zhang et al. (BMC Bioinformatics 5:16, 2004). Significance values for GO categories were estimated using the hypergeometric test. GO terms level 1-8 were included in the analysis, representing a total of 18,496 unique GO IDs. There was no correction applied for multiple testing in this analysis. The algorithm was implemented on a local server as the web based tool web tool is limited to 500 entries. Supplementary Table 16: Overlap of CNVs with OMIM disease genes Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive? Chr. 1

Homozygous mutant mice display a variety of defects including hippocampal dysgenesis, Tumour supressor; imprinted May play a role in certain cancers chr1:3,608,198- chr1:3,592,286- 3' end (12 of 13 hydrocephalus, chronic infections Gain is not expected to cause a 1p36.32 6 *601990 tumor protein p73 TP73 Cancer Affy 1 Gain 1 CEU No (tissue-specific maternal (in combination with p53), but no 3,678,693 3,673,013 exons) and inflammation, abnormal phenotype expression) mutations have been reported pheromone sensory pathways, eye abnormalities, impaired growth, and female infertility

Homozygous mutant mice are lethal Charcot-Marie-Tooth N-terminal-type motor protein (2 at birth (nervous system defects); chr1:10,172,336- kinesin family chr1:10,205,097- Mutation has been found to cause Loss of this gene would expect to 1p36.22 10 *605995 KIF1B Disease, Axonal, Type AD Sanger entire gene 2 Loss 2 YRI No major isoforms with different cargo- heterozygotes have transport/motor 10,516,820 member 1B 10,375,920 CMT type 2A1 cause some phenotype 2A1 binding domain) defect and muscle weakness similar to human neuropathies

Missense mutation can cause Zellweger syndrome; chr1:10,172,336- peroxisomal chr1:10,469,285- Membrane-bound peroxisomal Homozygous disruption of this Gain of first 2 exons is not 1p36.22 10 *601791 PEX14 Zellweger Syndrome AR Sanger 5' end (2 of 9 exons) 1 Gain 1 JPT WSSD overexpression in normal skin 10,516,820 biogenesis factor 14 10,625,079 protein locus results in embryonic lethality expected to cause a phenotype fibroblasts led to some peroxisome mislocalization

succinate chr1:16,509,639- chr1:17,090,559- Paraganglioma 4; Affy/Sanger Iron sulfur protein, subunit of Mutations have been reported in Inactivation may lead to greater 1p36.13 15 *185470 dehydrogenase SDHB entire gene 4 Loss 1 JPT, 3 YRI No None 17,229,287 17,125,952 Pheochromacytoma (Sanger) complex II in mitochondria paragangliomas and other cancers susceptibility to some cancers complex, subunit B

Homozygotes for targeted null mutations exhibit Missense mutations found in alkaline hypophosphatemia, growth chr1:21,481,490- chr1:21,581,175- Alkaline phosphatase of liver, bone, hypophosphatasia (can be AD or Deletion of this gene may have 1p36.12 16 *171760 phosphatase, ALPL Hypophosphatasia AR and AD Sanger entire gene 1 Gain, 1 Loss 2 YRI No impairment, elevated pyridoxal 5'- 21,687,720 21,650,208 kidney and skin fibroblasts AR; AD may be due to dominant- some clinical relevance liver/bone/kidney phosphate levels, seizures, poorly negative effects) mineralized bone and teeth, and preweaning lethality

Schwartz-Jampel syndrome, Type 1; Heparan sulfate proteoglycan; Mutations can cause Schwartz- 40% of homozygous mice died at Deletion will probably not cause chr1:21,967,827- heparan sulfate chr1:21,894,043- 5' end (2 of 97 1p36.12 17 *142461 HSPG2 Dyssegmental AR Sanger 1 Loss 1 CEU WSSD component of basement Jampel syndrome (a rare AR embryonic day 10.5 with defective phenotype unless associated with 22,158,163 proteoglycan 2 22,009,053 exons) Dysplasia, Silverman- membranes disease) cephalic development additional mutation Handmaker Type

Homozygous mice are viable and fertile, but developed spasticity (a Small glycoprotein that removes Deletion will probably not cause chr1:39,894,236- palmitoyl-protein chr1:40,207,477- Ceroid Lipofucinosis, 'clasping' phenotype) at a median 1p34.2 23 *600722 PPT1 AR Sanger entire gene 1 Loss 1 YRI No palmitate groups from cysteine Mutations cause CLN1 phenotype unless associated with 40,329,525 thioesterase 1 40,232,061 Neuronal, 1 age of 21 weeks (motor residues in lipid-modified proteins additional mutation abnormalities progressed, leading to death at 10 months)

amylo-1, 6- Involved in glycogen degradation Deletion will probably not cause chr1:100,071,676- glucosidase, 4- chr1:100,027,661- Glycogen storage 3' end (10 of 34 Mutations can cause glycogen 1p21.2 42 +232400 AGL AR Sanger 1 Loss 1 CEU No and has two independent catalytic None phenotype unless associated with 100,210,363 alpha- 100,101,597 disease, Type III exons) storage disease activities additional mutation glucanotransferase

Susceptibilty to insulin- dependent diabetes Protein tyrosine phosphatases 22; SNP associated with insulin- Homozygous mice are viable with protein tyrosine 1p13.2- chr1:112,869,177- chr1:114,068,481- mellitus, rheumatoid Affy/Sanger 1 Loss (S) 1 YRI (S) may be an effector and/or regulator dependent diabetes mellitus and some differences in immune cells; No indication that this gene is 52 *600716 phosphatase, non- PTPN22 entire gene No 1p13.1 116,453,414 114,126,376 arthritis, systemic lupus (Both) 1 Loss (A) 1 YRI (A) of CSK in T cells and other R.arthritis (+ other autoimmune older mice developed splenomegaly dosage sensitive receptor type 22 erythematosus, + other hematopoietic cells disorders) and lymphadenopathy autoimmune

One of the predominant molecular Also called transcriptional lesions in papillary thyroid 1p13.2- chr1:112,869,177- tripartite motif- chr1:114,647,443- papillary thyroid Affy/Sanger 1 Loss (S) 1 YRI (S) intermediary factor-1-gamma No indication that this gene is 52 *605769 TRIM33 entire gene No carcinomas occurs occurs when None 1p13.1 116,453,414 containing 33 114,765,823 carcinomas (Both) 1 Loss (A) 1 YRI (A) (TIF1G); thought to be a dosage sensitive this gene is fused with RET transcriptional corepressor protooncogene

catalyzes the deamination of AMP adenosine Mutations cause myopathy; 1p13.2- chr1:112,869,177- chr1:114,927,764- myopathy (AMPD Affy/Sanger 1 Loss (S) 1 YRI (S) to IMP in skeletal muscle and plays Deletion may unmask relatively 52 +102770 monophosphate AMPD1 AR entire gene No heterozygotes may be common for None 1p13.1 116,453,414 114,950,218 deficiency) (Both) 1 Loss (A) 1 YRI (A) an important role in the purine common recessive allele deaminase 1 this gene (>10% in caucasians) nucleotide cycle

Mice homozygous for a targeted mutation are viable and fertile with no gross morphological or histological abnormalities, or multiple myeloid neuroblastoma RAS defects in peripheral blood cell May predisopose for cancers 1p13.2- chr1:112,869,177- chr1:114,961,627- myeloma; primary Affy/Sanger 1 Loss (S) 1 YRI (S) Oncogene that is part of the RAS Mutations play a major role in 52 *164790 viral (v-ras) NRAS entire gene No populations; loss (-/- or +/-) when associated with other 1p13.1 116,453,414 114,971,557 plasma cell leukemia; (Both) 1 Loss (A) 1 YRI (A) gene family oncogenesis of certain cancers oncogene homolog together with RB1 +/- give findings mutations colorectal cancer that suggest that the loss of the Nras in certain cellular contexts can promote malignant tumor progression

Mutations (common in affected Deletion will probably not cause 1p13.2- chr1:112,869,177- thyroid stimulating chr1:115,284,457- Affy/Sanger 1 Loss (S) 1 YRI (S) The beta chain of the thyroid- families, but uncommon in general 52 *188540 TSHB thyrotropin deficiency AR entire gene No None phenotype unless associated with 1p13.1 116,453,414 hormone, beta 115,288,983 (Both) 1 Loss (A) 1 YRI (A) stimulating hormone population) can cause thyrotropin additional mutation deficiency

A member of the NGF-beta family and encodes a secreted protein Homozygous null mutants exhibit which homodimerizes and is elevated pain threshold, loss of incorporated into a larger complex; neurons in both sensory and hereditary sensory and Mutations cause a rare recessive Deletion will probably not cause 1p13.2- chr1:112,869,177- nerve growth factor, chr1:115,540,579- Affy/Sanger 1 Gain, 1 Loss (S) 1 CEU, 1 YRI (S) this protein has nerve growth sympathetic ganglia, but diminished 52 *162030 NGFB autonomic neuropathy, AR entire gene No disorder called hereditary sensory phenotype unless associated with 1p13.1 116,453,414 beta polypeptide 115,592,899 (Both) 1 Gain, 1 Loss (A) 1 CEU, 1 YRI (A) stimulating activity and the complex apoptosis in the retina and spinal type V and autonomic neuropathy, type V additional mutation is involved in the regulation of cord. Heterozygotes exhibit a growth and the differentiation of substantially reduced number of sympathetic and certain sensory sympathetic neurons neurons

The major calcium ion reservoir Missense mutations cause a rare Deletion will probably not cause 1p13.2- chr1:112,869,177- chr1:115,954,685- Affy/Sanger entire genei (S) 1 Gain, 1 Loss (S) 1 CEU, 1 YRI (S) 52 *114251 calsequestrin 2 CASQ2 ventricular tachycardia AR No within the sarcoplasmic reticulum of recessive form of ventricular None phenotype unless associated with 1p13.1 116,453,414 116,023,312 (Both) entire gene (A) 1 Loss (A) 1 YRI (A) cardiac myocytes tachycardia additional mutation

phosphoglycerate Catalyzes the first and rate-limiting Missense mutations cause 1p12- chr1:119,979,355- phosphoglycerate chr1:119,966,552- 3' end (9 of 12 Gain of 3' end is not expected to 55 *606879 PHGDH dehydrogenase AR Sanger 2 Gain 2 YRI No step in the phosphorylated pathway phosphoglycerate dehydrogenase None 1p11.2 120,958,392 dehydrogenase 119,998,878 exons) cause any phenotype deficiency of serine biosynthesis deficiency

3-hydroxy-3- 1p12- chr1:119,979,355- methylglutaryl- chr1:120,003,047- HMG-CoA synthase Mutations cause HMG-CoA Gain is not expected to cause a 55 *600234 HMGCS2 AR Sanger entire gene 2 Gain 2 YRI No The first enzyme of ketogenesis None 1p11.2 120,958,392 Coenzyme A 120,023,560 deficiency synthase deficiency phenotype synthase 2

Gain is not expected to cause a 7 CEU, 1 CHB, 3 1q12- chr1:141,387,477- hemochromatosis chr1:142,902,322- juvenile Affy/Sanger entire genei (S) 25 Gain (S) Mutations cause juvenile phenotype; but loss may cause 56 #602390 HFE2 AR JPT, 14 YRI (S) No Crucial to iron metabolism None 1q21.1 143,032,961 type 2 142,906,589 hemochromatosis (Both) entire gene (A) 2 Loss (A) hemochromatosis phenotype when present with 2 YRI (A) another mutation

5 CEU, 30 CHB, 34 Homozygous mutation of this gene Mutation causes change, but no Fc fragment of IgG, High-affinity Fc-gamma receptor Nonsense mutation affects 1q21.1- chr1:144,800,023- chr1:146,567,361- lack of phagocyte Affy/Sanger 185 Gain, 5 Loss (S) JPT, 71 YRI (S) results immune response defects noticeable disease state; 58 *146760 high affinity Ia, FCGR1A unclear entire gene Yes that plays a pivotal role in the expression/stability of CD64 (but 1q21.2 146,809,052 146,577,146 expression of CD64 (Both) 2 Gain, 13 Loss (A) 7 CEU, 3 CHB, 3 including a decreased inflammatory Gain/Loss is not expected to receptor immune response these patients are healthy) JPT, 2 YRI (A) response cause a phenotype

encodes a lysosomal membrane Gain is not expected to cause a Homozygous mice had less than protein that cleaves the beta- mutations cause different forms of phenotype; however, an additional chr1:151,908,051- glucosidase, beta; chr1:152,017,317- 4% of normal glucocerebrosidase 1q22 61 *606463 GBA Gaucher disease AR Sanger entire gene 5 Gain 5 YRI Yes glucosidic linkage of Gaucher disease (severity depends copy of the pseudogene may lead 152,127,880 acid 152,027,561 activity and died within 24 hours of glycosylceramide, an intermediate on the type of mutation) to greater chance of GC leading to birth in glycolipid metabolism mutations

Mouse model shows splenomegaly mutations cause hereditary A glycolytic enzyme that is the last and nonspherocytic hemolytic hereditary hemolytic hemolytic anemia due to pyruvate Gain is not expected to cause a chr1:151,908,051- pyruvate kinase, chr1:152,072,703- step of the glycolytic pathway; anemia due to deficiency of red 1q22 61 *609712 PKLR anemia due to pyruvate AR Sanger entire gene 5 Gain 5 YRI No kinase deficiency (AR); pyruvate phenotype; may be associated 152,127,880 liver and RBC 152,084,298 codes for both the liver and red blood cell pyruvate kinase; kinase deficiency kinase deficiency may be protective with increased malaria resistance blood cell isozymes heterozygous inactivating mutation against malaria in humans can underlie malaria resistance Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

Mutants show increased antibody response, passive cutaneous Susceptibility to Lupus analphylaxis, autoantibodies and 15 CEU, 7 CHB, 4 Polymorphism may cause Fc fragment of IgG, Nephritis (and Fc-gamma receptor, essential role arthritis susceptibility. On C57BL/6, chr1:158,157,328- chr1:158,288,275- Affy/Sanger entire gene (S) 2 Gain, 53 Loss (S) JPT, 29 YRI (S) susceptibility for SLE (and infection Gain/loss is not expected to cause 1q23.3 62 *146790 low affinity IIa, FCGR2A Pseudomonas WSSD in the protection of the organism mice die by 9 months with anemia, 158,413,210 158,302,415 (Both) entire genei (A) 7 Gain, 4 Loss (A) 4 CEU, 3 CHB, 2 with P. aeruginosa. in Cystic a phenotype receptor aeruginosa infection in against foreign antigens proteinuria, glomerulonephritis, and JPT, 2 YRI (A) Fibrosis) Cystic Fibrosis) inflammatory disease. A strain variant controls expression in germinal center B cells

Some polymorphisms associated 15 CEU, 7 CHB, 4 Fc fragment of IgG, immune diseases Fc-gamma receptor, required for with alloimmune neonatal chr1:158,157,328- chr1:158,324,608- Affy/Sanger entire gene (S) 2 Gain, 53 Loss (S) JPT, 29 YRI (S) Gain/loss is not expected to cause 1q23.3 62 *146740 low affinity IIIa, FCGR3A (such as SLE or WSSD high affinity binding to non- neutropenia and recurrent viral None 158,413,210 158,332,873 (Both) entire genei (A) 27 Gain, 22 Loss (A) 17 CEU, 11 CHB, 9 a phenotype receptor recurrent infections) fucosylated IgG glycoforms infections; abnormalities may also JPT, 12 YRI (A) cause SLE

Partial restoration in B cells of lupus- Fc fragment of IgG, Gain may help immune system chr1:158,157,328- chr1:158,364,611- systemic lupus Affy/Sanger 18 CEU, 10 CHB, 9 Homozygosity for polymorphism prone mouse strains is sufficient to 1q23.3 62 *604590 low affinity IIb, FCGR2B entire genei 27 Gain, 23 Loss WSSD Fc-gamma receptor; when in combination with certain 158,413,210 158,379,618 erythematosus (SLE) (Affy) JPT, 13 YRI causes susceptibility for SLE restore tolerance and prevent receptor alleles autoimmunity

Homozygotes for a targeted null Serine (or cysteine) proteinase mutation exhibit extensive inhibitor; also called antithrombin III; subcutaneous hemorrhage, fibrin antithrombin III serpin peptidase antithrombin III deficiency can Mutations and large gene deletions deposits in the myocardium and deficiency Deletion of this gene has been chr1:170,542,299- inhibitor, clade C chr1:158,364,611- manifest as a wide range of clinical have been found in disorders liver, and lethality by embryonic day 1q25.1 68 +107300 SERPINC1 (thrombophlebitis, AR and AD Sanger entire gene 1 Loss 1 YRI No shown to cause disease; loss may 170,687,600 (antithrombin), 158,379,618 phenotypes (many factors, associated with antithrombin III 16.5; heterozygotes challenged with thrombosis, cause phenotype member 1 including oral contraception in deficiency lipopolysaccharide show increased thrombophilia) females may be related to fibrin deposits; drosophila with point phenotype) mutations have neonatal thrombosis

Mutations cause factor H deficiency factor H deficiency, (AR); mutations also cause HUS Homozygous mice develop Hemolytic-Uremic 19 CEU, 8 CHB, 9 Complement factor H, a serum (AR, but also can be AD); deletion membranoproliferative Deletion could cause increase risk entire genei (S) chr1:193,322,494- complement factor chr1:193,352,798- Syndrome (HUS), Affy/Sanger 37 Gain, 18 Loss (S) JPT, 19 YRI (S) glycoprotein that controls the of exon 2 causing null (50% glomerulonephritis spontaneously to HUS and other diseases; this is 1q31.3 80 *134370 CFH AR and AD 3' end (5 of 21 Yes 193,901,429 H 193,448,288 susceptibility to age- (Both) i 2 Gain, 19 Loss (A) 4 CEU, 1 JPT, 16 function of the alternative expression) has been seen in HUS; and are hypersensitive to an important gene and disruption related macular exons) (A) YRI (A) complement pathway association has also been detected developing renal injury caused by may have several consequences degeneration between variants in the gene and immune complexes age-related macular degeneration

Factor XIII is a proenzyme for Recessive mutations can cause Deletion will probably not cause chr1:193,322,494- coagulation factor chr1:193,739,978- absence of the B Affy/Sanger 1 Loss (S) 1 CEU (S) fibrinoligase; this is the gene for the disease (bleeding); polymorphisms 1q31.3 80 +134580 F13B AR entire gene No None phenotype unless associated with 193,901,429 XIII, beta subunit 193,768,021 subunit of factor XIII (Both) 1 Loss (A) 1 YRI (A) Beta subunit (active form has 2 A may be related to risk for arterial additional mutation and 2 B) thrombotic events

asp (abnormal entire gene (S) Deletion will probably not cause chr1:193,322,494- spindle)-like, chr1:193,785,111- Affy/Sanger 1 Loss (S) 1 CEU (S) Essential for normal mitotic spindle Recessive mutations cause primary 1q31.3 80 *605481 ASPM primary microcephaly AR 3' end (10 of 26 WSSD None phenotype unless associated with 193,901,429 microcephaly 193,847,224 (Both) 1 Loss (A) 1 YRI (A) function in embryonic neuroblasts microcephaly exons) (A) additional mutation associated

Homozygotes for targeted null Complement component receptor 1; Deficiency may associate with SLE mutations exhibit impaired humoral a monomeric single-pass type I complement (disputed); deficiency may cause immune responses to T cell- chr1:203,946,290- chr1:204,057,897- SLE (maybe); membrane glycoprotein found on Deletion may cause resistance to 1q32.2 84 *120620 component (3b/4b) CR1 Sanger entire genei 5 Gain, 1 Loss 4 CEU, 2 YRI Yes mesangiocapillary dependent antigens, with limited 204,313,462 204,202,381 susceptibility to malaria erythrocytes, leukocytes, malaria receptor 1 glomerulonephritis; associated with affinity maturation, and reduced glomerular podocytes, and splenic susceptibility to malaria memory B cell and germinal center follicular dendritic cells formation

Encodes a protein with multiple A family with inherited coiled coil motifs which is located in 5' end (6 of 13 schizophrenia was found to have a Susceptibilty to the nucleus, cytoplasm and RNA interference in mouse led to chr1:227,931,495- disrupted in chr1:228,069,296- Affy/Sanger exons) (S) 2 Gain (S) 2 CEU (S) translocation that disrupted this Gain is not expected to cause a 1q42.2 95 *605210 DISC1 schizoaffective No mitochondria; the protein is impaired cerebral cortex 228,222,731 schizophrenia 1 228,483,751 (Both) 5' end (1 of 13 2 Gain (A) 2 CEU (A) gene; 1 marker in gene showed phenotype disorder involved in neurite outgrowth and development exons)i (A) strong linkage to schizophrenia in cortical development through its Finnish population interaction with other proteins

Arrhythmogenic right Mice homozygous for a ventricular dysplasia Mutations cause Arrhythmogenic phosphorylation defective allele chr1:234,267,835- ryanodine receptor chr1:233,531,743- Affy/Sanger 3' end (13 of 105 Ryanodine receptor found on the Gain is not expected to cause a 1q43 99 *180902 RYR2 type 2 and other heart AD 1 Gain 1 CHB No right ventricular dysplasia type 2 display decreased susceptibility to 235,094,143 2 234,322,694 (Sanger) exons) sarcoplasmic reticulum phenotype phenotypes (ventricular (and other cardiac phenotypes) myocardial infarction-induced heart tachycardia) failure

Chr. 2

chr2:1,410,597- chr2:1,396,242- total iodine middle (10 of 17 Thyroid peroxidase plays a central Mutations cause total iodine Gain is not expected to cause a 2p25.3 108 *606765 thyroid peroxidase TPO AR Affy 1 Gain 1 YRI No None 1,484,084 1,525,502 organification defect exons) role in thyroid gland function organification defect phenotype

Also called PHF9; represents an FA Homozygous mice are less fertile Fanconi anemia, 2p16.1- chr2:58,306,194- chr2:58,298,031- Affy/Sanger 5' end (7 of 13 1 Gain (S) 1 CEU (S) complementation group (L); the and have defective proliferation of Gain of 5' end is not expected to 145 +608111 complementation FANCL Fanconi Anemia No Disruption may cause FA 2p15 61,252,101 58,380,165 (Both) exons) 1 Gain (A) 1 CEU (A) likely catalytic subunit required for germ cells (similar to other FA KO cause a phenotype group L monoubiquitination of FANCD2 mice)

peroxisome biogenesis Mutations cause peroxisome A docking factor for the Homozygous mouse pups exhibited 2p16.1- chr2:58,306,194- peroxisome chr2:61,156,521- disorder; Zellweger Affy/Sanger 1 Gain (S) 1 CEU (S) biogenesis disorder (complement Gain is not expected to cause a 145 +601789 PEX13 AR entire gene No predominantly cytoplasmic PTS1 many of the clinical features of 2p15 61,252,101 biogenesis factor 13 61,188,042 syndrome; neonatal (Both) 1 Gain (A) 1 CEU (A) group H); mutations also cause phenotype receptor Zellweger syndrome adrenoleukodystrophy Zellweger syndrome and NALD

Homozygous null mice display obesity starting after puberty, Encodes a protein containing a chr2:73,628,687- chr2:73,524,541- 3' end (13 of 22 hypogonadism, hyperinsulinemia, Gain is not expected to cause a 2p13.1 151 *606844 Alstrom syndrome 1 ALMS1 Alstrom syndrome AR Sanger 6 Gain 2 CHB, 4 JPT Yes large tandem-repeat domain that Mutations cause Alstrom syndrome 73,990,247 73,748,701 exons)i male-specific hyperglycemia, retinal phenotype contains no cysteine residues dysfunction, and late-onset hearing loss

Overexpression of dynamitin, the Mutation associated with slowly Although dominant disorder, lower motor neuron Subunit of dynactin that is required p50 subunit of the dynactin progressive, autosomal dominant dominant phenotype might be chr2:74,391,579- chr2:74,499,937- disease and 4 CHB, 2 JPT, 14 for the cytoplasmic dynein-driven complex, disrupts the complex and 2p13.1 152 *601143 dynactin 1 DCTN1 AD Sanger entire gene 20 Loss No form of motor neuron disease caused by dominant/negative 74,674,080 74,519,619 amyotrophic lateral YRI movement of organelles along produces a late-onset, progressive without sensory symptoms and effect; deletion still may be of sclerosis (ALS) microtubules motor neuron disease in transgenic amyotrophic lateral sclerosis interest mice

Mutation found in a neonate with Deletion will probably not cause chr2:74,391,579- chr2:74,599,851- glucosidase I 4 CHB, 2 JPT, 14 Initiates processing of N-linked 2p13.1 152 *601336 glucosidase I GCS1 AR Sanger entire gene 20 Loss No severe generalized hypotonia and None phenotype unless associated with 74,674,080 74,604,161 deficiency YRI glycoproteins dysmorphic features additional mutation

zeta-chain (TCR) selective T-cell defect; zeta-chain associated protein Mutations found in patients with chr2:96,992,983- chr2:97,788,549- Affy/Sanger 5' end (2 of 14 Mouse model with recessive Gain of 5' end is not expected to 2q11.2 168 +176947 associated protein ZAP70 severe combined AR 1 Gain 1 CEU No kinase that may play a roll in T-cell SCID; recessive loss of gene can 97,795,025 97,814,841 (Sanger) exons) mutation shows chronic arthritis cause a phenotype kinase 70kDa immunodeficiency activation and response cause selective T-cell defect (STD)

Large (250 kb) homozygous Encodes a protein with src deletions cause juvenile entire gene (S) homology domain 3 (SH3) patterns; nephronophthisis; common deletion chr2:110,050,731- chr2:110,237,281- juvenile Affy/Sanger 1 Gain, 1 Loss (S) 1 CHB, 1 JPT (S) Known genomic disorder caused 2q13 173 *607100 nephronophthisis 1 NPHP1 AR 3' end (18 of 20 No part of multifunctional complex surrounded by seg dups; known None 110,558,272 110,319,969 nephronophthisis (Both) 1 Gain (A) 1 JPT (A) by deletion exons) (A) localized in actin- and microtubule- genomic disorder; mutations can based structures also cause the disorder when only 1 deletion is present

Homozygotes for targeted null Mutations in this gene have been mutations show increased A member of the MER/AXL/TYRO3 associated with disruption of the sensitivity to LPS-induced shock, receptor kinase family and encodes retinal pigment epithelium (RPE) defective phagocytosis of apoptotic AR (maybe c-mer proto- a transmembrane protein with two phagocytosis pathway and onset of cells, lupus-like autoimmunity, chr2:111,616,014- chr2:112,372,422- also AD in 5' end (8 of 19 Gain is not expected to cause a 2q13 174 +604705 oncogene tyrosine MERTK retinitis pigmentosa Sanger 4 Gain 3 CEU, 1 JPT WSSD fibronectin type-III domains, two Ig- autosomal recessive retinitis degeneration of photoreceptors, 112,463,168 112,503,176 certain exons) phenotype kinase like C2-type (immunoglobulin-like) pigmentosa; heterzygous nonsense decreased platelet aggregation and mutations) domains, and one tyrosine kinase mutation also seen in one patient protection from induced pulmonary domain (no other mutation identified; could thromboembolism and thrombosis; be AD form of this disease) rat with deletion of this gene has RP symptoms

Loss-of-function mutations cause EGF-CFC proteins act as cofactors heterotaxic phenotypes 2 CEU, 1 CHB, 1 for Nodal-related signals; proteins Deletion may cause phenotype 2q21.1- chr2:130,063,068- cripto, FRL-1, chr2:130,995,066- Affy/Sanger 7 Loss (S) (randomized organ positioning); 183 *605194 CFC1 heterotaxy syndrome AD entire gene JPT, 3 YRI (S) No play key roles in intercellular None (since disease is dominant) but 2q21.2 133,031,735 cryptic family 1 131,001,813 (Both) 1 Gain (A) mutations cause heterotaxy 1 CHB (A) signaling pathways during might be incomplete penetrance syndrome (dominant, but vertebrate embryogenesis incomplete penetrance) Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

Recessive lethal mutation in zebrafish has been studied; homozygous mutant mice show embryogenesis defects in Mutations cause dominantly Disease state is often dominant frontonasal mass, first branchial cardiomyopathy; Tibial Titin, or connectin, is a giant muscle inherited forms of cardiomyopathy; (some may be dominant-negative, chr2:179,234,579- chr2:179,216,227- middle (237 of 312 arch and somites, and vascular, 2q31.2 194 +188840 titin TTN muscular dystrophy; AD Sanger 1 Loss 1 CHB No protein expressed in the cardiac mutations have also been seen in but others appear to be 179,433,748 179,497,655 exons) cardiac and skeletal muscle defects Edstrom myopathy and skeletal muscles some muscular dystrophies and inactivating); Deletion may cause causing growth retardation, muscle myopathies phenotype weakness, abnormal posture, and premature death ranging from embryonic day 11.5 to 8 weeks of age

Missense mutation at the C- Homozygous mutation of this gene female-specific chr2:183,263,206- frizzled-related chr2:183,524,243- Affy/Sanger 1 Gain (S) 1 YRI (S) terminus was associated with hip results in defects in motor Gain is not expected to cause a 2q32.1 195 *605083 FRZB susceptibility to entire gene No Frizzled-related protein 183,660,590 protein 183,557,004 (Both) 1 Gain (A) 1 YRI (A) osteoarthritis in the female coordination and capability and a phenotype osteoarthritis probands in linkage study decrease in thermal pain sensation

Deficient mice show increased A glycoprotein on the surface of Fibronectin deficiency can cause neuronal apoptosis and larger Deletion of this gene could cause chr2:216,116,776- chr2:216,050,687- Ehlers-Danlos Affy/Sanger 5' end (6 of 46 fibroblasts; role in cell adhesion, Ehlers-Danlos syndrome (type X) infarction areas following transient Ehlers-Danos syndrome 2q35 205 *135600 fibronectin 1 FN1 AD 1 Loss 1 YRI No 216,276,027 216,126,297 syndrome (type X) (Sanger) exons) morphology, and surface (Adominant, with protein levels 1/2 focal cerebral ischemia; plasma (however, at the edge of CNV so architecture normal) (no mutations reported) fibronectin is not essential for skin- may loss may not overlap gene) wound healing or hemostasis

Member of the calpain family, a well- conserved family of calcium- chr2:241,085,111- chr2:241,246,142- Susceptibility to Affy/Sanger SNPs in the region show linkage Gain is not expected to cause a 2q37.3 210 *605286 calpain 10 CAPN10 entire gene 1 Gain 1 JPT No dependent, cysteine proteases; None 241,308,861 241,277,112 Diabetes mellitus (Sanger) with diabetes risk phenotype involved in the pathophysiology of diabetes

D-2- Deletion will probably not cause chr2:242,415,890- chr2:242,394,045- D-2-hydroxyglutaric Affy/Sanger 3' end (1 of 10 D-2-hydroxyglutarate Mutations cause D-2- 2q37.3 212 *609186 hydroxyglutarate D2HGDH AR 1 Loss 1 CEU Yes None phenotype unless associated with 242,787,722 242,428,214 aciduria (Affy) exons) dehydrogenase hydroxyglutaric aciduria dehydrogenase additional mutation

Chr. 3

multiple sulfatase Hetero- and homozygosity for Deletion may reduce sulfatase chr3:4,113,369- sulfatase modifying chr3:4,377,830- deficiency (MSD); Affy/Sanger Both an essential and a limiting 3p26.1 217 *607939 SUMF1 AR and AD 3' end (2 of 9 exons) 1 Loss 1 CHB No mutations (including microdeletions None activity, resulting in some 4,395,357 factor 1 4,483,954 lysosomal storage (Sanger) factor for sulfatases and splicing errors) cause MSD phenotype disorder

Located in a chromosomal segment deleted in lung and Expression significantly suppressed that is commonly deleted in various chr3:37,806,487- chr3:38,055,700- 5' end (5 of 33 Deletion of this gene may 3p22.3 231 *604050 esophageal cancer DLEC1 Various carcinomas Sanger 8 Loss 4 CEU, 2 CHB, 2 YRI No the growth of 4 different cancer cell carcinomas; aberrant transcription None 38,079,228 38,139,233 exons) predispose for some cancers 1 lines; may be involved in carcinogenesis of the lung, esophagus, and kidney

2 independent mutations in this Required for normal postnatal Deletion will probably not cause chr3:46,655,456- transmembrane chr3:46,717,827- Neurosensory Mutations (including small in/dels) gene are the cause of hearing loss 3p21.31 238 *607237 TMIE AR Sanger entire gene 29 Loss 1 CEU, 28 YRI No maturation of sensory hair cells in phenotype unless associated with 46,947,493 inner ear 46,727,205 deafness were found to cause hearing loss and vestibular dysfunction in the cochlea additional mutation 'spinner' mice

Metaphyseal chondrodysplasia, PTHR1 gene encodes a receptor Mutations were found to cause Murk Jansen type; Loss may affect parathyroid chr3:46,655,456- parathyroid chr3:46,894,240- for both parathyroid hormone and Murk Jansen (AD) and Ollier types Homozygyous mutant mice died in 3p21.31 238 *168468 PTHR1 Chondrodysplasia, AD; AR; AR Sanger entire gene 30 Loss 1 CEU, 29 YRI No hormone concentrations, resulting 46,947,493 hormone receptor 1 46,920,291 parathyroid hormone-related (AR); mutations were also found to mid-gestation Blomstrand type; in a metabolic phenotype protein; cause Blomstrand type Enchondromatosis, Ollier type

Encodes myosin light chain 3, an alkali light chain also referred to in Hetero- and homogygous mutations chr3:46,655,456- myosin, light chr3:46,874,371- Familiar hypertrophic Loss may cause cardiac 3p21.31 238 *160790 MYL3 AR and AD Sanger entire gene 30 Loss 1 CEU, 29 YRI No the literature as both the ventricular were found to cause hypertrophic None 46,947,493 polypeptide 3, alkali 46,879,935 cardiomyopathy phenotype isoform and the slow skeletal cardiomiopathy muscle isoform

Triple-knockout mice (for Gnat, Subunit of transducin, a 3-subunit Cnga3, Opn4), in which the rod- guanine nucleotide guanine nucleotide-binding protein cone and melanopsin systems were binding protein (G (G protein) which stimulates the Deletion will probably not cause chr3:50,173,482- chr3:50,204,047- congenital stationary Missense mutation was found to both silenced, had an intact retina 3p21.31 239 *139330 protein), alpha GNAT1 AD Sanger entire gene 3 Loss 1 CEU, 1 JPT, 1 YRI No coupling of rhodopsin and cGMP- phenotype unless associated with 50,346,381 50,208,953 night blindness cause night blindess but failed to show any significant transducing activity phoshodiesterase during visual additional mutation pupil reflex, to entrain to light/dark polypeptide 1 impulses; this gene encodes the cycles, and to show any masking alpha subunit in rods response to light

guanine nucleotide Adrenal cortical tumor; Mutations were found in adrenal binding protein (G ACTH-secreting Guanine nucleotide binding protein cortex and endocrine tumors of the Deletion will probably not cause chr3:50,173,482- chr3:50,248,651- 3p21.31 239 *139360 protein), alpha GNAI2 pituitary adenoma; Sanger entire gene 3 Loss 1 CEU, 1 JPT, 1 YRI No (G protein), alpha inhibiting activity ovary, and in pituitary adenoma; None phenotype unless associated with 50,346,381 50,271,790 inhibiting activity Idiopathic ventricular polypeptide 2 also seen in idiopathic VT (just 1 additional mutation polypeptide 2 tachycardia case of somatic mutation)

Encodes a lysosomal muco- hyaluronidase; intracellularly Deletion will probably not cause chr3:50,173,482- hyalurono- chr3:50,312,325- Mutations were found to cause 3p21.31 239 *607071 HYAL1 polysaccharidosis type AR Sanger entire gene 3 Loss 1 CEU, 1 JPT, 1 YRI No degrade hyaluronan, one of the None phenotype unless associated with 50,346,381 glucosaminidase 1 50,324,816 mucopolysaccharidosis type IX IX major glycosaminoglycans of the additional mutation extracellular matrix

Major hypothalamic mediator of TRH deficiency can cause Homozygous null mice exhibit Loss may cause low TRH release, chr3:131,142,165- thyrotropin chr3:131,176,261- Affy/Sanger release of thyroid-stimulating 3q21.3 268 +275120 TRH TRH deficiency entire gene 2 Loss 2 CEU No hypothyroidism and short stature teritary hypothyroidism, elevated causing hypothyroidism or related 131,422,680 releasing hormone 131,179,478 (Sanger) hormone; also stimulates the (no mutations reported) TSH levels and hyperglycemia phenotype release of prolactin

Histidine-rich glycoprotein Missense mutation was found in a containing two cystatin-like domains patient with thrombophelia due to Loss may cause low plasma HRG chr3:187,819,836- histidine-rich chr3:187,866,500- Thrombophelia due to Affy/Sanger entire gene (S) 2 Loss (S) 2 CEU (S) 3q27.3 297 +142640 HRG AD No and located in plasma and platelets; HRG deficiency (affect may be None level, causing thrombophelia or 188,050,028 glycoprotein 187,878,724 HRG deficiency (Both) entire genei (A) 2 Loss (A) 2 CEU (A) known that the protein binds heme, induced by oral contraceptive related phenotype dyes and divalent metal ions treatment)

Homozygous mutations (including Inhibits ERK-dependent T cell in/dels) were found to cause Deletion will probably not cause chr3:187,819,836- chr3:187,917,822- high molecular weight Affy/Sanger proliferation, which suggests that it 3q27.3 297 +228960 kininogen 1 KNG1 AR entire gene 2 Loss 2 CEU No kininogen deficiency (individual with None phenotype unless associated with 188,050,028 187,944,443 kininogen deficiency (Sanger) might have a role in heterozygous mutation had normal additional mutation immunosenescence HK)

Missense mutation was found in a Knockout mice exhibited severe Adiponectin regulates energy patient with adiponectin deficiency diet-induced insulin resistance; in Loss may cause low adiponectin adiponectin, C1Q homeostasis and glucose and lipid (coronary artery disease, lung adiponectin-null mice observed levels, which could result in chr3:187,819,836- chr3:188,043,165- Affy/Sanger 3q27.3 297 +605441 and collagen ADIPOQ adiponectin deficiency AD 5' end (1 of 3 exons) 2 Loss 2 CEU No metabolism; has antiinflammatory thrombosis, and autoimmune increased myocardial infarct size, phenotypes, including coronary 188,050,028 188,058,952 (Sanger) domain containing effects on the cellular components disease); also there may be an myocardial apoptosis, and TNF artery disease, lung thrombosis, of the vascular wall association between variants and expression compared to wildtype and autoimmune disease obesity (high body mass index) mice

Optic atrophy A nuclear-encoded mitochondrial chr3:194,716,602- chr3:194,793,814- (with/without 5' end (26 of 28 protein with similarity to dynamin- Mutations were found to cause Gain is not expected to cause a 3q29 303 *605290 optic atrophy 1 OPA1 AD Sanger 1 Gain 1 CEU No None 194,886,348 194,898,017 deafness); normal exons) related GTPases; a component of optic atrophy phenotype tension glaucoma the mitochondrial network

Chr. 4

Missense mutations and homozygous 71-bp tandem Mice homozygous for the rd phosphodiesterase retinitis pigmentosa; duplication in exon 1 (causing a mutation display hereditary retinal chr4:593,208- chr4:609,395- Beta subunit of phosphodiesterase Loss is not expected to cause a 4p16.3 308 *180072 6B, cGMP-specific, PDE6B congenital stationary AR Sanger entire gene 1 Loss 1 JPT No premature stop codon) were found degeneration which has been 921,184 654,542 6B, cGMP-specific found in the rod phenotype rod, beta night blindness to cause AR retinitis pigmentosa considered a model for human (mutations may be responsible for retinitis pigmentosa only about 5% of cases of ARRP)

achondroplasia (ACH); thanatophoric dysplasia, type I & II; Mutations were found to cause Heterozygous mice showed no hypochondroplasia; ACH (AD, familiar or sporadic), phenotypic abnormalitlies; Crouzon A member of the fibroblast growth hanatophoric dysplasia, type I & II homozygous mice had phenotypic craniosynostosis in factor receptor family; binds acidic (AD), hypochondroplasia (AR or effects restricted to bones; mice chr4:1,592,784- fibroblast growth chr4:1,762,854- association with Gain is not expected to cause a 4p16.3 309 *134934 FGFR3 AD; AR Sanger entire gene 1 Gain 1 CEU No and basic fibroblast growth AD), Crouzon craniosynostosis with heterozygous for K644E mutation 1,782,006 factor receptor 3 1,777,829 acanthosis nigricans; phenotype hormone and plays a role in bone acanthosis nigrican, Muenke showed mild bone dysplasia (20% Muenke syndrome; development and maintenance syndrome; Saddan dysplasia; of the wildtype level), and mice Saddan dysplasia; multple myeloma; mutations have homozygous for the mutation had multple myeloma; also been found in some cancers more severe phenotype colorectal cancer, thanatrophic dysplasia including bladd

Alpha-2-adrenergic receptors have a critical role in regulating Mice homozygous for targeted Homozygousity for 4-bp deletion chr4:3,431,313- adrenergic, alpha- chr4:3,805,265- susceptibility to Affy/Sanger Merged (no clone or no direct overlap with neurotransmitter release from mutations that inactivate the gene Not expected to cause a 4p16.3 310 *104250 ADRA2C entire gene No may increase susceptibility to 4,469,058 2C-, receptor 3,807,220 congenital heart failure (Neither) SNP coverage) individual CNV calls sympathetic nerves and from are viable and fertile and appear phenotype congenital heart failure adrenergic neurons in the central grossly normal nervous system Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

An allele 2 of the dinucleotide was found to have an increased blepharospasm, G-protein coupled receptor which Homozygous null mice develop frequency in blepharospasm cases chr4:8,640,244- dopamine receptor chr4:9,459,872- including primary Affy/Sanger 1 Gain (S) 1 JPT (S) stimulates adenylyl cyclase; hypertension and exhibit elevated Gain is not expected to cause a 4p16.1 313 +126453 DRD5 entire gene Yes compared with controls (but not in 9,952,736 D5 9,461,901 cervical dystonia; (Both) 2 Gain (A) 1 CEU, 1 JPT (A) receptor is expressed in neurons in blood pressure caused by phenotype German & French patients in susceptibility to ADHD the limbic regions of the brain increased sympathetic tone another study); microsatellite 18.5 kb upstream is linked to ADHD

Neuronal-specific form of c-Jun N- terminal kinases (JNKs); through its Patient with epileptic Targeted deletion reduced stress- developmental epileptic phosphorylation and nuclear Deletion of this gene may cause chr4:87,432,938- mitogen-activated chr4:87,294,811- middle (2 of 14 encephalopathy had de novo induced JNK activity and protected 4q21.3 354 *602897 MAPK10 encephalopathy of the Affy 2 Loss 2 CEU No localization, this kinase plays some phenotypes (JNK3 87,495,944 protein kinase 10 87,731,462 exons)i balanced translocation which mice from brain injury after cerebral Lennox-Gaustaut type regulatory roles in the signaling haploinsufficiency) disrupted JNK3 at intron 9 ischemia-hypoxia pathways during neuronal apoptosis (stress-induced)

Member of the polycystin protein family; may be an integral membrane protein involved in cell- cell/matrix interactions; may entire gene (S) Mutations (including large deletions Homozygous mice die in utero; chr4:89,275,730- polycystic kidney chr4:89,285,999- Affy/Sanger 2 Gain (S) 2 CEU (S) function in renal tubular Gain is not expected to cause a 4q22.1 357 +173910 PKD2 polycystic kidney type 2 AD 5' end (12 of 15 No encompassing most of the gene) heterozygous mice had mild renal 89,570,298 disease 2 89,356,107 (Both) 1 Gain (A) 1 CEU (A) development, morphology, and phenotype exons) (A) were found to cause PCK cystic lesion function, and may modulate intracellular calcium homoeostasis and other signal transduction pathways

Member of the 3-hydroxyacyl-CoA dehydrogenase gene family; L-3-hydroxyacyl- HAD deficiency; functions in the mitochondrial matrix Deletion will probably not cause chr4:109,298,778- Coenzyme A chr4:109,268,606- familiar to catalyze the oxidation of straight- Mutations were found to cause 4q25 363 *601609 HADHSC AR Affy middle (1 of 8 exons) 1 Loss 1 JPT No None phenotype unless associated with 109,305,695 dehydrogenase, 109,313,927 hyperinsulinemic chain 3-hydroxyacyl-CoAs as part hyperinsulinemic hypoglycemia additional mutation short chain hypoglycemia of the beta-oxidation pathway; enzymatic activity is highest with medium-chain-length fatty acids

A member of the trypsin family of serine proteases; may be involved Mice homozygous for a targeted chr4:118,836,451- chr4:119,560,020- Affy/Sanger Mutation was found to cause Gain is not expected to cause a 4q26 370 *606709 protease, serine, 12 PRSS12 mental retardation AR entire gene 1 Gain 1 CEU No in structural reorganizations mutation display hypoactivity and 120,032,345 119,631,525 (Affy) mental retardation phenotype associated with learning and increased anxiety memory

1 CEU, 3 CHB, 13 Major sialoglycoprotein of the chr4:144,705,898- chr4:145,274,862- Affy/Sanger entire gene (S) 6 Gain, 11 Loss (S) YRI (S) human erythrocyte membrane Many variants seen; often caused Gain/loss is not expected to cause 4q31.21 379 +111740 glycophorin B GYPB Ss blood group Yes None 145,489,197 145,298,101 (Both) entire genei (A) 4 Gain, 13 Loss (A) 1 CEU, 3 CHB, 13 which bears the antigenic by recombination with GYPA a phenotype YRI (A) determinants for the Ss blood group

Mice homozygous for a targeted Major sialoglycoprotein of the null mutation are viable and fertile; 1 CEU, 3 CHB, 13 human erythrocyte membrane however, mutant erythrocytes had a chr4:144,705,898- chr4:145,388,062- Affy/Sanger entire genei (S) 6 Gain, 11 Loss (S) YRI (S) Many variants seen; often caused Gain/loss is not expected to cause 4q31.21 379 +111300 glycophorin A GYPA MN blood group Yes which bears the antigenic reduced percentage of O-linked 145,489,197 145,419,449 (Both) i 4 Gain, 4 Loss (A) 1 CEU, 3 CHB, 4 YRI by recombination with GYPB a phenotype entire gene (A) determinants for the MN blood glycoproteins in the membranes, (A) group and were sensitive to hypoosmotic stress

A massive accumulation of Involved in the catabolism of N- aspartylglucosamine was detected linked oligosaccharides of in Aga-null mice at the age of 5 to Mutations were found to cause chr4:178,540,618- aspartyl- chr4:178,727,073- Aspartyl- Affy/Sanger glycoproteins; cleaves asparagine 10 months; the general condition of Gain is not expected to cause a 4q34.3 395 +208400 AGA AR entire gene 1 Gain 1 JPT No AGU (patient with deletion of 4q33- 178,780,523 glucosaminidase 178,738,740 glucosaminuria (AGU) (Sanger) from N-acetylglucosamines as one the null mutant mice gradually phenotype qter has been reported) of the final steps in the lysosomal deteriorated after the age of 10 breakdown of glycoproteins months, suffering from progressive motor impairment

Chr. 5

Subunit of complex II of the succinate Leigh syndrome due to respiratory chain, which is Mutations cause Leigh syndrome Deletion will probably not cause chr5:70,263- dehydrogenase chr5:271,447- 5p15.33 406 *600857 SDHA mitochondrial complex AR Sanger entire gene 12 Loss 7 CEU, 1 JPT, 4 YRI Yes specifically involved in the oxidation due to mitochondrial complex II None phenotype unless associated with 648,955 complex, subunit A, 309,792 II deficiency of succinate; localized in the deficiency additional mutation flavoprotein mitochondrial inner membrane

The family of natriuretic peptides Three mutations were found in natriuretic peptide elicit a number of vascular, renal, candidate for transgenic mice exhibited a skeletal chr5:32,281,118- receptor chr5:32,747,422- and endocrine effects that are Loss is not expected to cause a 5p13.3 429 *108962 NPR3 overgrowth syndromes Sanger 5' end (2 of 8 exons) 1 Loss 1 YRI No No mutations have been reported overgrowth phenotype; NPR3 gene 32,774,401 C/guanylate cyclase 32,823,009 important in the maintenance of phenotype (due to mouse model) became a candidate for overgrowth C blood pressure and extracellular syndromes in the human fluid volume

Component of the complement Mutations were found in C7 Deletion will probably not cause chr5:40,909,835- complement chr5:40,945,356- system. It participates in the 5p13.1 432 *217070 C7 C7 deficiency AR Affy entire gene 1 Loss 1 CHB No deficiency patients; variants may be None phenotype unless associated with 41,045,039 component 7 41,018,796 formation of Membrane Attack associated with risk for infection additional mutation Complex (MAC)

Localizes to both the cytoplasm and the nucleus (within the nucleus, the Homozygous mice died during the protein localizes to subnuclear Large deletions (spanning exons 7 periimplantation stage; the severity spinal muscular bodies called gems); forms chr5:69,109,876- survival of motor chr5:70,256,524- 67 CEU, 23 CHB, 22 & 8) are common in SMA patients; of the pathologic changes in these Deletion of this gene has been 5q13.2 439 *600354 SMN1 atrophy (SMA), types AR Sanger entire gene 147 Gain, 6 Loss Yes heteromeric complexes with 70,831,640 neuron 1 70,284,593 JPT, 51 YRI mutations and smaller deletions are mice correlated with the amount of shown to cause disease I, II, III, and IV proteins known to be involved in the also seen in these patients SMN protein that contained the biogenesis of snRNPs; witihin a 500 region encoded by exon 7 kb inverted duplication on chromosome 5q13

Although dominant disorder, Differentially modulates the dominant phenotype might be chr5:135,193,500- transforming growth chr5:135,392,597- Affy/Sanger Missense mutations were found to 5q31.1 471 *601692 TGFBI corneal dystrophy AD entire gene 1 Loss 1 CHB No aggregation of collagen VI with None caused by dominant/negative 135,502,898 factor, beta-induced 135,427,406 (Sanger) cause corneal dystrphies biglycan and decorin effect; deletion still may be of interest

protein Belongs to the phosphatase 2 chr5:146,410,036- phosphatase 2, chr5:145,949,262- spinocerebellar ataxia 5' end (1 of 11 regulatory subunit B family; Expanded CAG repeat was found Dominant disorder, but most likely 5q32 476 *604325 PPP2R2B AD Affy 1 Loss 1 JPT No None 146,519,693 regulatory subunit 146,441,207 (SCA) exons) implicated in the negative control of in patients with SCA dominant-negative B, beta isoform cell growth and division

Might participate in the formation of clathrin-coated vesicles at the level susceptibility to a Markers on this gene were found to chr5:156,930,186- chr5:157,145,875- 3' end (6 of 12 of the trans-Golgi network and Loss is not expected to cause a 5q33.3 480 *607265 enthoprotin ENTH subtype of Sanger 1 Loss 1 CEU No be significantly associated with None 157,165,622 157,218,746 exons) remains associated with the phenotype schizophrenia schizophrenia vesicles longer than clathrin and adaptors

Enhances androgen receptor (AR) transactivation, and this Known genomic disorder; 77% of enhancement can be increased Sotos syndrome had either large Homozygotes for targeted null Known genomic disorder caused Sotos syndrome; nuclear receptor further in the presence of other deletions (encompassing the entire mutations exhibit excess apoptosis by deletion; gain may be chr5:176,550,923- chr5:176,493,532- Weaver syndrome; 3' end (21 of 23 9 CEU, 2 CHB, 5 5q35.3 487 *606681 binding SET domain NSD1 AR and AD Sanger 54 Gain No androgen receptor associated gene) or point mutations in the and retarded growth, fail to associated with susceptibility for 176,735,050 176,655,367 Beckwith-Wiedemann exons) JPT, 38 YRI protein 1 coregulators; may act as a nucleus- NSD1 gene; microdeletion may be complete gastrulation, and are further rearrangements (such as syndrome localized, basic transcriptional more common in some populations resorbed by embryonic day 10 disease causing deletion) factor and also as a bifunctional (Japanese) transcriptional regulator

Member of the ADAMTS (a ADAM 5' end (3 of 21 disintegrin and metalloproteinase Homozygous mutation of this gene metallopeptidase chr5:178,593,872- chr5:178,473,474- Ehlers-Danlos Affy/Sanger exons) (S) 2 Gain (S) 2 JPT (S) with thrombospondin motifs) protein Missense mutations were found to results in a short snout, male Gain is not expected to cause a 5q35.3 488 *604539 with ADAMTS2 AR No 178,970,135 178,704,935 syndrome type VIIC (Both) 5' end (2 of 21 2 Gain (A) 2 JPT (A) family; excises the N-propeptide of cause EDS ype VIIC infertility, and thin skin that is torn phenotype thrombospondin exons)i (A) type I, type II and type V by scratching or handling type 1 motif, 2 procollagens

Chr. 6

Mutant mice began to develop 50 CEU, 23 CHB, 23 A member of a gene family known Translocation reported that causes generalized lymphadenopathy with interferon regulatory chr6:336,760- oncogene in multiple Affy/Sanger entire genei (S) 158 Gain, 6 Loss (S) JPT, 68 YRI (S) Gain/loss is not expected to cause 6p25.3 492 chr6:5,001-720,274 *601900 IRF4 No to be active in the control of B-cell overexpression which contributes expansion of both T and B factor 4 356,193 myelomas (Both) i 55 Gain (A) 6 CEU, 1 JPT, 48 a phenotype entire gene (A) proliferation and differentiation; to tumorigenesis lymphocytes and other problems in YRI (A) T/B lymphocyte function

Encodes the enzyme responsible Molecular defects cause adult i glucosaminyl (N- for formation of the blood group I blood group phenotype and adult i blood group entire gene (S) Deletion will probably not cause 6p24.3- chr6:10,551,783- acetyl) transferase chr6:10,636,575- Affy/Sanger 1 Loss (S) 1 CEU (S) antigen; responsible for the congenital cataracts (recessive); 497 *600429 GCNT2 phenotype with AR 5' end (1 of 3 exons)i No None phenotype unless associated with 6p24.2 10,751,118 2, I-branching 10,737,586 (Both) 2 Loss (A) 2 CEU (A) conversion of fetal i antigen to adult homozygous deletions of this gene congenital cataracts (A) additional mutation enzyme I antigen in erythrocytes during (in consagineous marriage) have embryonic development been reported

Increase in expression may increase susceptibility to tumours; Increase/decrease in expression HLA-G Belongs to the HLA class I heavy linkage to asthma has been may increase susceptibility to 6p22.1- chr6:29,900,413- chr6:29,903,497- Cancer; susceptibility Affy/Sanger 10 CEU, 1 CHB, 5 503 *142871 histocompatibility HLA-G entire gene 18 Gain, 3 Loss Yes chain paralogues; involved in reported; functional assays show None certain tumours (however, at the 6p21.33 30,083,123 29,906,859 to asthma (Sanger) JPT, 5 YRI antigen, class I, G inhibiting natural killer cell function that aberrant expression of HLA-G edge CNV so may not overlap may contribute to immune escape CNV) in human glioblastoma Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

Hypotrichosis simplex Encodes a protein found in Mutations cause Hypotrichosis chr6:31,136,269- chr6:31,190,849- of the scalp; Affy/Sanger corneodesmosomes, which localize simplex of the scalp; SNP shown to Gain is not expected to cause a 6p21.33 505 *602593 corneodesmosin CDSN AD entire gene 12 Gain 9 CEU, 3 YRI No None 31,650,287 31,196,202 susceptibility to (Sanger) to human epidermis and other provide risk in psoriasis phenotype psoriasis cornified squamous epithelia susceptibility (disputed)

complex immune Alleles are involved in protection major response; susceptibility 5 CEU, 2 CHB, 2 Belongs to the HLA class I heavy Very complex part of immune chr6:31,136,269- chr6:31,429,630- Affy/Sanger 8 Gain, 2 Loss (S) against malaria (also AIDS 6p21.33 505 *142830 histocompatibility HLA-B to ankylosing entire gene JPT, 1 YRI (S) Yes chain paralogues; part of the major None response; gain/loss is not 31,650,287 31,432,914 (Both) 1 Gain, 2 Loss (A) infection); related to susceptibility complex, class I, B spondylitis and other 2 CHB, 1 JPT (A) histocompatibility complex expected to cause a phenotype to ankylosing spondylitis immune diseases

nuclear factor of kappa light Encodes a divergent member of the chr6:31,136,269- chr6:31,623,351- susceptibility to Affy/Sanger Polymorphism related to Loss is not expected to cause a 6p21.33 505 *601022 polypeptide gene NFKBIL1 entire gene 1 Loss 1 YRI No I-kappa-B family of proteins. Its None 31,650,287 31,634,584 rheumatoid arthritis (Affy) susceptibility to rheumatoid arthritis phenotype enhancer in B-cells function has not been determined inhibitor-like

Considerable perivascular infiltration of activated T Polymorphisms associated with lymphocytes was seen in tissues colitis and Crohn's Secreted by activated lymphocytes chr6:31,136,269- chr6:31,648,072- Affy/Sanger colitis and Crohn's disease; SNPs from homozygous mice; presence Loss is not expected to cause a 6p21.33 505 *153440 lymphotoxin alpha LTA disease; myocardial entire gene 1 Loss 1 YRI No and presumed to act as a 31,650,287 31,650,077 (Affy) also associated with myocardial of LTA and/or lymph nodes phenotype infarction modulator in the immune response infarction accelerates the initiation of immune responses and protects the host from larger viral challenges

C2 deficiency has been seen in many other disorders, including Henoch-Schonlein purpura, lupus C2 deficiency (can Deletion could be present with 6p21.33- chr6:31,979,491- complement chr6:32,003,473- 10 CEU, 4 CHB, 3 Part of the classical pathway of erythematosus, polyarteritis and 506 +217000 C2 cause other immune AD Sanger entire gene 4 Gain, 30 Loss No None more common inactivating allele 6p21.32 32,317,091 component 2 32,021,427 JPT, 17 YRI complement system membranoproliferative diseases) and cause C2 deficiency glomerulonephritis; heterozygous deficiency is fairly common (but not due to deletion)

Known deletion of this gene (and Encodes the basic form of C4A and CYP21A2) have been Homozygous C4 deficient mice 6p21.33- chr6:31,979,491- complement chr6:32,057,813- SLE and other immune 10 CEU, 4 CHB, 3 Known deletion of this gene; 506 *120820 C4B Sanger entire gene 4 Gain, 31 Loss WSSD complement factor 4, part of the reported and associated with lupus have compromised immune 6p21.32 32,317,091 component 4B 32,078,435 disorders JPT, 18 YRI associated with immune disorders classical activation pathway (SLE); deletions (30-38 kb) in both responses controls and patients

encodes the acidic form of Within a known deletion (see Homozygous C4 deficient mice Known to have a lot of variation 6p21.33- chr6:31,979,491- complement chr6:32,090,550- 10 CEU, 4 CHB, 3 506 +120810 C4A SLE and diabetes AR Sanger entire gene 4 Gain, 31 Loss WSSD complement factor 4, part of the above); homozygous deficiency have compromised immune and associated with immune 6p21.32 32,317,091 component 4A 32,111,173 JPT, 18 YRI classical activation pathway associated with SLE and diabetes responses disorders

Within a known deletion (see Encodes a member of the above); mutations (and deletions) cytochrome P450 superfamily of cytochrome P450, cause CAH (genomic disease may Very complex with several gene 6p21.33- chr6:31,979,491- chr6:32,114,061- Congenital adrenal 10 CEU, 4 CHB, 3 enzymes; localizes to the 506 +201910 family 21, subfamily CYP21A2 AR and AD Sanger entire gene 4 Gain, 31 Loss WSSD sometimes be caused by gene None duplications and known 6p21.32 32,317,091 32,117,398 hyperplasia (CAH) JPT, 18 YRI endoplasmic reticulum and A, polypeptide 2 conversion with pseudogene or mutations/known deletions hydroxylates steroids at the 21 NAHR mediated deletion); common position AR disorder

Deletion reported (same as above, Extracellular matrix protein; can cause fusion gene); Homozygous mice showed congenital adrenal Again deletion of this region has 6p21.33- chr6:31,979,491- chr6:32,116,911- 10 CEU, 4 CHB, 3 encodes a member of the tenascin homozygous/heterozygous progressive skin hyperextensibility, 506 *600985 tenascin XB TNXB hyperplasia; Ehlers- AR Sanger entire genei 4 Gain, 31 Loss Yes been reported and is associated 6p21.32 32,317,091 32,185,131 JPT, 18 YRI family of extracellular matrix deletions can be seen in Ehlers- similar to that of individuals with Danlos syndrome with disease proteins; overlaps CYP21A2 Danlos syndrome; mutations also Ehlers-Danlos syndrome reported

May be related to susceptibility, chr6:32,479,731- chr6:32,470,491- susceptibility to 25 CEU, 7 CHB, 8 Linked to susceptibility to 6p21.32 507 *606000 butyrophilin-like 2 BTNL2 Sanger 5' end (2 of 6 exons) 46 Gain, 22 Loss No MHC class II associated protein None but no obvious correlation 32,813,412 32,482,878 sarcoidosis JPT, 28 YRI sarcoidosis between CNV and disease

immune disease and major Subunit of cell surface alpha/beta Some alleles associated with infections; Additional copy may be important chr6:32,479,731- histocompatibility chr6:32,470,491- 23 CEU, 8 CHB, 10 heterodimeric proteins whose protection from severe malaria; 6p21.32 507 *142857 HLA-DRB1 cardiomyopathy; Sanger entire genei 51 Gain, 8 Loss No None for malarial resistance or for graft- 32,813,412 complex, class II, 32,482,878 JPT, 18 YRI function is to present processed alleles may be associated with risk rheumatoid arthritis; vs-host rejection disease DR beta 1 foreign antigens to T cells for sarcoidosis sarcoidosis

Homozygous mice exhibited an early-onset retinal degeneration with a progressive, rapid loss of Member of a family of tubby-like Mutations cause rare form of chr6:35,571,719- chr6:35,573,632- photoreceptors, further supporting Gain is not expected to cause a 6p21.31 511 *602280 tubby like protein 1 TULP1 Retinitis pigmentosa AR Sanger entire gene 1 Gain 1 YRI No genes (TULPs) that encode autosomal recessive retinitis 35,914,482 35,588,623 the notion that previously identified phenotype proteins of unknown function pigmentosa mutations within the human TULP1 gene are indeed causative of retinitis pigmentosa

A member of the immunophilin Significant associations of response Susceptibility to protein family, which play a role in to antidepressants and the Gain may increase susceptibility increased recurrence chr6:35,571,719- FK506 binding chr6:35,649,346- immunoregulation and basic cellular recurrence of depressive episodes for neurological disorders if the 6p21.31 511 *602623 FKBP5 of depressive episodes Sanger entire genei 4 Gain 3 CEU, 1 YRI No None 35,914,482 protein 5 35,764,692 processes involving protein folding with SNPs in this gene (also increased expression is truly the in major depressive and trafficking; thought to mediate associated with increased cause of the disorder disorder calcineurin inhibition expression)

Gene was upregulated approximately 1.6-fold in brain tissue of a transgenic mouse model Increased expression may be A glutathione-binding protein Polymorphism may be a of Alzheimer disease and chr6:38,696,947- chr6:38,751,698- Autism; anxiety; 2 CEU, 1 CHB, 2 associated with increased anxiety 6p21.2 512 *138750 glyoxalase 1 GLO1 Sanger entire gene 5 Gain, 1 Loss No involved in the detoxification of susceptibility factor for the frontotemporal dementia; 38,819,063 38,778,895 Alzheimers JPT, 1 YRI or Alzheimers disease (based on methylglyoxal development of autism overexpression in the mouse brain mouse models) resulted in increased anxiety-like behavior, while local inhibition of express

Common mutation (27% heterozygosity in Japanese Since inactivating mutation is PAF Acetylhydrolase A secreted enzyme that catalyzes population) causes recessive PAF common, deletion could be chr6:46,808,141- phospholipase A2, chr6:46,780,237- Deficiency; 5' exon (1 of 12 2 CEU, 3 CHB, 2 6p12.3 516 +601690 PLA2G7 AR Sanger 8 Gain, 1 Loss No the degradation of PAF to inactive Acetylhydrolase Deficiency (carriers None another cause of disease 47,036,030 group VII 46,811,055 Susceptibility to exons) JPT, 2 YRI products may have mild phenotype); (however, at the edge of CNV so Asthma and Atopy polymorphisms associated with may not be within CNV) susceptibility to asthma and atopy

Homozygotes for targeted and Part of a heterotrimeric extracellular spontaneous mutations exhibit matrix protein; thought to mediate progressive growth retardation, congenital merosin- the attachment, migration, and Mutations cause congenital chr6:129,315,361- chr6:129,246,035- middle (3 of 72 ataxia, muscle atrophy and Gain of 3 exons is not expected to 6q22.33 560 *156225 laminin, alpha 2 LAMA2 deficient muscular AR Sanger 3 Gain 2 CHB, 1 JPT No organization of cells into tissues merosin-deficient muscular 129,484,648 129,879,401 exons) degeneration, infertility, and cause a phenotype dystrophy type 1A during embryonic development by dystrophy type 1A premature lethality; muscle fiber interacting with other extracellular degeneration is evident as early as matrix components the first week of life

autosomal dominant Mutations were responsible for hearing loss and A member of the eyes absent postlingual, progressive, autosomal Deletion of 5' end of gene could dilated cardiomyopathy (EYA) family of proteins; may act as dominant hearing loss; 5 kb Knockdown in zebrafish produced chr6:133,486,412- eyes absent chr6:133,604,206- 5' end (2 of 18 cause hearing loss and/or 6q23.2 561 *603550 EYA4 and heart failure AD Sanger 1 Loss 1 CEU No a transciptional activator and be deletion (exons 9 to 10) cause morphologic and hemodynamic 133,669,057 homolog 4 133,892,353 exons) cardiomyopathy (since they are preceded by important for continued function of dilated cardiomyopathy and heart features of heart failure dominant diseases) sensorineural hearing the mature organ of Corti failure preceded by sensorineural loss hearing loss

Autosomal recessive familial susceptibility to immunologic defect predisposing to Encodes the ligand-binding chain Deletion will probably not cause chr6:137,501,221- interferon gamma chr6:137,560,315- mycobacteria infection infection with a range of In homozygous mice there is failure 6q23.3 564 *107470 IFNGR1 AR Sanger entire gene 1 Loss 1 JPT No (alpha) of the heterodimeric gamma phenotype unless associated with 137,615,031 receptor 1 137,582,200 (eg: BCG infection from mycobacteria; mutations can cause to control BCG growth interferon receptor additional mutation vaccine) BCG vaccine to cause lethal infection

ACAT2 deficiency Patients with deficiency have chr6:159,974,242- acetyl-Coenzyme A chr6:160,153,496- 6 CEU, 1 CHB, 1 Enzyme involved in lipid Gain is not expected to cause a 6q25.3 574 +100678 ACAT2 (mental retardation and Sanger entire gene 12 Gain No shown severe mental retardation None 160,185,562 acetyltransferase 2 160,170,496 JPT, 4 YRI metabolism phenotype hypotonus) and hypotonus

Polypeptide hormone with structural Gain might be interesting because homologies to insulin; may be 70% of human hepatocellular entire gene (S) this is an imprinted gene, but most 6q25.3- chr6:160,342,655- insulin-like growth chr6:160,360,542- hepatocellular and Affy/Sanger 1 Gain (S) 1 JPT (S) polymorphically imprinted in human; tumors have loss of heterozygosity Mice with maternal deletion die 575 *147280 IGF2R 3' end (43 of 47 No likely the gain is of the 3' end only 6q26 161,205,076 factor 2 receptor 160,497,992 other tumors (Both) 1 Gain (A) 1 JPT (A) may functions as a tumor at this locus; mutations have also during early development exons) (A) (as seen on Affy). Therefore, not suppressor in human liver been seen in the other allele expected to cause a phenotype carcinogenesis

Absence of apolipoprotein(a) from coronary artery May be associated with coronary virtually all species other than disease; Has a role in homocysteine- artery disease; known to be size primates precludes the use of CNV may be due to known size 3' end (44 of 45 atherosclerosis 68 CEU, 42 CHB, 38 enhanced antifibrinolysis in human polymorphic in repeats within gene convenient animal models; but polymorphism of repeats within 6q25.3- chr6:160,342,655- chr6:160,922,926- Affy/Sanger exons)i (S) 202 Gain, 2 Loss (S) 575 +152200 lipoprotein, Lp(a) LPA (myocardial infarction, JPT, 56 YRI (S) Yes plasma; known to have variable = variability in expression; transgenic mice expressing human this gene; this size polymorphism 6q26 161,205,076 161,055,702 (Both) 3' end (43 of 45 1 Gain (A) stroke, restenosis); 1 JPT (A) sequence, which causes wide increased levels associated with apolipoprotein(a) are more is associated with many cardiac exons) (A) arterial or venous variation in Lp(a) levels increased risk for atherosclerosis susceptible than control mice to the phenotypes thrombosis and its manifestations development of lipid-staining lesions in the aorta Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

Homozygous mice develop multiple spontaneous thrombotic lesions leading to severe organ damage Deficiency causes thrombophilia and high morbidity or mortality at an 6q25.3- chr6:160,342,655- chr6:161,093,694- thrombophilia; Affy/Sanger The zymogen in the circulating and Ligneous conjunctivitis early age; double KO combination Gain is not expected to cause a 575 +173350 plasminogen PLG AR and AD entire gene 1 Gain 1 JPT Yes 6q26 161,205,076 161,144,749 Ligneous conjunctivitis (Sanger) blood from which plasmin is formed (sometimes with tracheobronchial of plasminogen deficiency and phenotype fibrin deposition) fibrinogen deficiency prevents corneal fibrin deposits and associated inflammatory reactions and restores normal wound healing

chr6:161,906,087- chr6:161,740,082- 6q26 576 Affy intronic 1 Gain 1 CEU No 161,907,120 163,119,211

chr6:162,161,167- chr6:161,740,082- middle (2 of 12 6q26 577 Sanger 1 Gain 1 CHB No 162,381,661 163,119,211 exons) Mutations seen in autosomal Deletions may have phenotypic recessive juvenile parkinsonism; autosomal recessive consequence, but since they are chr6:162,461,349- chr6:161,740,082- Involved in protein degradation as a hemizygous or homozygous Homozygous mice show motor and 6q26 578 *602544 parkin PARK2 juvenile parkinsonism; AR Affy intronic 1 Loss 1 YRI No only in introns, this is unlikely; gain 162,478,101 163,119,211 ubiquitin-protein ligase deletions have been seen in some cognitive deficits cancer is not expected to cause a cancers; deletions of some exons phenotype also seen in Parkinsons disease chr6:162,706,292- chr6:161,740,082- 6q26 579 Affy intronic 2 Loss 1 CHB, 1 JPT No 162,710,176 163,119,211

5' end (2 of 12 chr6:162,811,333- chr6:161,740,082- Affy/Sanger exons) (S) 1 Gain (S) 1 CHB (S) 6q26 580 No 163,203,672 163,119,211 (Both) middle (1 of 12 1 Gain (A) 1 CHB (A) exons) (A)

Xenopus embryos without detectable Tbp initiated gastrulation complex neurologic but died before completing Unclear if gain/loss of these gene Expansion of CAG repeat can disorder with cerebellar Tata-box binding protein, is the gastrulation; homozygous mice would be important; CAG chr6:170,499,383- TATA box binding chr6:170,781,103- cause neurologic disorder 6q27 588 *600075 TBP ataxia, pyramidal signs, AD Sanger entire gene 1 Gain, 1 Loss 1 CHB, 1 YRI No DNA-binding subunit of TFIID; has fetuses died in midgestation from expansion is probably dominant- 170,927,551 protein 170,799,578 manifested by ataxia and and severe intellectual polymorphic CAG repeat; an apparent defect in the placenta; negative so deletion may not give intellectual deterioration impairment (SCA17) heterozygous mice were born in the same phenotype expected mendelian frequency and were of normal

Chr. 7

An allele is associated with Transgenic mice carrying the multiple myeloma, T- increased expression susceptibility human IL6 gene showed reduced cell lymphoma, ovarian Has a role in insulin signal for lipid abnormalities (Obesity), Deletion may be associated with chr7:22,528,824- chr7:22,540,060- growth (50-70% of non-traqnsgenic 7p15.3 609 *147620 interleukin 6 IL6 cell carcinoma, Kaposi Sanger entire gene 1 Loss 1 CEU No transduction via insulin receptor diabetes, hyperandrogenic susceptibility for metabolic 22,694,150 22,544,856 mice) and decreased IGFI sarcoma; osteopenia, substrate-1 in skeletal muscle cells disorders, and some other disorders and cancer production; chronic inflammation osteoporosis phenotypes; also some association affects growth with different cancers

Encodes a nuclear protein with juxtaposed with Fusion with JJAZ1 (due to recurrent 7p15.2- chr7:27,566,856- chr7:27,643,432- endometrial stromal three C2H2-type zinc fingers, and Loss is not expected to cause a 611 *606246 another zinc finger JAZF1 Sanger 3' end (3 of 5 exons) 1 Loss 1 CHB No translocation) was present in all None 7p15.1 27,746,109 27,993,465 sarcomas functions as a transcriptional phenotype gene 1 types of endometrial stromal tumors repressor

chromosome 7 nonphotosensitive Also called C7orf11; may be Mutations (including small Deletion will probably not cause chr7:39,833,420- chr7:27,643,432- 7p14.1 616 *609188 open reading frame TTDN1 trichothiodystrophy AR Affy entire gene 1 Gain 1 CHB No involved in transcription but not deletions) were found in TTDN1 None phenotype unless associated with 40,042,823 27,993,465 11 (TTDN1) DNA repair patients additional mutation

Encodes a member of a highly Mutations (including gene conserved protein family that exists conversion mutations which chr7:65,845,580- Shwachman-Bodian- chr7:65,896,840- Shwachman-Diamond Gain is not expected to cause a 7q11.21 626 *607444 SBDS AR Sanger entire gene 2 Gain 2 JPT Yes from archaea to vertebrates and accounted for 74.4% of disease None 66,303,403 Diamond syndrome 65,904,738 syndrome (AR) phenotype plants; may function in RNA alleles) cause Shwachman- metabolism Diamond syndrome

Mouse gene is associated with a novel autoimmune mechanism Mutations were found to cause leading to severe destructive chronic granulomatous Loss of gene may be associated Cytosolic subunit of the multi- CGD; WBS deletion can sometimes arthritis (rheumatoid arthritis in chr7:73,439,084- neutrophil cytosolic chr7:74,017,097- disease (AR, b- Affy/Sanger with prevention of hypertension; in 7q11.23 629 *608512 NCF1 AR entire gene 4 Gain, 1 Loss 3 CEU, 1 JPT, 1 YRI Yes protein complex known as NADPH contain this gene (hypertension is human); Mutated mice (with a point 76,494,030 factor 1 74,032,410 positive, Type I); WBS (Sanger) WBS region, so gain may have oxidase found in neutrophils significantly less prevalent in WBS mutation in the splice site for exon 8 & hypertention some consequence also patients hemizygous for NCF1) of the Ncf1 gene) showed augmented severity of collagen- induced

Homozygous mutants may exhibit A membrane-associated protein axial skeleton defects, that colocalizes with huntingtin; has PDGFRB/HIP1 fusion gene hematopotietic abnormalities, and Gain is not expected to cause chronic chr7:73,439,084- huntingtin chr7:74,808,060- Affy/Sanger 3' end (31 of 32 similarities to cytoskeleton proteins (caused by a translocation) was testicular degeneration with phenotype (although may be 7q11.23 629 *601767 HIP1 myelomonocytic 11 Gain 2 CEU, 1 JPT, 8 YRI No 76,494,030 interacting protein 1 75,012,930 (Sanger) exons) and its interaction with huntingtin is found in a patient with chronic increased apoptosis of postmeiotic associated with susceptibility to leukemia (CMML) thought to play a functional role in myelomonocytic leukemia spermatids; one line showed some cancers) the cell filament network microphthalmia and cataracts, whereas others did not

Homozygotes for targeted null P450 oxidoreductase mutations exhibit defects of the Mutations were found to cause (POR) deficiency; Encodes an endoplasmic reticulum neural tube, eye, heart, and limbs, POR deficiency; mutations were chr7:73,439,084- P450 (cytochrome) chr7:75,227,958- Disordered Affy/Sanger membrane oxidoreductase with an retarded growth, and prenatal Gain is not expected to cause 7q11.23 629 *124015 POR AR and AD entire gene 6 Gain 1 CEU, 5 YRI No also found to cause disordered 76,494,030 oxidoreductase 75,260,823 steroidogenesis; (Sanger) FAD-binding domain and a lethality; liver-specific knockouts phenotype steroidogenesis and congenital congenital adrenal flavodoxin-like domain exhibit increased liver weight, adrenal hyperplasia hyperplasia hepatic lipidosis, and impaired drug metabolism

Charcot-marie-Tooth Mutations were found to cause chr7:73,439,084- chr7:75,576,574- disease type 2F, Affy/Sanger entire gene (does not Hits merged - not Hits merged - not Heat-shock protein of endothelial disease including Charcot-Marie- Not expected to cause a 7q11.23 629 *602195 heat shock protein 1 HSPB1 AD No None 76,494,030 75,578,263 xDistal heretitary motor (Neither) hit CNVs) individual CNV calls individual CNV calls cells Tooth disease type 2F and distal phenotype neuropathy HSPB type hereditary motor neuropathy

Hydrolyzes the neurotransmitter, Homozygous mice were found with 4-bp deletion polymorphism in acetylcholine at neuromuscular drastic reductions in expression of Deletion will probably not cause chr7:100,000,141- acetyl- chr7:100,132,269- Acute hypersensitivity ACHE promotor (17kb upstream) 7q22.1 638 +100740 ACHE Sanger entire gene 1 Loss 1 JPT No junctions and brain cholinergic several muscarinic ACh receptors phenotype unless associated with 100,342,681 cholinesterase 100,138,147 to anti-AChEs causes acute hypersensitivity to synapses, and thus terminates in brain regions associated with additional mutation anti-AChEs signal transmission learning and memory

Encodes a trypsinogen; secreted by 4 CEU, 14 CHB, 9 the pancreas and cleaved to its chr7:141,610,138- protease, serine, 1 chr7:141,943,619- hereditary & idiopathic Affy/Sanger 28 Loss (S) JPT, 1 YRI (S) active form in the small intestine; Mutations were found to cause Since disorder is dominant, 7q34 660 +276000 PRSS1 AD entire gene Yes None 142,240,984 (trypsin 1) 141,947,210 chronic pancreatitis (Both) 4 Loss (A) 2 CEU, 1 CHB, 1 active on peptide linkages involving pancreatitis deletion may cause phenotype JPT (A) the carboxyl group of lysine or arginine

Encodes a type II transmembrane Kell blood group, chr7:141,610,138- chr7:142,155,040- Affy/Sanger glycoprotein that is the highly Point mutations cause different Kell Loss is not expected to cause a 7q34 660 +110900 metallo- KEL Kell null entire gene 1 Loss 1 CEU No None 142,240,984 142,176,340 (Sanger) polymorphic Kell blood group null phenotypes phenotype endopeptidase antigen

Long QT syndrome 2 potassium voltage- Deletion may cause some (familiar, sporadic, Homozygous mice manifested chr7:149,976,469- gated channel, chr7:150,079,697- Encodes a Ca(2+)-modulated Mutations were found to cause phenotypes (due to channel 7q36.1 665 +152427 KCNH2 acquired, bradycardia- AD Sanger entire gene 1 Loss 1 CEU No abrupt spontaneous episodes of 150,101,345 subfamily H (eag- 150,112,662 potassium channel LQT2; mutations also cause SQT1 dysfunction; although this may be induced); Short QT sinus brachycardia related), member 2 dominant-negative disorder) syndrome 1 (familiar)

Chr. 8

A potential oncogene containing malignant fibrous domains which are structural or Overexpression may be oncogenic Gain may increase expression chr8:8,745,049- histiocytoma chr8:8,680,942- Malignant fibrous 8p23.1 682 *605352 MFHAS1 Affy 5' end (1 of 3 exons) 1 Gain 1 JPT No functional elements for interactions in some malignant fibrous None and may be associated with some 8,785,304 amplified sequence 8,787,978 histiocytoma among proteins related to the cell histiocytomas (MFH) cancers 1 cycle

A candidate tumor suppressor gene; expressed in most Homozygous deletion (large, maybe Deletion will probably not cause chr8:14,670,571- tumor suppressor chr8:15,442,101- metastatic prostate Affy/Sanger 2 Loss (S) 2 CEU (S) 8p22 689 *601385 TUSC3 entire gene No nonlymphoid human tissues >700 kb) seen in metastatic None phenotype unless associated with 15,809,077 candidate 3 15,666,364 cancer (Both) 2 Loss (A) 2 CEU (A) including prostate, lung, liver, and prostate cancer additional mutation colon

Region is commonly deleted in Encodes a protein with significant colorectal cancer, hepatocellular platelet-derived sequence similarity to the ligand chr8:17,335,551- chr8:17,478,986- Affy/Sanger entire gene (S) 1 Loss (S) 1 JPT (S) carcinoma, non-small cell lung Deletion may be associated with 8p22 691 *604584 growth factor PDGFRL cancers No binding domain of platelet-derived None 17,685,810 17,544,903 (Both) entire genei (A) 2 Loss (A) 1 JPT, 1 YRI (A) cancer; mutations were also found some cancers receptor-like growth factor receptor beta; may in colorectal cancer, hepatocellular function as a tumor suppressor carcinoma

Mutations were found in families congenital universal Deletion will probably not cause chr8:20,577,324- chr8:22,027,879- Affy/Sanger 1 Loss (S) 1 CEU (S) Encodes a protein whose function with congenital universal alopecia; 8p21.3 695 *602302 hairless homolog HR alopecia; atrichia with AR entire gene No None phenotype unless associated with 23,167,554 22,043,975 (Both) 1 Loss (A) 1 CEU (A) has been linked to hair growth other mutations were found to papular lesions additional mutation cause atrichia with papular lesions Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

desquamative Homozygous mice were viable at Mutations were found to cause interstitial pneumonitis; birth and grew normally to surfactant, A hydrophobic surfactant protein; chronic interstitial lung disease (and pulmonary alveolar adulthood without apparent Deletion may cause lung chr8:20,577,324- pulmonary- chr8:22,075,113- Affy/Sanger 1 Loss (S) 1 CEU (S) promotes rapid surface film other lung phenotypes); certain 8p21.3 695 *178620 SFTPC proteinosis; familial AD entire gene No pulmonary abnormalities; other phenotype or act as risk factor for 23,167,554 associated protein 22,077,928 (Both) 1 Loss (A) 1 CEU (A) formation by simple mixtures of alleles may be risk factors for idiopathic pulmonary surfactant proteins (A, B, D) in respiratory distress C phospholipids respiratory distress syndrome and fibrosis; deficiency of alveolar lavage were comparable to bronchopulmonary dysplasia surfactant protein C those in wildtype mice

Nonsense mutation was found in Homozygous mutants exhibit tumor necrosis SCC; 8p21 region contains a enhanced innate immune head and neck A member of the TNF-receptor Deletion of this region seen in chr8:20,577,324- factor receptor chr8:22,075,113- Affy/Sanger number of putative tumor responses, including increased 8p21.3 695 *603612 TNFRSF10B squamous cell entire gene 1 Loss 1 CEU WSSD superfamily, and contains an some cancer; loss may increase 23,167,554 superfamily, 22,077,928 (Sanger) suppressor genes and is a frequent clearance of cytomegalovirus and carcinoma (SCC) intracelluar death domain susceptibility member 10b site of translocations in head and increased levels of IL-12, IFN-alpha neck tumors and IFN-gamma after viral infection

Deficiency of this gene causes familial hypogonadotropic Hypogonadism in the hpg A key molecule in the hypothalamic- gonadotropin- hypogonadism (no mutations have (hypogonadal) mouse is caused by Loss of this gene could cause chr8:25,324,942- chr8:25,332,693- hypogonadotropic pituitary-gonadal axis that controls 8p21.2 697 *152760 releasing hormone GNRH1 AR Sanger entire gene 1 Loss 1 JPT No been identified); most cases of a deletional mutation of at least deficiency leading to 25,478,051 25,337,836 hypogonadism human reproduction; stimulates the 1 GNRH deficiency in humans are 33.5 kb encompassing the distal hypogonadism secretion of both LH and FSH sporadic and, thus, could represent half of the gene new mutation

Mutations at this locus effect genome stability, radiation encodes the catalytic subunit of a sensitivity and DNA repair; Loss of this gene could cause protein kinase, DNA- nuclear DNA-dependent PRKDC deficiency may be involved nonsense (scid) and null chr8:48,950,846- chr8:48,848,222- 5' end (38 of 86 PRKDC deficiency which may be 8q11.21 702 *600899 activated, catalytic PRKDC PRKDC deficiency Sanger 2 Loss 2 YRI No serine/threonine protein kinase; in apoptosis and/or cancer (no homozygotes have severe 49,170,567 49,035,296 exons) associated with increased risk of polypeptide involved in DNA repair, apoptosis, mutations reported) combined immunodeficiency; a cancer transcriptional regulation BALB/c variant allele reduces enzyme activity and predisposes to breast cancer

Encodes an accessory enzyme 2,4-Dienoyl-CoA reductase Loss of this gene may cause chr8:91,069,962- 2,4-dienoyl CoA chr8:91,082,756- 2,4-Dienoyl-CoA Affy/Sanger which participates in the beta- 8q21.3 719 +222745 DECR1 entire gene 1 Loss 1 JPT No deficiency causes persistent None deficiency which could be 91,398,845 reductase 1 91,133,403 reductase deficiency (Sanger) oxidation and metabolism of hypotonia (no mutations reported) associated with hypotonia unsaturated fatty enoyl-CoA esters

5' end (14 of 62 chr8:100,098,024- chr8:100,094,670- 1 CEU, 2 CHB, 1 A potential transmembrane protein Gain is not expected to cause a 8q22.2 723 Sanger exons) (one entire 9 Gain No 100,265,857 100,958,983 JPT, 5 YRI that may function in vesicle- phenotype isoform in CNV) mediated transport and sorting of vacuolar protein proteins within the cell; may play a Mutations were found in patients *607817 VPS13B Cohen syndrome AR None sorting 13B role in the development and the with Cohen syndrome function of the eye, hematological Deletion will probably not cause chr8:100,473,327- chr8:100,094,670- middle (25 of 62 8q22.2 724 Sanger 17 Loss 7 CEU, 5 CHB, 5 YRI No system, and central nervous phenotype unless associated with 100,907,800 100,958,983 exons)i system additional mutation

progressive A member of a family of Mutations were found in patients chr8:102,678,650- chr8:102,574,162- nonsyndromic middle (5 of 16 transcription factor genes; a Disorder is dominant; therefore, 8q22.3 726 *608576 grainyhead-like 2 GRHL2 AD Affy 3 Loss 3 YRI No with progressive nonsyndromic None 102,718,857 102,750,995 sensorineural hearing exons)i mammalian ortholog of the loss may cause phenotype sensorineural hearing loss loss Drosophila gene 'grainyhead'

Large deletions (100 kb A member of the TNF-receptor tumor necrosis encompassing this gene) have Large deletions of this gene have superfamily; an osteoblast-secreted Homozygous mice showed chr8:120,012,490- factor receptor chr8:102,574,162- Juvenile Paget disease been reported to cause Juvenile been identified; could cause 8q24.12 730 *602643 TNFRSF11B AR Sanger 5' end (2 of 5 exons)i 2 Gain 1 CHB, 1 YRI No decoy receptor that functions as a elevated osteoclastogenesis and a 120,344,931 superfamily, 102,750,995 (JPD) Paget disease (JPD); smaller (3-bp) disorder when homozygous or negative regulator of bone consequent osteoporotic phenotype member 11b deletion also seen to cause this when other mutations are present resorption disease

potassium voltage- Epilepsy is dominant; however A member of a family of voltage- chr8:133,470,532- gated channel, KQT- chr8:133,210,438- benign familial neonatal 5' end (1 of 15 48 CEU, 26 CHB, 24 Mutation was found in family with may be dominant-negative; 8q24.22 733 *602232 KCNQ3 AD Sanger 3 Gain, 149 Loss WSSD gated potassium channels; None 133,754,071 like subfamily, 133,562,186 epilepsy exons) JPT, 54 YRI benign familial neonatal epilepsy deletion may still predispose for expressed in the brain member 3 epilepsy

solute carrier family chr8:145,494,501- 39 (zinc chr8:145,608,607- acrodermatitis A candidate intestinal zinc-specific Mutations were found to cause Gain/loss is not expected to cause 8q24.3 743 *607059 SLC39A4 AR Sanger entire gene 1 Gain, 1 Loss 1 CHB, 1 JPT No None 145,668,486 transporter), 145,613,081 enteropathica transporter acrodermatitis enteropathica a phenotype member 4

Chr. 9

Males homozygous for null Expressed only in testis; high mutations are sterile and exhibit a doublesex and mab- Loss of this gene should cause XY expression is necessary for Hemizygosity for this gene (and complete loss of germ cells chr9:514,413- 3 related chr9:831,690- Affy/Sanger sex reversal (however, at the 9p24.3 746 *602424 DMRT1 XY sex reversal AD 5' end (2 of 5 exons) 2 Loss 2 YRI No testicular differentiation, whereas DMRT2) due to distal 9p between postnatal days 7-14, 843,033 transcription factor 959,088 (Sanger) edge of CNV, so may not be within lower expression is compatible with monosomy cause XY sex reversal disorganized seminiferous tubules, 1 CNV) ovarian differentiation and degeneration of Leydig cells; females are normal and fertile

solute carrier family 1 Mice homozygous for disruptions in High-affinity glutamate transporter (neuronal/epithelial Mutations in this gene may be this gene display reduced chr9:4,517,262- chr9:4,480,444- dicarboxylicamino that plays an essential role in Intronic loss, so not expected to 9p24.2 750 *133550 high affinity SLC1A1 Affy intronic 2 Loss 1 CHB, 1 JPT No responsible for dicarboxylicamino locomotor activity and excessive 4,518,816 4,577,469 aciduria; familial ALS transporting glutamate across cause a phenotype glutamate aciduria & familial ALS excretion of glutamate and plasma membranes transporter, system aspartate Xag), member 1

glycine Mutations and homozygous One of 4 protein components Deletion will probably not cause chr9:6,566,991- glycine chr9:6,522,469- encephalopathy; Affy/Sanger 5' end (14 of 25 deletions (at least 30 kb) were 9p24.1 752 *238300 GLDC AR and AD 1 Loss 1 CEU No composing the glycine cleavage None phenotype unless associated with 6,835,561 dehydrogenase 6,635,650 nonketotic (Sanger) exons) found to cause glycine system (protein P) additional mutation hyperglycinemia encephalopathy

oculocutaneous Sequence variants in the Tyrp1 albinism, type III; Mutations have been found to Deletion will probably not cause chr9:12,225,048- tyrosinase-related chr9:12,683,449- Affy/Sanger Involved in the production of gene caused the 'chocolate' and 9p23 762 *115501 TYRP1 Rufous AR entire gene 1 Loss 1 CEU No cause oculocutaneous albinism phenotype unless associated with 12,774,092 protein 1 12,700,258 (Sanger) melanin 'cinnamon' alleles of the brown oculocutaneous type 3 (and other forms of albinism) additional mutation locus in domestic cat albinism (ROCA)

2-bp deletion in C5 of A/J and Deficiency of C5 leads to an AKR/J mice with C5 deficiency had Component 5 of the compliment C5 deficiency; antiinflammatory phenotype; airway hyperresponsiveness, Loss may decrease C5 activity chr9:120,727,751- complement chr9:120,794,169- system; a key mediator of 9q33.2 804 +120900 C5 susceptibilty to liver AD Sanger entire gene 1 Loss 1 JPT No mutations were found to cause C5 whereas C5-sufficient strains did and may affect antiinflammatory 120,922,549 component 5 120,892,108 meconium-induced neutrophil fibrosis deficiency with heterozygous not develop asthma; in mouse response activation mutations showed 50% C5 activity models, C5 deficiency attenuates liver fibrogenesis

Protooncogene encodes a Recurrent translocation occurs in Mice homozygous for mutations in v-abl Abelson cytoplasmic and nuclear protein greater than 90% of CML and ALL chronic myeloid Abl display increased perinatal Loss is not expected to cause a 9q34.12- chr9:130,767,120- murine leukemia chr9:130,618,822- 3' end (8 of 11 tyrosine kinase that has been cases; can cause BCR/ABL fusion 808 *189980 ABL1 leukemia; acute Sanger 1 Loss 1 CEU No mortality and defects in the phenotype; but may be associated 9q34.13 131,058,115 viral oncogene 130,792,614 exons) implicated in processes of cell gene; mutations in ABL domain of lymphoblastic leukemia maturation of B cells in bone with some cancers homolog 1 differentiation, cell division, cell the BCR-ABL fusion were found in marrow adhesion, and stress response patients with CML, ALL

A component of the nuclear pore complex in eukaryotic cells; Fusion genes (NUP214/DEK, localized to the cytoplasmic face of NUP214/ABL1, DEK/NUP214) Essential for embryonic Loss is not expected to cause a 9q34.12- chr9:130,767,120- chr9:131,030,535- acute nonlymphocytic 5' end (17 of 36 808 *114350 nucleoporin 214kDa NUP214 Sanger 1 Loss 1 CEU No the nuclear pore complex where it caused by translocations were development; homozygous ES cells phenotype; but may be associated 9q34.13 131,058,115 131,138,644 leukemia exons) is required for proper cell cycle found in acute nonlymphocytic are not viable with some cancers progression and nucleocytoplasmic leukemia transport

Initiates O-mannosylation, an Homozygous null mice suffered important protein modification in Walker-Warburg Mutations were found to cause developmental arrest around eukaryotes; in yeast, these chr9:131,300,676- protein-O-mannosyl- chr9:131,407,866- syndrome; limb-girdle Affy/Sanger 1 Gain (S) 1 JPT (S) Walker-Warburg syndrome and embryonic day (E) 7.5 and died Gain is not expected to cause a 9q34.13 809 *607423 POMT1 AR entire gene No enzymes are located in the 131,508,504 transferase 1 131,428,746 muscular dystrophy, (Both) 1 Gain (A) 1 JPT (A) limb-girdle muscular dystrophy, between E7.5 and E9.5 (due to phenotype endoplasmic reticulum (ER) and are type 2K type 2K defects in the formation of the required for cell integrity and cell Reichert membrane) wall rigidity

1-acylglycerol-3- Converts lysophosphatidic acid Mutations were found to cause Deletion will probably not cause chr9:136,526,666- chr9:136,843,432- congenital generalized 9q34.3 811 *603100 phosphate O- AGPAT2 AR Sanger entire gene 9 Loss 9 CEU No (LPA) to PA, the second step in de congenital generalized None phenotype unless associated with 137,102,322 136,857,748 lipodystrophy, type I acyltransferase 2 novo phospholipid biosynthesis lipodystrophy, type I additional mutation

Alterations play a role in the Regulates cell fate decisions during chr9:136,526,666- Notch gene chr9:136,664,734- T-cell lymphoblastic pathogenesis of some T-cell Homozygous embryos die during Loss may be associated with 9q34.3 811 *190198 NOTCH1 Sanger entire gene 1 Loss 1 CEU No development; is important for 137,102,322 homolog 1 136,716,075 leukemia neoplasms; many recurrent gestation leukemia normal lymphocyte function translocations seen in T-ALL

Chr. 10

A ligand-dependent AR-associated protein that functions in human Rearrangements (such as prostate cancer cells as an translocations) cause fusion genes Gain/loss is not expected to cause chr10:50,641,980- nuclear receptor chr10:51,242,373- papillary thyroid 12 CEU, 1 CHB, 2 10q11.23 840 *601984 NCOA4 Sanger entire gene 1 Gain, 21 Loss Yes activator to enhance AR with RET that were detected in None a phenotype; but may be 51,595,172 coactivator 4 51,260,738 carcinoma JPT, 7 YRI transcriptional activity 10-fold in the sporadic and radiation-associated associated with some cancers presence of dihydrotestosterone or PTC testosterone Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

chr10:55,027,142- chr10:55,250,866- Affy/Sanger 3' end (2 of 33 Homozygotes for severe mutations 10q21.1 844 1 Loss 1 YRI Yes 55,256,936 56,231,057 (Sanger) exons) A member of the cadherin exhibit circling, head-tossing, superfamily; localized in inner ear hyperactivity, impaired swimming Usher syndrome type Mutations were found to cause hair cell stereocilia and in retinal and profound deafness; mice have Gain/loss is not expected to cause *605514 protocadherin 15 PCDH15 IF; Autosomal AR hearing loss consistent with Usher photoreceptors; plays an essential defects in cochlea and a phenotype recessive deafness syndrome, Type F 5' end (2 of 30 role in maintenance of normal degeneration of hair cells, spiral chr10:56,078,033- chr10:55,250,866- Affy/Sanger 2 Loss (S) 1 CEU, 1 YRI (S) 10q21.1 845 exons) (S) Yes retinal and cochlear function ganglion cells and saccular macula; 56,236,143 56,231,057 (Both) 12 Gain (A) 12 CEU (A) intronic (A) females are poor mothers

If a female has loss on her preeclampsia 10q21.3- chr10:70,127,725- chr10:70,257,387- Mutations on the maternal allele maternal allele, she may have 855 *609397 storkhead box 1 STOX1 (gestational proteinuric AD Sanger 5' end (1 of 4 exons) 3 Loss 3 YRI No Storkhead box gene 1 None 10q22.1 70,301,318 70,322,821 were found to cause preeclampsia increased risk for preeclampsia hypertension) phenotype

Homozygous mutant mice exhibit hemolytic anemia due Deletion may cause decrease in chr10:70,708,723- chr10:70,699,762- middle (2 of 20 Hexokinase catalyzes the first step Mutations cause hemolytic anemia hemolytic anemia with extensive 10q22.1 856 *142600 hexokinase 1 HK1 to hexokinase AD Affy 1 Loss 1 YRI No HK1 activity which may cause 70,722,894 70,831,641 exons) in glucose metabolism due to hexokinase deficiency tissue iron deposition and deficiency some anemia phenotypes reticulocytosis and female infertility

A member of the cadherin superfamily; a large, single-pass transmembrane protein composed of an extracellular domain Usher syndrome type containing 27 repeats that show Mutations were found to cause Mutant mice exhibit circling Deletion will probably not cause chr10:72,907,909- chr10:72,826,697- middle (3 of 68 10q22.1 857 *605516 cadherin-like 23 CDH23 ID; Autosomal AR Affy 1 Loss 1 YRI No significant homology to the cadherin Usher syndrome and AR hearing behavior, tilting of the head and are phenotype unless associated with 72,956,161 73,245,659 exons) recessive deafness ectodomain; expressed in the loss deaf additional mutation neurosensory epithelium, the protein is thought to be involved in stereocilia organization and hair bundle formation

Large-conductance voltage- and potassium large Homozygous mice (targeted generalized epilepsy 5' end (1 of 29 Ca(2+)-activated K+ channel, also conductance disruption) had normal life chr10:78,781,397- chr10:78,299,368- and paroxysmal Affy/Sanger exons)i (S) 1 Gain, 1 Loss (S) 1 CHB, 1 YRI (S) called the BK channel; can be Mutations were found in family with Disorder is dominant; therefore, 10q22.3 860 *605516 calcium-activated KCNMA1 AD No expectancy compared with wildtype 79,263,477 79,067,583 nonkinesigenic (Both) 5' end (1 of 29 1 Gain (A) 1 CHB (A) activated by both intracellular GEPD loss may cause phenotype channel, subfamily littermates, but showed obvious dyskinesia (GEPD) exons) (A) Ca(2+) ions and by membrane M, alpha member 1 ataxia. depolarization

Member of the MAGUK (membrane- associated guanylate kinase) family; localizes to the plasma membrane and cytoplasm, and Variant showed a significant 3' end (15 of 31 interacts with components of difference in association with Crohn chr10:78,781,397- discs, large chr10:79,220,557- susceptibility to Crohn Affy/Sanger exons) (S) 1 Gain (S) 1 CHB (S) Gain is not expected to cause a 10q22.3 860 *604090 DLG5 No adherens junctions and the disease in affected individuals None 79,263,477 homolog 5 79,298,959 disease (Both) 3' end (23 of 31 1 Gain (A) 1 CHB (A) phenotype cytoskeleton; proposed to function carrying risk-associated CARD15 exons) (A) in the transmission of extracellular alleles signals to the cytoskeleton and in the maintenance of epithelial cell structure

Homozygotes for targeted null mutations exhibit impaired lung surfactant, susceptibility to response to hyperventilation, Gain/loss is not expected to cause chr10:80,945,468- pulmonary- chr10:81,040,718- Affy/Sanger 9 CEU, 1 CHB, 1 Plays a role in innate host defense Variant was found to be associated 10q22.3 861 *178630 SFTPA1 diopathic pulmonary entire gene 1 Gain, 13 Loss Yes reduced resistance to pulmonary a phenotype, but may be 81,810,835 associated protein 81,043,975 (Sanger) JPT, 3 CEU in the lung with pulmonary fibrosis fibrosis infections, and enhanced associated with pulmonary fibrosis A1 pulmonary inflammatory response to lipopolysaccharide

Hydrolyzes the abundant multiple inositol metabolites inositol entire gene (S) 20 CEU, 6 CHB, 4 LOH or mutations at the MINPP1 Deficient mice were fertile, lacked 10q23.2- chr10:88,505,038- polyphosphate chr10:89,254,633- follicular thyroid Affy/Sanger 6 Gain, 39 Loss (S) pentakisphosphate and inositol Deletion may be associated 865 *605391 MINPP1 5' end (4 of 5 exons) JPT, 15 CEU (S) No locus were found in patients with obvious defects, and had normal 10q23.31 89,299,742 histidine 89,303,124 adenoma (Both) 1 Gain (A) hexakisphosphate; has the ability to tumours (A) 1 CHB (A) FTA tumours chondrocyte differentiation phosphatase, 1 remove 3-phosphate from inositol phosphate substrates

Homozygous null mutants die by juvenile polyposis embryonic day 9.5, are smaller than bone Germline mutations have been syndrome; Cowden-like normal, and form no mesoderm; a 10q23.2- chr10:88,505,038- morphogenetic chr10:88,506,376- Affy/Sanger 19 CEU, 3 CHB, 4 Receptors for the bone identified in juvenile polyposis Deletion may cause 865 *601299 BMPR1A syndrome; hereditary AD entire genei 1 Gain, 31 Loss No conditional knockout resulted in 10q23.31 89,299,742 protein receptor, 88,674,924 (Sanger) JPT, 6 YRI morphogenetic proteins patients; tumors also show LOH of phenotype/disease mixed polyposis gross malformations of the limbs type 1A this region in these patients syndrome with complete agenesis of the hindlimb

Has a central role in nitrogen familiar metabolism; catalyzes the oxidative Deletion may cause abnormal in hyperinsulinemic deamination of 1-glutamate to 2- Mutations cause hyperinsulinemic nigrogen metabolism (eg: 10q23.2- chr10:88,505,038- glutamate chr10:88,800,225- hypoglycemia Affy/Sanger 53 CEU, 25 CHB, 28 865 *138130 GLUD1 AD entire gene 3 Gain, 164 Loss Yes oxoglutarate (GLUD); glutamate, hypoglycemia and None diminished inhibitory effect of 10q23.31 89,299,742 dehydrogenase 1 88,844,603 (hyperinsulinemic (Sanger) JPT, 61 YRI the main substrate of GLUD, is hyperammonemia guanosine triphosphate on hypoglycemia and present in brain in concentrations glutamate dehydrogenase activity) hyperammonemia) higher than in other organs

Homozygous knockout mice The lysosomal acid lipase (also produced no Lip1 mRNA, protein, known as cholesterol ester or enzyme activity, and were lipase A, lysosomal cholesteryl ester strage Loss may cause decreased chr10:90,825,044- chr10:90,963,309- hydrolase); functions in the Mutations were found in CESD and normal at birth, followed normal 10q23.31 866 +278000 acid, cholesterol LIPA disease (CESD); AR Sanger entire gene 1 Loss 1 CEU No enzyme activity without lipid 91,007,466 91,001,640 lysosome to catalyze the hydrolysis Wolman disease development into adulthood; esterase Wolman disease accumulation of cholesteryl esters and however, massive accumulation of triglycerides triglycerides and cholesteryl esters occurred in several organs

Homozygous targeted and spontaneous null mutants show impaired to absent development of renal-coloboma Believed to be a target of Mutations have been seen to cause chr10:102,141,840- chr10:102,495,322- Affy/Sanger 5' end (6 of 11 optic nerve, retina, kidney, ureters, Deletion may cause renal 10q24.31 870 *167409 paired box gene 2 PAX2 syndrome; bilateral AD 1 Loss 1 YRI No transcriptional supression by the renal-coloboma syndrome and 102,555,726 102,579,687 (Sanger) exons) genital tracts, inner ear and phenotype renal hypoplasia tumor supressor gene WT1 bilateral renal hypoplasia midhindbrain; heterozygotes show milder defects of the optic nerve, retina and kidney

bromodomain and A candidate tumor suppressor gene chr10:122,625,702- chr10:122,600,685- 3' end (18 of 29 LOH of this region was seen in Loss may be associated with 10q26.12 875 *606417 WD repeat domain BRWD2 glioblastoma Sanger 2 Loss 2 YRI No involved in tumorigenesis of glial None 122,891,863 122,659,026 exons) glioblastomas some glioblastomas containing 2 and other tumors

A glycoprotein containing multiple scavenger receptor cysteine-rich (SRCR) domains separated by Homozygous null mice display chr10:124,253,065- deleted in malignant chr10:124,310,171- 2 CEU, 6 CHB, 6 SRCR-interspersed domains (SID); Mutations and LOH were seen in Loss may be associated with 10q26.13 877 *601969 DMBT1 glioblastoma multiforme Sanger entire gene 10 Gain, 13 Loss Yes embryonic lethality and an 124,444,805 brain tumors 1 124,393,242 JPT, 9 YRI not be a classical tumor supressor glioblastomas some glioblastomas abnormal inner cell mass gene, but rather play a role in the interaction of tumor cells and the immune system

Gunther disease Responsible for the conversion of chr10:127,443,890- uroporphyrinogen III chr10:127,467,142- (congenital the linear tetrapyrrole, Mutations were found to cause Gain is not expected to cause a 10q26.2 879 *606938 UROS AR Sanger entire gene 2 Gain 2 YRI No None 127,776,692 synthase 127,501,757 erythropoietic hydroxymethylbilane, to the cyclic CEP phenotype porphyria, or CEP) tetrapyrrole, uroporphyrinogen III

Chr. 11

Mice homozygous for targeted null mutations are viable and fertile with Mutations have been identified in no gross morphological or Loss of gene may increase v-Ha-ras Harvey rat One of the RAS oncogenes; different forms of cancer; germline histological abnormalities, defects susceptibility to cancer; however, chr11:399,846- chr11:522,243- Cancers; susceptibility 11p15.5 885 *190020 sarcoma viral HRAS Sanger entire gene 1 Loss 1 CEU No probably plays a role in normal cell mutations in HRAS perturb human in neuronal development or defects mutations in this gene that are 1,313,968 525,550 to Costello syndrome oncogene homolog growth or differentiation development and increase in lymphocyte cell populations; a associated with cancer may be susceptibility to tumors decreased susceptibility to DMBA dominant-negative effects induced skin papillomas was also demonstrated

Homozygous have less active than Known variants mayb underlie Susceptibility to several wildtype controls in open field tests Might not be in CNV; even if it is in A G-protein coupled receptor which individual differences in neurological and Sanger (no in both novel and familiar CNV, no obvious phenotype would chr11:399,846- dopamine receptor chr11:627,305- No overlap (maybe inhibits adenylyl cyclase; a target susceptibility to neuropsychiatric 11p15.5 885 *126452 DRD4 behavioural diseases clones None (maybe Loss) None (maybe 1 CEU) No environments; also displayed be caused by deletion of this 1,313,968 D4 630,703 entire gene) for drugs which treat schizophrenia disease and in responsiveness to (ADHD, perhaps overlap gene) locomotor supersensitivity to gene; may subtely affect and Parkinson disease antipsychotic medication (ADHD, alcoholism) ethanol, cocaine, and neurology/behaviour alcoholism) methamphetamine

Might not be in CNV; even if it is, Sanger (no Transaldolase deficiency was seen chr11:399,846- chr11:737,432- transaldolase No overlap (maybe None (maybe 1 YRI Key enzyme of the pentose deletion of this gene is not 11p15.5 885 *602063 transaldolase 1 TALDO1 AR clones None (maybe Loss) No caused by a homozygous 3-bp None 1,313,968 755,023 deficiency entire gene) or 1 CEU) phosphate pathway predicted to give a phenotype overlap gene) deletion (because disorder is recessive)

early-onset severe Mitochondrial carrier that transports Missense mutations seen in early- Deletion will probably not cause chr11:399,846- solute carrier family chr11:780,476- 11p15.5 885 *609302 SLC25A22 seizures and neonatal AR Sanger entire gene 1 Loss 1 YRI No a variety of metabolites across the onset severe seizures and neonatal None phenotype unless associated with 1,313,968 25, member 22 786,221 hypotonia inner mitochondrial membrane hypotonia additional mutation Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

A member of the transmembrane 4 superfamily; a cell surface Homozygous mice were viable, glycoprotein that is known to fertile, and healthy, with normal Nephropathy with complex with integrins and other Homozygous insertion causes Deletion will probably not cause chr11:399,846- chr11:822,986- blood and marrow cell counts and 11p15.5 885 *602243 CD151 molecule CD151 pretibial epidermolysis AR Sanger entire gene 1 Loss 1 YRI No transmembrane 4 superfamily Nephropathy with pretibial phenotype unless associated with 1,313,968 828,834 normal tissue morphology and bullosa and deafness proteins; involved in cellular epidermolysis bullosa and deafness additional mutation integrin expression in skin; some processes including cell adhesion other mild phenotypes seen and may regulate integrin trafficking and/or function

Mutant protein expressed in type 1 long QT Mutations cause type 1 long QT potassium voltage- Encodes a protein for a voltage- Xenopus with wildtype protein syndrome; Jervell and syndrome (dominant-negative 11p15.5- chr11:2,745,620- gated channel, KQT- chr11:2,422,797- AD (dominant- 3' end (5 of 15 gated potassium channel required abolish protein activity (dominant- Gain of 3' end is not expected to 886 *607542 KCNQ1 Lange-Nielsen Sanger 2 Gain 2 CEU No effect); different mutations also 11p15.4 2,920,188 like subfamily, 2,826,915 negative); AR exons) for the repolarization phase of the negative); homozygous-null mice cause a phenotype cardioauditory cause recessive Jervell and Lange- member 1 cardiac action potential were deaf and exhibited a shaker- syndrome Nielsen cardioauditory syndrome waltzer phenotype

Homozygous mutants or heterozygotes with a mutant Potent tight-binding inhibitor of maternal allele have developmental Beckwith-Wiedemann several G1 cyclin/Cdk complexes, Mutations cause BWS, suggested Most imprinted genes are dosage defects including cleft palate, 11p15.5- chr11:2,745,620- cyclin-dependent chr11:2,861,441- syndrome; maybe and is a negative regulator of cell that normal variation may sensitive. If gain leads to 886 *600856 CDKN1C AD Sanger entire gene 2 Gain 2 CEU No gastrointestinal defects and short 11p15.4 2,920,188 kinase inhibitor 1C 2,863,537 susceptibility to some proliferation; incompletely imprinted predispose to some tumours increased expression this may limbs; most mutants die at birth; tumours gene (preferential maternal (disputed) cause phenotype survivors are growth retarded and expression) have immature reproductive systems

Cancer (Wilms tumour, One of several tumor-suppressing Another imprinted gene; breast cancer); subtransferable fragments located Some mutations are associated associated with different forms of 11p15.5- chr11:2,745,620- solute carrier family chr11:2,877,527- 886 *602631 SLC22A18 associated with Sanger entire gene 2 Gain 2 CEU No in the imprinted gene domain of with tumours (such as Wilms None cancer; unclear whether increased 11p15.4 2,920,188 22, member 18 2,903,051 Beckwith-Wiedemann 11p15.5; "leaky" maternal tumour); Maybe involved in BWS expression would cause syndrome expression (paternal imprinting) phenotype

Disruption of this gene (by Recurrent translocations (and translocation) has been seen in chr11:3,193,088- chr11:3,652,817- Affy/Sanger 3' end (29 of 31 12 CEU, 14 CHB, 11 Protein that functions in the nuclear protein fusions) seen in some many translocation (translocation 11p15.4 887 *601021 nucleoporin 98kDa NUP98 Myeloid leukemia 1 Gain, 71 Loss No None 3,758,005 3,775,468 (Sanger) exons)i JPT, 35 YRI transport of protein and RNA myeloid leukemia and other hotspot); deletion may also cause cancers phenotype or be associated/risk for leukemia

pyruvate neonatal lactic Deletion will probably not cause chr11:34,869,891- dehydrogenase chr11:34,894,741- acidemia and 5' end (2 of 11 Component X of the pyruvate Mutations cause neonatal lactic 11p13 908 *608769 PDHX AR Affy 1 Loss 1 CEU No None phenotype unless associated with 34,920,304 complex, 34,974,092 deficiency of the exons) dehydrogenase (PDH) complex acidemia additional mutation component X component X protein

Splice variants may be associated Integral cell membrane glycoprotein 5' end (10 of 18) with metastasis; expression on with a postulated role in matrix chr11:34,986,509- chr11:35,116,993- problems with Affy/Sanger exons (S) 1 Loss (S) 1 YRI (S) activated monocytes was reduced Arteriogenesis was severely Loss is not expected to cause a 11p13 909 *107269 CD44 molecule CD44 No adhesion, lymphocyte activation 35,195,154 35,210,524 arteriogenesis (Both) 5' end (15 of 18 1 Loss (A) 1 YRI (A) in patients with poor impaired in homozygous null mice phenotype and lymph node homing; pivotal exons) (A) collateralization compared to role in arteriogenesis patients with good collateralization

Thought to be involved in damage-specific Encodes the large subunit of DNA chr11:60,671,936- chr11:60,823,500- 3' end (11 of 27 39 CEU, 39 CHB, 41 xeroderma pigmentosa, but Gain/loss of 3' end of this gene not 11q12.2 922 *600045 DNA binding protein DDB1 None Sanger 180 Gain, 2 Loss WSSD damage-binding protein; functions None 60,837,233 60,857,125 exons) JPT, 63 YRI mutations were instead found in expected to cause a phenotype 1 in nucleotide-excision repair DDB2

NADH Deletion will probably not cause chr11:67,229,481- dehydrogenase chr11:67,554,685- Affy/Sanger 2 Loss (S) 1 CEU, 1 CHB (S) Component of NADH-Ubiquinone 11q13.2 926 *602141 NDUFS8 Leigh syndrome AR entire gene No Mutations cause Leigh syndrome None phenotype unless associated with 67,647,865 (ubiquinone) Fe-S 67,560,690 (Both) 1 Loss (A) 1 CHB (A) oxidoreductase additional mutation protein 8

Infantile malignant Subunit of an enzyme that mediates Deletion will probably not cause chr11:67,229,481- T-cell, immune chr11:67,563,059- Affy/Sanger 2 Loss (S) 1 CEU, 1 CHB (S) Mutations cause Infantile malignant Inactivation in mice caused 11q13.2 926 *604592 TCIRG1 autosomal recessive AR entire gene No acidification of eukaryotic phenotype unless associated with 67,647,865 regulator 1 67,574,941 (Both) 1 Loss (A) 1 CHB (A) autosomal recessive osteopetrosis osteoclast-rich osteopetrosis osteopetrosis intracellular organelles additional mutation

Encodes a member of the potassium channel, voltage-gated, isk-related subfamily; a type I potassium voltage- membrane protein, and a beta chr11:73,520,257- gated channel, Isk- chr11:73,843,536- Affy/Sanger 1 Gain (S) 1 CHB (S) Mutations cause periodic paralysis Gain is not expected to cause a 11q13.4 928 *604433 KCNE3 periodic paralysis AR entire gene No subunit that assembles with a None 74,235,245 related family, 73,856,186 (Both) 1 Gain (A) 1 CHB (A) (may be dominant) phenotype potassium channel alpha-subunit to member 3 modulate the gating kinetics and enhance stability of the multimeric complex

Chr. 12

Suggested role in the development Hereditary sensory and chr12:205,271- hereditary sensory chr12:847,257- Affy/Sanger and/or maintenance of peripheral Mutations found in patients with Gain is not expected to cause a 12p13.33 966 *608620 HSN2 autonomic neuropathy AR entire gene 1 Gain 1 YRI No None 860,805 neuropathy, type II 848,561 (Sanger) sensory neurons or their supporting HSAN II phenotype type II Schwann cells

Mutations identified causing one form of pseudohypoaldosteronism Heterozygous mice displayed a 5' end (12 of 28 type II, an autosomal dominant significant decrease in blood WNK lysine Pseudo- Encodes a cytoplasmic serine- Gain is not expected to cause a chr12:205,271- chr12:732,993- Affy/Sanger exons) (S) 1 Gain (S) 1 YRI (S) disorder characterized by pressure; homozygous mice for the 12p13.33 966 *605232 deficient protein WNK1 hypoaldosteronism AD No threonine kinase expressed in distal phenotype (disease caused by 860,805 888,219 (Both) 5' end (4 of 28 1 Gain (A) 1 YRI (A) hypertension, hyperkalemia, and Wnk1 mutation died during kinase 1 type II nephron deletion) exons) (A) renal tubular acidosis; patients embryonic development before day carried deletions of 22 and 41kb, in 13 of gestation. intron one of the gene

Subunit, containing 2 transmembrane spanning domains, Mutations identified in patients with Deficient neonates developed sodium channel, Pseudo- chr12:6,324,145- chr12:6,326,276- Affy/Sanger of sodium channel (ENaC), which is pseudohypoaldosteronism type I; respiratory distress and died within Gain is not expected to cause a 12p13.31 967 *600228 nonvoltage-gated 1 SCNN1A hypoaldosteronism AR Entire gene 1 Gain 1 YRI No 6,534,096 6,354,976 (Sanger) expressed in the distal nephron and variants could lead to an increased 40 hours of birth from failure to phenotype alpha type I regulated by aldosterone; supports risk of hypertension clear their lungs of liquid. sodium conductance

Mutations seen in patients with Muscle Tarui disease, a deficiency of this phosphofructokinase Catalyzes the irreversible chr12:46,715,969- phospho- chr12:46,802,815- Affy/Sanger protein which causes muscle Gain is not expected to cause a 12q13.11 989 +232800 PFKM deficiency (glycogen AR Entire gene 1 Gain 1 CHB No conversion of fructose 6-phosphate None 47,111,766 fructokinase 46,826,154 (Sanger) cramps with exertion and phenotype storage disease VII or to fructose 1,6-bisphosphate myoglobinuria with extreme exertion Tarui disease) in patients

Basic protein which chr12:50,849,531- keratin, hair, basic, chr12:50,965,966- Affy/Sanger 1 Gain (S) 1 CEU (S) Mutations are seen in the rare Gain is not expected to cause a 12q13.13 990 *602153 KRTHB1 Monilethrix AD Entire gene No heterodimerizes with type I keratins None 51,071,786 1 50,971,566 (Both) 1 Gain (A) 1 CEU (A) disease Monilethrix phenotype to form hair and nails

Basic protein which chr12:50,849,531- keratin, hair, basic, chr12:50,981,916- Affy/Sanger 1 Gain (S) 1 CEU (S) Mutations are seen in the rare Gain is not expected to cause a 12q13.13 990 *601928 KRTHB6 Monilethrix AD Entire gene WSSD heterodimerizes with type I keratins None 51,071,786 6 50,989,212 (Both) 1 Gain (A) 1 CEU (A) disease Monilethrix phenotype to form hair and nails

Homozygotes for a targeted null Kinesins are microtubule-based mutation die at birth; most mutants Gain may be tolerated. Interesting Mutations in this gene cause chr12:56,116,000- kinesin family chr12:56,230,114- Hereditary spastic 5 CHB, 6 JPT, 26 motor proteins involved in the for a postnatal conditional knockout lack of CEU, but no population 12q13.3 992 *602821 KIF5A AD Sanger Entire gene 37 Gain No autosomal dominant spastic 56,288,135 member 5A 56,264,821 paraplegia (SPG10) YRI transport of organelles in eukaryotic allele exhibit fatal seizures around 3 differences was mentioned paraplegia 10 cells. weeks of age, but about 1/4 survive regarding the disease to 3 months or older

Serves as a dominant-negative inhibitor of the transcription factors DNA-damage- Involved in cancer through a Possible that CNV increases risk chr12:56,116,000- chr12:56,196,640- 5 CHB, 6 JPT, 26 C/EBP and LAP. Activated by 12q13.3 992 +126337 inducible transcript DDIT3 Myxoid liposarcoma Sanger Entire gene 37 Gain No common translocation (that cause None for the translocation to occur; may 56,288,135 56,200,567 YRI endoplasmic reticulum (ER) stress 3 gene fusions) be associated with some cancers imposed by unfolded and malfolded proteins

Functions as a ligand-gated ion channel and is responsible for ATP- Mice homozygous for disruptions in dependent lysis of macrophages this gene are fertile and viable with through the formation of membrane Polymorphism may be associated no obvious phenotypic abnormality. purinergic receptor chr12:119,878,565- chr12:120,033,398- Susceptibility to chronic 5' end (1 of 13 pores permeable to large with chronic lymphatic leukemia Cellular responses of macrophages Loss is not expected to cause a 12q24.31 1008 *602566 P2X, ligand-gated P2RX7 Sanger 1 Loss 1 JPT Yes 120,047,533 120,086,591 lymphatic leukemia exons) molecules; activation of this nuclear (disputed; not replicated in to extracellular ATP are frequently phenotype ion channel, 7 receptor by ATP in the cytoplasm subsequent study) normal however; in addition, long may be a mechanism by which bones are thinner than normal in cellular activity can be coupled to adult mice changes in gene expression

Knockouts failed to thrive and died maturity-onset diabetes Mutations and small deletions chr12:119,878,565- transcription factor chr12:119,879,269- Transcription factor that regulates a around weaning after a progressive Loss may cause MODY3 or could 12q24.31 1008 *142410 TCF1 of the young, type III AD Sanger entire gene 1 Loss 1 JPT No cause MODY3; LOH of the gene is 120,047,533 1 119,903,032 large number of genes wasting syndrome with marked liver be associated with adenomas (MODY3) also often found in liver adenomas enlargement.

eukaryotic Leukoencephalopathy A GTP exchange factor that is Mutations seen in chr12:122,635,002- translation initiation chr12:122,630,451- Gain is not expected to cause a 12q24.31 1009 *606686 EIF2B1 with vanishing white AR Affy 5' end (6 of 9 exons)i 2 Gain 2 CEU No essential for protein synthesis; its leukoencephalopathy with None 122,720,736 factor 2B, subunit 1 122,643,127 phenotype matter substrate is EIF2 vanishing white matter alpha Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive? Chr. 13

A member of the fibroblast growth factor (FGF) family; members of this family possess broad mitogenic Early-onset tremor, Deficient mice were viable, fertile, and cell survival activities, and are Mutations cause early-onset chr13:101,459,508- fibroblast growth chr13:101,173,036- dyskinesia, and slowly and anatomically normal, but Intronic loss, so not expected to 13q33.1 1051 +601515 FGF14 AD Affy intronic 1 Loss 1 JPT No involved in a variety of biological tremor, dyskinesia, and slowly 101,483,261 factor 14 101,852,125 progressive cerebellar developed ataxia and a paroxysmal cause a phenotype processes, including embryonic progressive cerebellar ataxia ataxia (SCA27) hyperkinetic movement disorder development, cell growth, morphogenesis, tissue repair, tumor growth and invasion

Chr. 14

Homozygotes for a spontaneous Mutations cause defective protein mutation exhibit a severe microcytic Type I hereditary seen in many patients with anemia with erythrocyte fragility, Deletion will probably not cause chr14:64,324,218- chr14:64,282,755- middle (13 of 35 14q23.3 1085 +182870 spectrin, beta SPTB spherocytosis and AR Affy 1 Loss 1 YRI No An erythrocyte membrane protein abnormalities of red blood cell hepatomegaly, and jaundice; phenotype unless associated with 64,341,533 64,359,619 exons) elliptocytosis shape, including hereditary mutants die within a few days of additional mutation spherocytosis and elliptocytosis birth; heterozygotes are mildly anemic

Methylmalonate Catalyzes the irreversible oxidative aldehyde semialdehyde decarboxylation of malonate and Only one patient known to have chr14:73,620,134- chr14:73,596,626- 5' end (1 of 12 Gain is not expected to cause a 14q24.3 1088 +603178 dehydrogenase 6 ALDH6A1 dehydrogenase AR Affy 1 Gain 1 YRI No methylmalonate semialdehydes to mutations causing MMSDH None 73,676,171 73,620,949 exons) phenotype family, member A1 deficiency (MMSDH acetyl- and propionyl-CoA, deficiency deficiency) respectively

Homozygotes for spontaneous and targeted mutations exhibit tremors, progressive weakness, wasting, A lysosomal enzyme involved in the both central and peripheral Mutations give rise to Krabbe catabolism of galactosylceramide, a demyelination, massive Unmasking of recessive allele is chr14:87,460,869- galactosyl- chr14:87,469,113- 3' end (8 of 18 disease; common deletion of exons 14q31.3 1099 *606890 GALC Krabbe disease AR Affy 2 Loss 2 CEU WSSD major lipid in myelin, kidney, and accumulation of common when patients inherit 87,500,047 ceramidase 87,529,596 exons)i 11-17 has been reported (together epithelial cells of the small intestine galactosylceramide, abnormal deletion with a polymorphic transition) and colon macrophages, and death by 4 months of age; there are also naturally occuring dogs and rhesus monkey with mutations in the gene

Encodes a member of the X-ray repair RecA/Rad51-related protein family complementing Association studies showed link to Convincing evidence for chr14:103,217,278- chr14:103,233,708- that participates in homologous 14q32.33 1104 *600675 defective repair in XRCC3 Cancer Sanger entire gene 1 Loss 1 CEU No malign melanoma and breast None involvement in DNA repair, but 103,482,566 103,251,549 recombination to maintain Chinese hamster cancer association to cancer is weak. chromosome stability and repair cells 3 DNA damage

Chr. 15

Encodes a potential transmembrane protein which may non imprinted in function as a receptor or 15q11.1- chr15:18,263,733- Prader- chr15:20,594,720- spastic paraplegia-6 Affy/Sanger 1 Gain, 2 Loss (S) 1 CHB, 2 YRI (S) transporter molecule; may play a Mutations cause hereditary spastic Autosomal dominant disorder; 1107 *608145 NIPA1 AD entire gene No None 15q11.2 21,365,850 Willi/Angelman 20,637,877 (SPG6) (Both) 1 Gain, 2 Loss (A) 1 CHB, 2 YRI (A) role in nervous system paraplegia-6 deletion could cause phenotype syndrome 1 development and maintenance; widely expressed with highest levels in neuronal tissues

Bicistronic imprinted (paternally 0.9-kb deletion of exon 1 of mouse expressed) gene that encodes 2 Deletions of SNRPN exon 1 are Snrpn did not disrupt imprinting or Deletions of the 5' end of SNRPN small nuclear polypeptides; may be involved in associated with a block of the elicit any obvious phenotype; are known to cause PWS; these chr15:22,606,371- chr15:22,619,887- Prader-Willi syndrome, 5' end (3 of 12 15q11.2 1110 *182279 ribonucleoprotein SNRPN AD Affy 3 Loss 3 YRI No tissue-specific alternative RNA maternal-paternal imprint switch in overlapping 4.8-kb deletion caused CNVs are expected to cause 22,689,056 22,774,822 Angelman syndrome exons)i polypeptide N processing events; 5' end also several families with Prader-Willi a partial or mosaic imprinting defect phenotype, especially if paternally involved in expression of SNURF and Angelman syndromes and perinatal lethality when inherited and UBE3AS paternally inherited

Involved in regulating innate Gain/loss not expected to cause a 22 CEU, 9 CHB, 5 immune response (essential for Polymorphisms in this region show chr15:29,553,592- cholinergic receptor, chr15:30,110,018- Affy/Sanger entire genei (S) 7 Gain, 58 Loss (S) phenotype; maybe represent 15q13.3 1114 +118511 CHRNA7 schizophrenia, epilepsy JPT, 29 YRI (S) Yes inhibiting cytokine synthesis by the linkage with schizophrenia and None 30,773,871 nicotinic, alpha 7 30,248,525 (Both) entire gene (A) 3 Gain (A) susceptibility for complex 3 CEU (A) cholinergic antiinflammatory epilepsy disorders pathway)

Homozygotes for targeted null agenesis of the corpus mutations exhibit locomotor deficits, Suggested to play a critical role in Deletion will probably not cause chr15:32,330,313- solute carrier family chr15:32,312,958- callosum associated Affy/Sanger 5' end (10 of 25 74 CEU, 39 CHB, 31 reduced exploratory activity, 15q14 1115 *604878 SLC12A6 AR 205 Gain, 2 Loss No the development and maintenance Mutations cause ACCPN phenotype unless associated with 32,775,539 12, member 6 32,398,222 with peripheral (Sanger) exons)i JPT, 63 YRI progressive neurodegeneration, of the nervous system additional mutation neuropathy (ACCPN) hypertension, slow progressive deafness and failure to breed

Homozygous Rad51 null mutation Mutations found in familiar breast Forms a complex with BRCA1 and can be characterized as a chr15:38,619,837- chr15:38,774,661- 5' end (3 of 10 cancer patients; a SNP is thought Loss of gene (or part of gene) may 15q15.1 1117 *179617 RAD51 homolog RAD51 Breast cancer Sanger 1 Loss 1 JPT No BRCA2; functions in recombination preimplantational lethal mutation 38,782,403 38,811,646 exons) to be associated with increased risk increase the risk for breast cancer and in DNA repair that disrupts basic molecular for breask cancer functions of cells

Expressed in the sensory hair cells Mutations and large deletions have and is associated with the autosomal recessive 1 CEU, 2 JPT, 3 YRI been identified in patients with chr15:41,610,450- chr15:41,679,053- Affy/Sanger 2 Gain, 4 Loss (S) stereocilia, the stiff microvilli Deletions of this gene have been 15q15.3 1119 *606440 stereocilin STRC nonsyndromal AR entire gene (S) Yes nonsyndromal sensorineural None 41,935,933 41,698,290 (Both) 5 Loss (A) forming the structure for shown to cause deafness sensorineural deafness 1 CEU, 4 YRI (A) deafneMs; 70-kb deletions including mechanoreception of sound this gene have been reported stimulation

Mice homozygous for knockout of Can created amyloid fibres that the beta-2-microglobulin gene show Hemodialysis-related chr15:42,756,160- chr15:42,790,977- Affy/Sanger Microglobulin essential to cause Hemodialysis-related progressive hepatic iron overload, Gain may cause an increase in 15q21.1 1120 *109700 beta-2-microglobulin B2M amyloidosis (HRA); entire gene 1 Gain 1 YRI No 43,210,134 42,797,649 (Sanger) expression of HLA amyloidosis (HRA); mutations and indistinguishable from that amyloid fibres in certain tissues cancer deletions found in some cancers observed in human hemochromatosis

Deficiency may cause congenital Congenital cataracts; cataracts; reduced expression may Catalyzes the interconversion of Homozygous mice exhibit no chr15:42,756,160- sorbitol chr15:43,102,644- microvascular Affy/Sanger entire gene (S) 1 Gain (S) 1 YRI (S) increase sorbital levels which is Gain is not expected to cause a 15q21.1 1120 *182500 SORD Yes polyols and their corresponding obvious abnormalities in the kidney 43,210,134 dehydrogenase 43,154,330 complications in (Both) entire genei (A) 3 Gain (A) 3 YRI (A) implicated in the development of phenotype ketoses or in other physiological functions diabetic patients microvascular problems in some diabetic patients

A glycoprotein and a member of the Defect in thyroid NADPH oxidase family; part of a Mutations can cause defects in chr15:42,756,160- chr15:43,172,145- hormonogenesis; mild Affy/Sanger protein complex located at the Gain is not expected to cause a 15q21.1 1120 *606759 dual oxidase 2 DUOX2 AR and AD entire gene 1 Gain 1 YRI No thyroid hormonogenesis and mild None 43,210,134 43,193,651 transient congenital (Sanger) apical membrane of thyroid follicular phenotype transient congenital hypothyroidism hypothyroidism cells involved in the synthesis of thyroid hormone

A kidney-specific sodium-potassium- chloride cotransporter; found on the apical membrane of the thick Homozygous pups howed signs of chr15:46,296,330- solute carrier family chr15:46,287,190- antenatal Bartter 3' end (23 of 24 ascending limb of Henle's loop and Mutations are seen in patients with extracellular volume depletion with Autosomal dominant disorder; 15q21.1 1121 *600839 SLC12A1 AD Sanger 1 Loss 1 CHB No 46,451,070 12, member 1 46,382,417 syndrome exons) the macula densa; accounts for antenatal Bartter syndrome elevated hematocrits and fail to deletion could cause phenotype most of the NaCl resorption; thrive sensitive to such diuretics as furosemide and bumetanide

Mutations are known to cause Knockout mice showed abnormal Gain would be expected to have a cytochrome P450, aromatase deficiency; increased chr15:49,069,549- chr15:49,288,962- gynecomastia; Affy/Sanger 1 Gain (S) 1 JPT (S) Catalyzes the formation of aromatic sexual development and had significant effect on sexual 15q21.2 1122 +107910 family 19, subfamily CYP19A1 AD; AR entire gene No expression (caused by cryptic 49,617,631 49,418,086 aromatase deficiency (Both) 1 Gain (A) 1 JPT (A) C18 estrogens from C19 androgens increased adipocyte volume at development and may cause A, polypeptide 1 promoter via an inversion) causes gonadal and infrarenal sites symptoms similar to gynecomastia dominant gynecomastia

Mice lacking the Bbs4 protein had An adaptor of the p150(glued) Mutations, including partial gene major components of the human Deletion will probably not cause chr15:70,606,839- Bardet-Biedl chr15:70,765,588- Bardet-Biedl syndrome- 15q24.1 1130 *600374 BBS4 AR Sanger entire gene 2 Gain, 1 Loss 2 CEU, 1 YRI No subunit of the dynein transport deletions, are known to cause Bardet-Biedl syndrome-4 phenotype unless associated with 70,907,613 syndrome 4 70,817,869 4 machinery Bardet-Biedl syndrome phenotype, including obesity and additional mutation retinal degeneration

Chimeric PML-RARA fusion gene Potential transcription factor and Common translocations that result was created to initiate tumor suppressor; regulates in PML fusion genes have been Gain and/or loss of this gene may chr15:72,002,167- promyelocytic chr15:72,074,067- acute promyelocytic leukemogenesis; mice had 15q24.1 1131 *102578 PML Sanger entire gene 3 Gain, 3 Loss 3 CEU, 3 YRI No hemopoietic differentiation and found in leukemia; overexpression have a effect on susceptibility to 72,251,969 leukemia 72,127,206 leukemia (APL) abnormalities that appeared to be a controls cell growth and of PML induces senescence in a leukemia faithful reproduction of the human tumorigenesis p53-dependent manner disease

PAPA syndrome proline-serine- (pyogenic sterile Involved in in actin reorganization chr15:74,957,605- threonine chr15:75,074,609- Gain is not expected to cause a 15q24.3 1132 *606347 PSTPIP1 arthritis, pyoderma AD Sanger entire gene 1 Gain 1 CEU No during cytoskeletal-mediated Mutations cause PAPA syndrome None 75,160,503 phosphatase 75,116,726 phenotype gangrenosum, and events interacting protein 1 acne)

5 CEU, 3 CHB, 2 Involved in the degradation process chr15:99,537,666- chr15:99,628,737- Modulation of Affy/Sanger 7 Gain, 8 Loss (S) SNPs associated with modulation of May be responsible for some 15q26.3 1154 *607918 selenoprotein S SELS entire gene JPT, 5 YRI (S) No of misfolded endoplasmic reticulum None 99,872,978 99,635,223 inflammatory response (Both) 1 Gain (A) inflammatory response variation in inflammatory response 1 CEU (A) (ER) luminal proteins

Chr. 16 Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

Mutant homozygotes die at A cytoplasmic protein; functions as embryonic day 8-10, exhibiting 2-hit' mutation of AXIN1 seen in 5 a negative regulator of the wingless- neuroectodermal defects and axial chr16:266,993- chr16:277,441- Hepatocellular primary HCCs; LOH in 3 tumors (33- Loss may increase risk of 16p13.3 1157 *603816 axin 1 AXIN1 Sanger entire gene 1 Loss 1 CEU WSSD type MMTV integration site family, duplications; heterozygotes exhibit 1,111,069 342,465 carcinoma bp deletion in exon 3 and 12 carcinoma member 1 (WNT) signaling pathway skeletal, cardiac, and neurological missense mutations) and can induce apoptosis defects including short, bent tails, and deafness with circling behavior

Homozygotes for one null allele display decreased numbers of insulin positive cells in the Germline mutation may be involved pancreas; homozygotes for a Resistance to Possibly involved in abnormal chr16:266,993- somatostatin chr16:1,068,870- 29 CEU, 10 CHB, 16 Involved in modulating dopamine- in the resistant to treatment with the second null allele have normal 16p13.3 1157 *182455 SSTR5 somatostatin treatment AD Sanger entire gene 3 Gain, 61 Loss No movement disorders 1,111,069 receptor 5 1,069,964 JPT, 9 YRI mediated control of motor activity somatostatin analog octreotide in a pancreatic islet morphology but in Acromegaly patient (Parkinsons?) patient with Acromegaly increased insulin secretion, decreased blood insulin and glucose levels, and improved glucose tolerance

asparagine-linked 1 CEU, 1 JPT, 1 YRI Homozygous mutation causes Deletion will probably not cause chr16:4,912,851- chr16:5,061,821- Congenital disorder of Affy/Sanger 2 Gain, 1 Loss (S) Involved in the biosynthesis of lipid- 16p13.3 1160 *605907 glycosylation 1 ALG1 AR entire gene (S) Yes congenital disorder of glycosylation None phenotype unless associated with 5,364,830 5,075,588 glycosylation, type Ik (Both) 1 Gain (A) linked oligosaccharides homolog 1 YRI (A) type Ik additional mutation

Mutations can cause A member of the MRP subfamily Homozygous null mice display pseudoxanthoma elasticum; large which is involved in multi-drug patchy mineralization which may ATP-binding deletions have been reported; Loss of gene may cause PXE or 16p13.11- chr16:16,092,718- chr16:16,151,491- Pseudoxanthoma Affy/Sanger 3 CEU, 7 CHB, 9 resistance; functions as a include the capsule surrounding the 1171 *603234 cassette, sub-family ABCC6 AR and AD entire gene 12 Gain, 11 Loss Yes carriage of a sole ABCC6 mutation increase risk in populations where 16p12.3 16,831,289 16,224,815 elasticum (Sanger) JPT, 4 YRI modulator of ATP-sensitive sinuses of vibrissae, medium sized C, member 6 may be a cardiovascular risk factor; mutations are common (Afrikaner) potassium channels and insulin arteries, skin, retina, kidney, and high prevalence of PXE in the release interscapular brown fat Afrikaner population

Preferentially expressed in retina 16p12.2- chr16:21,212,772- chr16:21,177,344- nonsyndromic Affy/Sanger Mutations can cause nonsyndromic Gain is not expected to cause a 1174 *123740 crystallin, mu CRYM AD 5' end (1 of 9 exons) 2 Gain 1 JPT, 1 YRI No and brain, presumably in an None 16p12.1 21,856,623 21,221,918 deafness (Affy) deafness phenotype enzymatic role

26 CEU, 11 CHB, 7 Deletion will probably not cause 16p12.2- chr16:21,212,772- chr16:21,597,336- Deafness, autosomal Affy/Sanger entire gene (S) 69 Gain, 5 Loss (S) Noncollageneous glycoprotein of Mutations cause autosomal 1174 *607038 otoancorin OTOA AR JPT, 30 YRI (S) Yes None phenotype unless associated with 16p12.1 21,856,623 21,679,550 recessive 22 (Both) entire genei (A) 2 Gain, 1 Loss (A) the acellular gels of the inner ear recessive deafness 2 JPT, 1 YRI (A) additional mutation

Mutations cause Batten disease (most common is genomic deletion Homozygotes for targeted of 1.02 kb, although other deletions mutations show neuronal ceroid also occur); deletion may be lipofuscinosis, degeneration of the Deletion of this gene may unmask Functions as a chaperone involved ceroid- Batten disease (Ceroid- frequent in certain populations retina, cerebral cortex and mutations that are common in chr16:28,082,639- chr16:28,396,102- in the folding/unfolding or 16p11.2 1178 *607042 lipofuscinosis, CLN3 lipofuscinosis, neuronal- AR Sanger entire gene 4 Gain, 2 Loss 1 CEU, 1 JPT, 4 YRI No (Finnish); overexpressed in a cerebellum, hypertrophy of some populations; gain and loss 29,058,054 28,410,717 assembly/disassembly of other neuronal 3 3); Cancer variety of human cancer cell lines interneuron populations in the may affect viability and proteins (blocking its expression inhibited hippocampus, gliosis, mild susceptibility for some cancers growth and viability of cancer cells neurological symptoms and excess indicating this might be a treatment late mortality in some cancers)

Calcium-transporting ATPase found Sanger (gene ATPase, Ca++ in fast-twitch skeletal muscle fibers; Null mice had progressive cyanosis only hits None (gene only hits Deletion will probably not cause chr16:28,082,639- transporting, chr16:28,797,310- function to lower cytoplasmic Mutations found in Brody myopathy and gasping respiration and 16p11.2 1178 *108730 ATP2A1 Brody myopathy AR merged, not entire gene merged, not None No phenotype unless associated with 29,058,054 cardiac muscle, fast 28,823,331 Ca(2+) concentration by pumping patients succumbed from respiratory failure individual individual CNVs) additional mutation twitch 1 Ca(2+) to luminal or extracellular shortly after birth CNVs) spaces

Glycolytic enzyme that catalyzes the reversible conversion of chr16:29,981,456- aldolase A, fructose- chr16:29,971,992- 3' end (10 of 14 Mutations cause Aldolase A Gain is not expected to cause a 16p11.2 1180 +103850 ALDOA Aldolase A deficiency AR Sanger 9 Gain 3 CEU, 6 YRI No fructose-1,6-bisphosphate to None 30,290,781 bisphosphate 29,989,235 exons) deficiency phenotype glyceraldehyde 3-phosphate and dihydroxyacetone phosphate

Phosphorylase kinase Mutations cause phosphorylase chr16:45,819,013- phosphorylase chr16:46,052,739- Affy/Sanger 5' end (8 of 30 1 Gain (S) 1 JPT (S) Activates glycogen phosphorylases Gain is not expected to cause a 16q12.1 1182 *172490 PHKB deficiency of liver and AR WSSD kinase deficiency of liver and None 46,163,788 kinase, beta 46,291,755 (Both) exons) 1 Gain (A) 1 JPT (A) in muscle, liver, and other tissues phenotype muscle muscle

Norepinephrine homeostasis is Gene is a potential candidate for Mutation seen to cause orthostatic Involved in the rapid abnormal in homozygous mutant psychiatric disorders such as chr16:54,226,897- solute carrier family chr16:54,248,057- 1 CEU, 1 CHB, 2 intolerance; variants may effect 16q12.2 1187 *163970 SLC6A2 Orthostatic intolerance AD Sanger entire gene 4 Gain No reaccumulation of neurotransmitter mice; in addition to displaying manic depression; gain may affect 54,541,091 6, member 2 54,295,199 JPT sensitivity to cocaine and into presynaptic terminals altered behavior, mutant mice are sensitivity to or treatment of antidepressants hypersensitive to psychostimulants depression

Catalyzes the hydrolysis of a variety of compounds containing Monocyte esterase deficiency may chr16:54,226,897- chr16:54,394,267- monocyte esterase 1 CEU, 1 CHB, 2 Gain is not expected to cause a 16q12.2 1187 +114835 carboxylesterase 1 CES1 Sanger entire gene 4 Gain Yes ester and amide bonds; may play be associated with some cancers None 54,541,091 54,424,576 deficiency JPT phenotype an important role in lipid and drug and with rheumatoid arthritis metabolism

Different alleles may have associations with cardiovascular Prevents Hb-induced oxidative disease and diabetes; large Gain may be associated with chr16:70,533,845- chr16:70,646,009- Anhaptoglobinemia; tissue damage; just distal to 16q22.2 1192 *140100 haptoglobin HP AR and AD Sanger entire gene 20 Gain 20 YRI Yes deletion encompassing gene None cardiovascular disease and 70,831,848 70,652,458 Hypohaptoglobinemia fra16q22.1; polymorphic gene with reported to cause diabetes different alleles of different sizes anhaptoglobinemia and hypohaptoglobinemia

carbohydrate (N- Correlates with the presence of chr16:73,977,115- acetylglucosamine 6 chr16:74,064,526- Macular corneal Mutations cause MCD Type I; Gain is not expected to cause a 16q23.1 1195 *605294 CHST6 AR Sanger entire gene 2 Gain 2 YRI Yes sulfated keratan sulfate in the None 74,134,472 O) sulfotransferase 74,086,427 dystrophy (MCD) deletions can cause MCD Type II phenotype human cornea 6

chr16:76,811,430- chr16:76,691,052- Affy/Sanger middle (1 exon of an 2 Loss (S) 2 YRI (S) overexpression seen in breast 16q23.1 1198 No cancer cell lines; abnormalities 76,974,815 77,804,064 (Both) isoform) 3 Loss (A) 3 YRI (A) Losses of this gene have been WW domain affecting this gene at the genomic Potent suppressor of tumor growth; reported; at the FRA16D fragile *605131 containing WWOX Cancer and transcriptional level may be None found at FRA16D site; losses are associated with oxidoreductase relevant in carcinogenesis; chr16:77,607,617- chr16:76,691,052- some cancers 16q23.1 1199 Affy intronic 7 Loss 7 YRI No mutations and deletoins are seen in 77,626,238 77,804,064 some cancers and cell lines

9.5 kb deletions and other mutations reported to cause spastic Null mice were affected by a distal Proteolytic and chaperone-like chr16:87,970,408- chr16:88,102,306- 17 CEU, 7 CHB, 2 paraplegia-7; in region of frequent axonopathy of spinal and peripheral Gain is not expected to cause a 16q24.3 1208 *602783 spastic paraplegia 7 SPG7 Spastic paraplegia-7 AR Sanger entire gene 58 Gain No activities at the inner mitochondrial 88,179,649 88,151,674 JPT, 32 YRI loss of heterozygosity (LOH) in axons, characterized by axonal phenotype membrane sporadic breast and prostate swelling and degeneration cancer

Part of a nuclear multiprotein core Alu-mediated genomic deletions Null mice displayed FA-like Fanconi anemia, Fanconi anemia, complex which triggers activating have been reported; mutations and phenotypes including growth Deletion of this gene may unmask chr16:88,398,233- chr16:88,331,460- 5' end (7 of 40 16q24.3 1209 *607139 complementation FANCA complementation group Sanger 3 Loss 3 CEU No monoubiquitination; FA/BRCA deletions cause Fanconi anemia; retardation, microphthalmia, mutations that are common in 88,495,450 88,410,566 exons) group A A pathway is involved in the repair of large deletions have also been craniofacial malformations, and some populations DNA damage reported hypogonadism

Chr. 17

Cytochrome c oxidase (COX) Deletion will probably not cause entire gene (S) assembly protein; catalyzes the HNPP deletion results in a COX10 chr17:13,821,966- chr17:13,913,444- cytochrome c oxidase Affy/Sanger 1 Loss (S) 1 YRI (S) phenotype unless associated with 17p12 1213 *602125 COX10 homolog COX10 AR 5' end (4 of 7 exons) Yes farnesylation of a vinyl group at null allele; mutations can also None 14,069,281 14,052,717 deficiency (Both) 1 Loss (A) 1 YRI (A) additional mutation; loss does not (A) position C2; spans the distal cause COX deficiency appear to overlap CMT1A-REP CMT1A-REP

Mutations cause Sjogren-Larsson aldehyde Catalyzes the oxidation of long- Deletion will probably not cause chr17:19,426,327- chr17:19,492,656- Sjogren-Larsson 5' end (5 of 11 syndrome; mutations common in 17p11.2 1217 *609523 dehydrogenase 3 ALDH3A2 AR Affy 4 Loss 4 YRI No chain aldehydes derived from lipid None phenotype unless associated with 19,504,358 19,521,500 syndrome (SLS) exons)i certain populations (northern family, member A2 metabolism additional mutation Sweden)

hypertension Produces nitric oxide (NO) which is Polymorphisms may be associated chr17:22,902,614- nitric oxide chr17:23,107,920- susceptibility; Gain is not expected to cause a 17q11.2 1221 *163730 NOS2A Sanger entire gene 6 Gain 6 YRI Yes a messenger molecule with diverse with hypertension susceptibility and None 23,201,246 synthase 2A 23,151,682 resistance to severe phenotype functions throughout the body resistance to malaria malaria

NAHR between gene and Homozygous null mice are not pseudogene cause 1 of the viable and die during early recurrent deletions in NF1 (a postimplantation stages; embryonic Cct by forming multiprotein microdeletion disorder); neurofibromatosis 1; and extraembyronic structures do Gain may increase susceptibility chr17:27,245,834- suppressor of zeste chr17:27,288,185- complexes with repressive state of haploinsufficiency may contribute to 17q11.2 1222 *606245 SUZ12 endometrial stromal AD Sanger entire gene 1 Gain 1 YRI Yes not develop at E7.5 and E8.5 and for NAHR events causing NF1 27,562,095 12 homolog 27,352,162 homeotic genes throughout mental impairment in patients with tumors organogenesis does not initiate; a microdeletion disorder development; has a pseudogene constitutional NF1 microdeletions; decrease in cell proliferation and translocation causing a fusion gene increase in cell apoptosis is with JAZF1 cause endometrial observed in E7.5 embryos stromal tumors

Catalyzes the rate-limiting reaction chr17:32,642,843- acetyl-Coenzyme A chr17:32,516,040- acetyl-CoA 5' end (27 of 53 Deficiency causes hypotonic Gain is not expected to cause a 17q12 1225 +200350 ACACA Sanger 1 Gain 1 CEU No in the biogenesis of long-chain fatty Null mice were embryonic lethal 32,848,430 carboxylase alpha 32,841,015 carboxylase deficiency exons) myopathy and neurologic damage phenotype acids Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

Dominant-negative Tcf2 mutant inhibited Pkhd1 expression and produced renal cysts in transgenic Syndrome appears to be caused 5' end (5 of 9 exons) Member of the homeodomain- mice; homozygotes for targeted null by dominant-negative mutations; chr17:33,140,728- transcription factor chr17:33,120,548- renal cysts and Mutations cause renal cysts and 17q12 1226 *189907 TCF2 AD Sanger (one entire isoform in 2 Loss 2 CEU No containing superfamily of mutations exhibit reduced size, deletion probably does not cause 34,010,545 2 33,179,182 diabetes syndrome diabetes syndrome CNV) transcription factors impaired development of disease, but may increase extraembryonic membranes, lack of susceptibilty to diabetes visceral or parietal endoderm, and early post-implantation lethality

Member of the type I (acidic) Loss of gene may contribute to or chr17:36,554,901- chr17:36,910,760- Affy/Sanger 2 Loss (S) 2 YRI (S) Mutations cause rare white sponge 17q21.2 1228 *148065 keratin 13 KRT13 white sponge nevus AD entire gene No subfamily of genes characteristic of None cause white sponge nevus 37,150,369 36,915,391 (Both) 1 Gain (A) 1 CHB (A) nevus the internal stratified epithelia disease

An intermediate filament chain Syndrome appears to be caused Epidermolytic Dominant-negative mutations chr17:36,554,901- chr17:36,975,622- Affy/Sanger 2 Loss (S) 2 YRI (S) expressed only in the terminally by dominant-negative mutations; 17q21.2 1228 *607606 keratin 9 KRT9 palmoplantar AD entire gene No cause Epidermolytic palmoplantar None 37,150,369 36,981,836 (Both) 1 Gain (A) 1 CHB (A) differentiated epidermis of palms deletion probably does not cause keratoderma (EPPK) keratoderma (EPPK) and soles disease

Homozygotes for targeted null mutations develop extensive skin Some missense mutations are Usually found as a heterotetramer blistering after birth and die by 2 Syndrome appears to be caused dominant-negative and cause chr17:36,554,901- chr17:36,992,059- Epidermolysis bullosa Affy/Sanger 2 Loss (S) 2 YRI (S) with two keratin 5 molecules, a type days of age; if keratin 16 is also by dominant-negative mutations; 17q21.2 1228 *148066 keratin 14 KRT14 AR and AD entire gene Yes epidermolysis bullosa simplex, 37,150,369 36,996,673 simplex (Both) 1 Gain (A) 1 CHB (A) II keratin; together they form the expressed in skin, development is deletion probably does not cause others are required to be cytoskeleton of epithelial cells normal but later alopecia, chronic disease homozygous to cause disease skin ulcers and stratified epithelial defects occur

Jadassohn- A member of the keratin gene Lewandowsky type of family, proteins responsible for the Dominant-negative mutations Syndrome appears to be caused pachyonychia structural integrity of epithelial cells; cause Jadassohn-Lewandowsky chr17:36,554,901- chr17:37,019,559- Affy/Sanger 2 Loss (S) 2 YRI (S) by dominant-negative mutations; 17q21.2 1228 *148067 keratin 16 KRT16 congenita; AD entire gene Yes coexpressed with keratin 14 in a type of pachyonychia congenita and None 37,150,369 37,022,545 (Both) 1 Gain (A) 1 CHB (A) deletion probably does not cause nonepidermolytic number of epithelial tissues, nonepidermolytic palmoplantar disease palmoplantar including esophagus, tongue, and keratoderma keratoderma hair follicles

A member of the keratin gene Mutations cause pachyonychia Syndrome appears to be caused chr17:36,554,901- chr17:37,029,221- pachyonychia Affy/Sanger 2 Loss (S) 2 YRI (S) family; expressed in nail bed, hair congenita (most likely dominant- by dominant-negative mutations; 17q21.2 1228 *148069 keratin 17 KRT17 AD entire gene Yes None 37,150,369 37,034,335 congenita (Both) 1 Gain (A) 1 CHB (A) follicle, sebaceous glands, and negative like other keratin deletion probably does not cause other epidermal appendages disorders) disease

Frontotemporal Dementia with Mutations found to cause Mice expressing a repressible microtubule- Parkinsonism; frontotemoral dementia with human tau variant developed Gain may affect susceptibilty to 17q21.31- chr17:41,439,751- chr17:41,327,624- Affy/Sanger 3' end (4 of 14 Promotes microtubule assembly 1230 +157140 associated protein MAPT susceptibilty to other AD 33 Gain 33 CEU No Parkinsonism; also associated with progressive age-related dementia and other neurological 17q21.32 42,632,332 41,458,611 (Sanger) exons) and stability tau neurological disorders susceptibility to neurological neurofibrillary tangles, neuronal disorders (Alzheimer Disease, disorders loss, and behavioral impairments Parkinsons disease)

Mice developed a normal egg Implicated in primary axis formation wingless-type cylinder but did not form a primitive entire gene (S) 118 Gain, 32 Loss 45 CEU, 31 CHB, 31 during vertebrate embryogenesis; Key gene in embryogenesis; gain 17q21.31- chr17:41,439,751- MMTV integration chr17:42,196,859- Affy/Sanger Mutations cause autosomal streak, mesoderm, or node; provide 1230 *165330 WNT3 tetra-amelia AR 3' end (4 of 5 exons) (S) JPT, 43 YRI (S) No required at the early stages of limb or loss may have subtle effects on 17q21.32 42,632,332 site family, member 42,251,081 (Both) recessive tetra-amelia genetic proof for the requirement of (A) 2 Gain (A) 2 CEU (A) formation, as well as for craniofacial early development 3 Wnt3 in primary axis formation in and urogenital development the mouse

A member of the tripartite motif chr17:54,437,361- tripartite motif- chr17:54,414,793- 5' end (22 of 25 Gain is not expected to cause a 17q23.2 1237 *605073 TRIM37 mulibrey nanism AR Sanger 1 Gain 1 YRI No (TRIM) family; a peroxisomal Mutations cause mulibrey nanism None 54,780,416 containing 37 54,539,011 exons) phenotype protein

Chr. 18 Chr. 19

Mutations (nonsense, missense, early termination) are found to Peutz-Jeghers cause PJS and the other A member of the serine/threonine Homozygous mice die at syndrome; testicular No clone overlaps None (maybe 1 Gain, malignancies; deletions of exons 4 chr19:902,641- serine/threonine chr19:1,156,798- None (maybe 1 JPT, kinase family; regulates cell polarity midgestation; heterozygous mice If deletion overlaps this gene, may 19p13.3 1281 *602216 STK11 carcinoma, malignant AD Sanger gene (maybe entire 1 Loss); no clone No and 5 and an inversion of exons 6 1,495,933 kinase 11 1,179,434 1 YRI) and functions as a tumor developed multiple gastric cause disorder melatnoma, pancreatic gene) covering gene and 7 have been reported; suppressor adenomatous polyps cancer functional LKB1 is required for normal embryogenesis and that it is related to tumor development

NADH Leigh syndrome due to Mutation was found in 2 male sibs chr19:902,641- dehydrogenase chr19:1,334,906- Subunit of the NADH Gain/Loss is not expected to 19p13.3 1281 *601825 NDUFS7 mitochondrial complex I AD Sanger entire gene 1 Gain, 2 Loss 1 CEU, 1 JPT, 1 YRI No with Leigh syndrome due to None 1,495,933 (ubiquinone) Fe-S 1,346,582 dehydrogenase protein cause a phenotype deficiency mitochondrial complex I deficiency protein 7

Homozygous null mice display A methyltransferase that converts increased postnatal lethality; chr19:902,641- guanidinoacetate N- chr19:1,348,089- guanidoacetate to creatine, using S- reduced body weight, muscle Gain/Loss is not expected to 19p13.3 1281 +601240 GAMT GAMT deficiency AR Sanger entire gene 1 Gain, 2 Loss 1 CEU, 1 JPT, 1 YRI No Mutations cause GAMT deficiency 1,495,933 methyltransferase 1,352,552 adenosylmethionine as the methyl tension, and creatine cause a phenotype donor concentrations; infertility with impaired spermatogenesis

A bZIP transcription factor which can bind as a homodimer to certain promoters and enhancers; forms heterodimers with the related Homozygous mice died within the CCAAT/enhancer proteins CEBP-beta and CEBP- chr19:38,468,914- chr19:38,482,776- Affy/Sanger Mutations were found in patients first 20 hours after birth and had Gain is not expected to cause a 19q13.11 1293 *116897 binding protein CEBPA acute myeloid leukemia AD entire gene 2 Gain 2 YRI No gamma; binds to the promoter and 39,273,401 38,485,160 (Sanger) with AML defects in the control of hepatic phenotype (C/EBP), alpha modulates the expression of the growth and lung developmen gene encoding leptin; interacts with CDK2 and CDK4, thereby inhibiting these kinases and causing growth arrest in cultured cells.

A cytosolic dipeptidase that hydrolyzes dipeptides with proline or hydroxyproline at the carboxy chr19:38,468,914- chr19:38,569,699- Affy/Sanger entire gene (S) 2 Gain (S) 2 YRI (S) Mutations were found to cause Gain is not expected to cause a 19q13.11 1293 +170100 peptidase D PEPD prolidase deficiency AR No terminus (but not Pro-Pro); None 39,273,401 38,704,522 (Both) entire genei (A) 2 Gain (A) 2 YRI (A) prolidase deficiency phenotype important in collagen metabolism because of the high levels of iminoacids

hepcidin Hamp inhibited the iron Deletion will probably not cause chr19:40,402,918- chr19:40,465,250- juvenile hereditary Homozygous mutations were found 19q13.12 1296 *606464 antimicrobial HAMP AR Sanger entire gene 3 Loss 2 CEU, 1 CHB No A key regulator of iron absorption accumulation normally observed in phenotype unless associated with 40,578,953 40,467,883 hemochromatosis to cause JH peptide homozygous mice additional mutation

Deficient mice were insulin-resistant v-akt murine Enriched in insulin-responsive Mutation was seen in a family with and exhibited growth deficiency; diabetes mellitus type chr19:45,304,260- thymoma viral chr19:45,431,556- tissues and has been implicated in diabetes mellitus; overexpression deletion of the Akt2 gene in mice Gain may be associated with 19q13.2 1299 *164731 AKT2 II; ovarian and AD Sanger entire gene 1 Gain 1 JPT WSSD 45,531,360 oncogene homolog 45,483,034 the metabolic actions of the was seen in ovarian carcinoma and impaired platelet aggregation, some carcinomas pancreatic carcinoma 2 hormone pancreatic carcinomas fibrinogen binding, and granule secretion

Individuals carrying CYP2A6-null Significant increases in the alleles (heterozygotes) should have carcinogen-metabolizing enzymes cytochrome P450, tobacco-related Plays a major role in the oxidation a decreased risk of developing Loss may be associated with chr19:45,983,467- chr19:46,041,284- Affy/Sanger CYP1A1, CYP1A2, CYP3A, 19q13.2 1300 +122720 family 2, subfamily CYP2A6 diseases such as lung entire gene 3 Loss 3 JPT Yes of nicotine and coumarin in human tobacco-related cancers and other decreased risk of developing 46,237,908 46,048,180 (Sanger) CYP2B, and CYP2A were seen in A, polypeptide 6 cancer liver microsomes medical complications; genetic tabacco-related cancers the lungs of rats supplemented with polymorphism may reduce lung high doses of beta-carotene cancer risk

killer cell 8 CEU, 5 CHB, 2 immunoglobulin-like KIRs on NK cells regulate the Certain alleles are significantly chr19:59,359,391- chr19:59,989,605- delayed or rapid Affy/Sanger entire gene (S) 16 Gain, 5 Loss (S) JPT, 6 YRI (S) Gain/loss may have an effect on 19q13.42 1309 *604946 receptor, three KIR3DL1 Yes inhibition and activation of NK cell associated with more rapid or None 60,158,136 60,034,044 progression of AIDS (Both) entire genei (A) 6 Gain, 23 Loss (A) 3 CEU, 5 CHB, 1 the progression of AIDS domains, long responses delayed progression of AIDS JPT, 20 YRI (A) cytoplasmic tail, 1

Loss in a woman may cause A negative regulator of interleukin-1- NACHT, leucine phenotypes such as conceptuses, chr19:59,359,391- chr19:60,126,689- recurrent hydatidiform Affy/Sanger 7 CEU, 5 CHB, 2 beta that is abundant in the uterine Mutations were found to cause 19q13.42 1309 *609661 rich repeat and PYD NALP7 AR entire gene 16 Gain, 4 Loss WSSD None late spontaneous abortions, 60,158,136 60,150,679 moles (Sanger) JPT, 6 YRI milieu during the peri-implantation recurrent hydatidiform moles containing 7 stillbirths, and normal pregnancies period with intrauterine growth defect

Part of the tropomyosin-troponin chr19:60,229,274- chr19:60,336,009- Amish nemaline 3' end (5 of 14 complex which is responsible for Nonsense mutation was found in Gain is not expected to cause a 19q13.42 1310 *191041 troponin T type 1 TNNT1 AR Affy 1 Gain 1 CHB No None 60,342,499 60,352,386 myopathy exons) the calcium sensitivity of the Amish nemaline myopathy phenotype contractile apparatus

Chr. 20

thrombophilia due to Thrombomodulin is a specific Disruption of the mouse chr20:22,977,404- chr20:22,974,271- thrombomodulin defect; Affy/Sanger 5' end (part of single endothelial cell receptor that forms Mutations were found in patients thrombomodulin gene leads to Loss may be associated with 20p11.21 1327 +188040 thrombomodulin THBD AD 1 Loss 1 CEU No 23,127,604 22,978,301 susceptibility to (Sanger) exon gene) a 1:1 stoichiometric complex with with thrombotic events embryonic lethality caused by a thrombotic events myocardial infarction thrombin defect in the placenta Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

A member of the TNF-receptor Null mice lacked cell-dependent immunodeficiency with superfamily; essential in mediating immunoglobulin class switching and hyper-IgM, type 3; a broad variety of immune and Loss of gene appears to be germinal center formation; CD40 chr20:44,126,322- chr20:44,180,313- susceptibility to 33 CEU, 16 CHB, 14 inflammatory responses including T Homozygosity for mutations were frequent; homozygosity for 20q13.12 1334 *109535 CD40 molecule CD40 AR Sanger entire gene 108 Loss No expression was increased in murine 44,398,283 44,191,337 Alzheimers disease JPT, 45 YRI cell-dependent immunoglobulin found in patients with HIGM3 deletion may cause model of Alzheimers disease (may (suggested by mouse class switching, memory B cell immunodeficiency be involved in Alzheimers model) development, and germinal center pathogenesis) formation

Mice heterozygous for a gene trap chr20:49,756,024- chr20:49,833,992- Duane-radial ray Putative zinc finger transcription Mutations were found in patients allele of Sall4 showed limb and Disorder is dominant; therefore, 20q13.2 1338 *607343 sal-like 4 SALL4 AD Affy entire gene 1 Loss 1 YRI No 49,852,802 49,852,421 syndrome factor with DRRS heart defects that modeled human loss may cause phenotype disease

Mice homozygous for a null mutation die perinatally with pulmonary atelectasis, in the potassium voltage- absence of brain abnormalities, chr20:61,572,793- gated channel, KQT- chr20:61,502,011- benign neonatal 5' end (1 of 17 Important in the regulation of Mutations were found to cause signs of seizures or other Disorder is dominant; therefore, 20q13.33 1344 *602235 KCNQ2 AD Sanger 1 Loss 1 YRI No 61,846,811 like subfamily, 61,574,437 epilepsy exons) neuronal excitability benign neonatal epilepsy behavioral manifestations; loss may cause phenotype member 2 heterozygous null mice appear behaviorally normal but exhibit a hypersensitivity to the epileptic inducer pentylenetetrazole

Binds to the consensus sequence hypotrichosis- SRY (sex 5'-AACAAAG-3'; involved in the Mutations in Sox18 underlie the chr20:62,108,666- chr20:62,149,525- lymphedema- Mutations were found in patients Disorder is dominant; therefore, 20q13.33 1345 *601618 determining region SOX18 AR and AD Sanger entire gene 5 Gain, 6 Loss 3 CEU, 2 JPT, 6 YRI No regulation of embryonic cardiovascular and hair follicle 62,435,964 62,151,423 telangiectasia with HLTS loss may cause phenotype Y)-box 18 development and in the defects in ragged mice syndrome (HLTS) determination of the cell fate

Chr. 21 Chr. 22

neonatal Mutations were found patients with adrenoleukodystrophy chr22:16,926,349- peroxisome chr22:16,935,243- Affy/Sanger 16 CEU, 11 CHB, 8 Probably required for protein import neonatal adrenoleukodystrophy Gain/loss is not expected to cause 22q11.21 1362 +608666 PEX26 (NALD); Zellweger AR entire gene 23 Gain, 29 Loss No None 17,436,267 biogenesis factor 26 16,948,790 (Sanger) JPT, 17 YRI into peroxisomes (NALD), Zellweger syndrome and a phenotype syndrome; infantile infantile Refsum disease Refsum disease

GLUTATHIONURIA One of several gamma- gamma- Patients with No clone overlaps Mutations were found to cause chr22:16,926,349- chr22:17,135,729- Affy/Sanger glutamyltransferase genes located 22q11.21 1362 *137181 glutamyltransferase GGT2 cholestasis usually AD gene (maybe entire No clone coverage No clone coverage Yes significant elevation of GGT serum None Loss may cause elevation fo GGT 17,436,267 17,154,028 (Neither) on chromosome 22 (at least 2 of 2 have increased serum gene) concentration these appear to be transcribed) GGT concentrations

Deletion (350 kb in size) and proline hyperprolinemia, type I; AD (with 22 CEU,12 CHB, 9 Mitochondrial proline The hyperprolinemic Pro/Re mouse chr22:16,926,349- chr22:17,274,849- Affy/Sanger 29 Gain, 31 Loss (S) mutations were found to cause Deletion may cause 22q11.21 1362 *606810 dehydrogenase PRODH susceptibility to incomplete entire gene JPT, 17 YRI (S) Yes dehydrogenase is involved in the has serum proline levels 7 times 17,436,267 17,298,620 (Both) 3 Gain (A) hyperprolinemia with susceptibility hyperprolinemia to some degree (oxidase) 1 schizophrenia-4 penetrance) 3 CEU (A) degradation of proline normal to schizophrenia-4

Encodes the receptor for reticulon 4, oligodendrocyte myelin Mutations in mouse affect cessation glycoprotein and myelin-associated Two mutations that lead to putative of ocular dominance plasticity; NgR chr22:18,401,047- chr22:18,603,494- susceptibility to glycoprotein; mediates axonal structural alterations of the native is not essential for mediating Loss may may be associated with 22q11.21 1363 *605566 reticulon 4 receptor RTN4R AD Sanger entire gene 2 Loss 2 YRI Yes 18,684,001 18,630,370 schizophrenia growth inhibition and may play a protein were found in Italian family inhibitory signals from CNS myelin schizophrenia role in regulating axonal with schizophrenia and does not play a central role in regeneration and plasticity in the inhibition of axonal growth adult central nervous system

Crystallins are the dominant Homozygosity for mutation in 22q11.23- chr22:23,691,355- chr22:23,920,379- congenital nuclear Affy/Sanger 10 CEU, 4 CHB, 8 Gain/loss is not expected to cause 1367 *123630 crystallin, beta B3 CRYBB3 AR entire gene 14 Gain, 8 Loss No structural components of the CRYBB3 in 2 Pakistani families with None 22q12.1 24,371,067 23,927,878 cataract (Sanger) YRI a phenotype vertebrate eye lens AR congenital nuclear cataract

Mutations in this gene cause congenital cataract, progressive lens cataracts Dominant disorder, but most likely 10 CEU, 4 CHB, 8 Crystallins are the dominant 22q11.23- chr22:23,691,355- chr22:23,941,939- Cerulean type; sutural Affy/Sanger 14 Gain, 8 Loss (S) Mutations were found in families discernable at 12-15 days of age as dominant-negative; loss may 1367 *123620 crystallin, beta B2 CRYBB2 AD entire gene YRI (S) Yes structural components of the 22q12.1 24,371,067 23,952,378 cataract with punctate (Both) 1 Loss (A) with congenital cataract mild anterior or cortical opacity and increase susceptibility for 1 CEU (A) vertebrate eye lens and cerulean opacities progressing to total opacity by 6-12 cataracts weeks of age

Dominant disorder, but most likely chr22:25,223,053- chr22:25,319,916- Mutations cause pulverulent dominant-negative; loss may 22q12.1 1369 +600929 crystallin, beta B1 CRYBB1 pulverulent cataract AD Sanger entire gene 1 Loss 1 CEU No Member of the crystallin gene family None 25,354,450 25,338,545 cataract increase susceptibility for cataracts

chr22:32,193,499- chr22:31,993,617- 4 CEU, 1 CHB, 3 Homozygotes exhibit a progressive 22q12.3 1370 Sanger intronic 1 Gain, 10 Loss No myopathy, abnormal posture, 32,234,100 32,640,964 JPT, 3 YRI Part of the biosynthetic pathway to muscular dystrophy, A patient was identified with thoracic kyphosis, calcium deposits like-glycosyl- produce mature and functional Intronic CNV are not expected to *603590 LARGE congenital, 1D AR mutation causing muscular in muscle, loss of Schwann cells transferase dystroglycan; high-affinity laminin cause a phenotype (MDC1D) dystrophy and myelin, eye and CNS defects, chr22:32,494,349- chr22:31,993,617- receptor function 22q12.3 1371 Sanger intronic 1 Loss 1 JPT No deafness, reduced growth, and 32,528,033 32,640,964 death around 4 months

Homozygotes for targeted null mutations exhibit lung pathology 2 mutations may be associated with including lymphocytic infiltration, colony stimulating Deletion of this gene may cause chr22:35,499,654- chr22:35,642,722- Pulmonary alveolar Beta chain of the high affinity leukemia; mutations can also cause alveolar proteinosis-like areas, and 22q12.3 1375 *138981 factor 2 receptor, CSF2RB AD Sanger entire genei 5 Gain, 1 Loss 4 CEU, 1 CHB, 1 YRI No pulmonary phenotype or increase 35,685,405 35,659,318 proteinosis (PAP) receptor for interleukin-5 PAP (which may also be associated increased saturated beta, low-affinity risk for leukemia with some leukemias) phosphatidylcholine pool sizes; mutants also have low peripheral eosinophil numbers

Involved in the regulation of actin Mutations cause recessive Deletion will probably not cause chr22:36,328,377- TRIO and F-actin chr22:36,466,741- Deafness, autosomal 22q13.1 1376 *609761 TRIOBP AR Sanger entire gene 6 Loss 1 CEU, 5 YRI No cytoskeletal organization, cell nonsyndromic hearing loss None phenotype unless associated with 36,590,378 binding protein 36,495,347 recessive 28 growth, and cell migration designated DFNB28 additional mutation

entire gene (S) 4 CEU, 2 CHB, 4 chr22:41,091,699- cytochrome b5 chr22:41,339,319- Affy/Sanger 18 Gain (S) Mutations cause different forms of Gain/loss is not expected to cause 22q13.2 1377 +250800 CYB5R3 Methemoglobinemia AR 3' end (8 or 9 exons) JPT, 8 YRI (S) No Involved in heme group metabolism None 41,407,804 reductase 3 41,369,903 (Both) 1 Loss (A) methemoglobinemia a phenotype (A) 1 CHB (A)

Translocation disrupting gene Null mice have massive 5' end (1 of 17 Secreted glycoprotein that causes a complex type of hemorrhages in several tissues chr22:43,894,761- chr22:44,219,256- complex type of Affy/Sanger exons) (S) 1 Gain (S) 1 JPT (S) Gain is not expected to cause a 22q13.31 1381 *135820 fibulin 1 FBLN1 No becomes incorporated into a fibrillar synpolydactyly; entire gene is starting at midgestation, resulting in 44,245,703 44,317,551 synpolydactyly (Both) 5' end (4 of 17 1 Gain (A) 1 JPT (A) phenotype extracellular matrix deleted in chromosome 22q13.3 the death of almost all homozygous exons) (A) deletion syndrome embryos at birth

cardio- Catalyzes the transfer of reducing SCO cytochrome encephalomyopathy, equivalents from cytochrome c to Deletion will probably not cause chr22:49,219,663- chr22:49,252,143- 22q13.33 1390 *604272 oxidase deficient SCO2 fatal infantile, due to AR Sanger entire gene 1 Loss 1 CHB No molecular oxygen and pumps Mutations cause COX deficiency None phenotype unless associated with 49,307,552 49,254,116 homolog 2 cytochrome coxidase protons across the inner additional mutation deficiency mitochondrial membrane

mitochondrial Angiogenic factor; also known as Mutations cause mitochondrial Deletion will probably not cause chr22:49,219,663- endothelial cell chr22:49,254,325- neurogastrointestinal thymidine phosphorylase and as 22q13.33 1390 *131222 ECGF1 AR Sanger entire gene 1 Loss 1 CHB No neurogastrointestinal None phenotype unless associated with 49,307,552 growth factor 1 49,258,599 encephalomyopathy gliostatin, because it limits glial cell encephalomyopathy additional mutation (MNGIE) proliferation

Males homozygous for a targeted null mutation produce sperm that shows delayed fertilization in vitro. chr22:49,392,382- chr22:49,466,791- Male infertility due to 1 CEU, 5 CHB, 1 Major proteinase present in the Deficiency of acrosin is seen in Loss may have an effect on 22q13.33 1391 *102480 acrosin ACR AR Sanger entire genei 9 Loss Yes Sperm from mutant gonial cells are 49,495,206 49,473,870 acrosin deficiency JPT, 2 YRI acrosome of mature spermatozoa spermatids of infertile males fertility ineffective at fertilization in competition with normal sperm both in vitro and in vivo

Chr. X

entire gene (S) chrX:1,865,728- chrX:2,663,476- Affy/Sanger 1 Gain (S) 1 JPT (S) Polymorphisms and translocations Gain is not expected to cause a Xp22.33 1393 +314700 Xg blood group XG XG blood group X-linked D 3' end (6 of 10 Yes The XG blood group gene None 3,187,726 2,727,327 (Both) 2 Gain (A) 1 CEU, 1 JPT (A) have been reported in this gene phenotype exons) (A)

Essential for the correct chrX:1,865,728- chrX:2,846,213- chondrodysplasia Affy/Sanger Mutations cause chondrodysplasia Gain is not expected to cause a Xp22.33 1393 *300180 arylsulfatase E ARSE X-linked R entire gene 1 Gain 1 JPT No composition of cartilage and bone None 3,187,726 2,875,672 punctata (CDPX1) (Affy) punctata phenotype matrix during development

Deficiency causes ichthyosis; large X-linked ichthyosis Involved in the conversion of chrX:7,061,134- chrX:6,997,233- Affy/Sanger deletions of the entire gene have Also X-linked in mouse, may cause Deletions of this gene have Xp22.31 1396 +308100 steroid sulfatase STS (placental steroid X-linked R 3' end (4 of 9 exons) 1 Loss 1 CEU Yes sulfated steroid precursors to 7,483,618 7,132,416 (Sanger) been reported; also mutations hematologic abnormalities shown; may be carrier sulfatase deficiency) estrogens during pregnancy cause the disease

Fusion with DMD seen in X-linked R (but May regulate calcium-dependent Loss of gene may cause interleukin 1 contiguous gene deletion syndrome Xp21.3- chrX:27,751,188- chrX:6,997,233- X-linked mental carriers may Affy/Sanger exocytosis; may be involved in the neurological abnormalities 1403 *300206 receptor accessory IL1RAPL1 entire gene 1 Loss 1 CEU No with multiple phenotypes; inversion None Xp21.1 31,356,624 7,132,416 retardation have mild (Affy) physiologic processes underlying including mild mental retardation protein-like 1 and mutations disrupting gene phenotype) memory and learning abilities or learning disabilities causes mental retardation Merged Gene Dominant or Band Coordinates OMIM Gene Name Gene Coordinates Disease Platform Region of Gene Gain/Loss Frequency Seg Dup Gene Info Mutations or Association? Animal Models Comments CNV_ID Symbol Recessive?

Mutations that inactivate this X- linked gene result in abnormal repoductive development in the X-linked congenital Encoded protein acts as a Mutations cause X-linked hemizygote, ranging from defects in Disorders may be genetically nuclear receptor Xp21.3- chrX:27,751,188- chrX:30,082,243- adrenal hypoplasia; Affy/Sanger dominant-negative regulator of congenital adrenal hypoplasia and testes development and heterogeneous, but loss of this 1403 *300473 subfamily 0, group NR0B1 X-linked D entire gene 1 Loss 1 CEU No Xp21.1 31,356,624 30,087,149 hypogonadotropic (Affy) transcription which is mediated by hypogonadotropic hypogonadism; spermatogenesis to complete male gene is expected to give rise to B, member 1 hypogonadism the retinoic acid receptor gene deletions have been reported to female sex reversal, depending disorder on genetic background; homozygous mutant female mice are fertile

Mutant male mice appeared normal at birth, but exhibited postnatal growth retardation, altered fat Key enzyme in the regulation of metabolism with profound glycerol uptake and metabolism; Mutations and deletions (one >20 Loss should cause glycerol kinase Xp21.3- chrX:27,751,188- chrX:30,431,197- glycerol kinase Affy/Sanger hyperglycerolemia and elevated 1403 *300474 glycerol kinase GK X-linked R entire gene 1 Loss 1 CEU WSSD catalyzes the phosphorylation of kb in size) known to cause glycerol deficiency in male; if in female, Xp21.1 31,356,624 30,508,381 deficiency (Affy) free fatty acids, autonomous glycerol by ATP, yielding ADP and kinase deficiency should be carrier for the disorder glucocorticoid synthesis, and death glycerol-3-phosphate by 3 to 4 days of age; heterozygous females were healthy and biochemically normal

Hemizygous males and homozygous mutant females show progressive muscle atrophy, increased K+ and Ca+ levels in Known mutations and large middle (4 of 79 muscle with age, increased levels Duchenne muscular deletions are known to cause Loss should cause muscular Xp21.3- chrX:27,751,188- chrX:30,897,002- Affy/Sanger exons) (S) 1 Loss (S) 1 CEU (S) Important gene in the skeletal of blood pyruvate kinase, and other 1403 *300377 dystrophin DMD dystrophy; Becker X-linked R No Duchenne and Becker muscular dystrophy in male; if in female, Xp21.1 31,356,624 33,117,383 (Both) 3' end (22 of 79 1 Loss (A) 1 CEU (A) muscle Duchenne- and Becker-like muscular dystrophy dystrophies; duplications are also should be carrier for the disorder exons) (A) muscular dystrophy symptoms; seen in this gene alleles vary in their phenotypic severity and may include cardiovascular and digestive system effects

Rare mutations and a translocation Loss may cause symptoms of chrX:47,523,164- zinc finger protein chrX:47,452,555- X-linked mental Affy/Sanger disrupting the gene are a rare Xp11.23 1404 *314998 ZNF81 X-linked D 3' end (2 of 7 exons) 3 Gain, 1 Loss 1 CHB, 3 YRI WSSD Zinc finger protein gene None mental retardation or slight 47,902,964 81 47,537,860 retardation (Sanger) cause of X-linked mental neurological abnormalities retardation

May function as transcriptional repressors; also capable of eliciting spontaneously humoral and cellular Translocation causes fusion of this chrX:47,523,164- synovial sarcoma, X chrX:47,871,051- Affy/Sanger Gain/loss may be associated with Xp11.23 1404 +312820 SSX1 Synovial sarcoma entire gene 2 Gain, 1 Loss 1 CHB, 2 YRI Yes immune responses in cancer gene with SYT seen in synovial None 47,902,964 breakpoint 1 47,883,133 (Sanger) susceptibility for sarcoma patients, and are potentially useful sarcomas targets in cancer vaccine-based immunotherapy

Hemizygous mutant males are androgen-resistant and therefore Belongs to the class of nuclear have have small, undescended androgen insensitivity 5' end (1 of 8 exons) receptors called activated class I testes, and lack epididymal chrX:66,282,690- chrX:66,546,895- Affy/Sanger 1 Gain (S) 1 CEU (S) Mutations cause AIS and have Gain is not expected to cause a Xq12 1409 *313700 androgen receptor AR syndrome (AIS); X-linked R (S) No steroid receptors, which recognize structures, vas deferens, and male 67,102,115 66,727,140 (Both) 1 Gain (A) 1 CEU (A) been seen in prostate cancer phenotype prostate cancer entire gene (A) canonical androgen response accessory glands; mutants elements (AREs) resemble females physically and behaviorally, but lack female reproductive organs

Downregulation in CA1 neurons in Modulate cytoskeletal changes; Translocation disrupting gene and rat hippocampal slices resulted in a chrX:66,282,690- chrX:67,045,736- X-linked mental Affy/Sanger 3' end (7 of 24 may acts normally to repress the Gain is not expected to cause a Xq12 1409 *300127 oligophrenin 1 OPHN1 X-linked R 1 Gain 1 CEU No other mutations cause X-linked significant decrease in dendritic 67,102,115 67,436,668 retardation (Affy) exons) Rho signaling pathway to maintain phenotype mental retardation spine length (ranging from a 12 to dendritic spine length 18% decrease)

Mutations in this gene affect copper metabolism and, depending on the allele, result in abnormal ATPase, Cu++ Loss should cause disorder in chrX:77,031,055- chrX:76,972,344- Menkes disease; X- 3' end (21 of 22 Mutations cause Menkes disease pigmentation, vibrissae, hair, and Xq21.1 1412 *300011 transporting, alpha ATP7A X-linked R Sanger 1 Loss 1 YRI Yes Copper-binding protein male; if in female, should be 77,115,217 77,111,584 linked cutis laxa exons) and X-linked cutis laxa skeleton; behavior may be polypeptide carrier for the disorder abnormal and defects of collagen and elastin fibers are reported. Some alleles are hemizygous lethal.

Female heterozygotes for a acyl-CoA Mutations and large gene deletion targeted null mutation exhibit Loss should cause disorder in chrX:108,585,146- synthetase long- chrX:108,690,711- X-linked mental Converts free long chain fatty acids cause mental retardation (female accumulation of prostaglandins in Xq23 1421 *300157 ACSL4 X-linked R Sanger entire gene 2 Loss 2 YRI No male; if in female, should be 108,787,037 chain family 108,782,764 retardation into fatty acyl-CoA esters carriers have skewed X inactivation the uterus, reduced fertility with few carrier for the disorder member 4 in leukocytes) and small litters, and very low transmission of the mutant allele

Receptor for angiotensin II that Null mice developed normally but Translocation silencing this gene mediates programmed cell death; had an impaired drinking response chrX:115,037,017- angiotensin II chrX:115,113,885- X-linked mental causes moderate mental Gain is not expected to cause a Xq23 1424 +300034 AGTR2 X-linked R Affy entire gene 1 Gain 1 CEU No may have a role in cell to water deprivation as well as a 115,175,870 receptor, type 2 115,117,702 retardation retardation; mutations also cause phenotype morphogenesis and related events reduction in spontaneous MR in growth and development movements

Majority of hemizygous or Glycoprotein thought to protect the homozygous mutant mice die Mutations can cause Danon X-linked R (but lysosomal membrane from prematurely displaying lysosomal- disease and hypertrophic Loss should cause disorder in chrX:119,183,307- chrX:119,346,563- carriers may proteolytic enzymes within cardiomyopathy and accumulation Xq24 1427 *309060 associated LAMP2 Danon disease Sanger 3' end (6 of 9 exons) 1 Loss 1 YRI No cardiomyopathy; certain alleles may male; if in female, should be 119,364,831 119,385,043 have mild lysosomes and to act as a receptor of autophagic vacuoles in several membrane protein 2 be associated with insulin- carrier for the disorder phenotype) for proteins to be imported into tissues including liver, pancreas, dependent diabetes mellitus lysosomes spleen, kidney and skeletal and cardiac muscle

Phosphatidylinositol 4,5- Lowe Homozygous null mice do not bisphosphate-5-phosphatase Mutations and small deletions have Loss should cause disorder in chrX:128,423,110- oculocerebrorenal chrX:128,399,787- Oculocerebrorenal 3' end (12 of 23 12 CEU, 3 CHB, 5 develop any of the abnormalities Xq25 1431 *300535 OCRL X-linked R Sanger 18 Gain, 19 Loss No localized to the trans-Golgi network been found to cause OCRL and male; if in female, should be 128,689,620 syndrome of Lowe 128,452,063 Syndrome (OCRL); exons) JPT, 17 YRI associated with oculocerebrorenal that is involved in actin Dent disease carrier for the disorder Dent Disease syndrome of Lowe polymerization

Translocation disrupting this gene X-prolyl premature ovarian has been seen in premature chrX:128,423,110- aminopeptidase chrX:128,598,485- failure (POF); Hydrolase that is specific for N- Loss of this gene may increase Xq25 1431 *300145 XPNPEP2 Sanger entire gene 2 Loss 2 YRI No ovarian failure; SNPs associated None 128,689,620 (aminopeptidase P) 128,629,060 Angioedema (adverse terminal imido bonds risk of premature ovarian failure with life-threatening adverse 2 reaction to ACEi) reaction to ACEi treatment

Homozygotes for a targeted null Trinucleotide repeat expansions mutation exhibit macroorchidism fragile X mental cause fragile X mental retardation; associated with more rapid Sertoli Xq27.3- chrX:146,718,150- fragile X mental chrX:146,699,055- retardation 1; idiopathic 3' end (10 of 17 Associated with polysomes, might Gain is not expected to cause a 1437 +309550 FMR1 X-linked R Affy 1 Gain 1 JPT No premutations usually normal, but cell proliferation, altered dendritic Xq28 146,857,358 retardation 1 146,738,157 premature ovarian exons) be involved in transport of mRNA phenotype have been associated with spines of visual cortex pyramidal failure idiopathic premature ovarian failure cells, and subtle differences in a variety of behavioral tests

Heterozygous females exhibit a striped coat or skin hyperkeratotic lesions leaving bare patches on the NAD(P) dependent coat, with some mutations also chrX:151,572,622- chrX:151,670,079- Enzyme of post-squalene Gain is not expected to cause a Xq28 1439 *300275 steroid NSDHL CHILD syndrome X-linked D Affy 5' end (2 of 8 exons) 1 Gain 1 YRI No Mutations cause CHILD syndrome resulting in skeletal dysplasia and 151,688,320 151,708,475 cholesterol biosynthesis phenotype dehydrogenase-like eye defects; hemizygous male and homozygous female mice die before birth, presumably due to placental defects

Chr. Y

Deletions of DAZ genes have been Gene required for reported, and may cause or Yq11.223- chrY:22,936,103- deleted in chrY:25,318,189- Male infertility 2 CEU, 5 CHB, 12 Gain/loss may have an effect on 1447 *400003 DAZ1 Y-linked Sanger entire genei 11 Gain, 30 Loss Yes spermatogenesis; exists in multiple increase susceptibility for infertility None Yq11.23 26,838,610 azoospermia 1 25,391,306 (azoospermia) JPT, 22 YRI male fertility highly similar copies depending on the size of the deletion

Supplementary Table 16: Genes associated with a defined disease phenotype (OMIM morbid map) were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi). A total of 1961 unique genes representing 2,025 diseases were used. Overlap between genes and CNVs were extracted using the merged data from both WGTP and 500KEA platforms. The list of overlapping entries was then manually curated, and the number of gains and losses at the sample level was recorded for each platform, respectively. Information about each gene and associated phenotype was extracted from the full OMIM database entry. Supplemental Talbe 16B: OMIM regions summary # OMIM Region CNP_ID Chromosome Start End Info # Genes Accessions GeneID Gene Symbol OMIM ID Class Transcripts 1 6 chr1 3,608,198 3,678,693 Affy 1 1 NM_005427 7161 TP73 601990 spanOne NM_015074 23095 2 10 chr1 10,172,336 10,516,820 Sanger 2 3 NM_183416 23095 KIF1B KIF1B 605995 605995 within within NM_004565 5195 PEX14 601791 spanOne 3 15 chr1 16,509,639 17,229,287 Both 1 1 NM_003000 6390 SDHB 185470 within 4 16 chr1 21,481,490 21,687,720 Sanger 1 1 NM_000478 249 ALPL 171760 within 5 17 chr1 21,967,827 22,158,163 Sanger 1 1 NM_005529 3339 HSPG2 142461 spanOne 6 23 chr1 39,894,236 40,329,525 Sanger 1 1 NM_000310 5538 PPT1 600722 within NM_000643 NM_000028 NM_000646 7 42 chr1 100,071,676 100,210,363 Sanger 1 6 NM_000642 178 178 AGL AGL 232400 232400 spanOne spanOne NM_000645 178 178 AGL AGL 232400 232400 spanOne spanOne NM_000644 178 178 AGL AGL 232400 232400 spanOne spanOne NM_002506 NM_002524 4803 NM_015906 4893 NGFB NRAS 162030 164790 NM_015967 51592 TRIM33 605769 8 52 chr1 112,869,177 116,453,414 Both 7 9 NM_033020 26191 PTPN22 222100,600716 within within NM_012411 51592 TRIM33 605769 within within NM_000036 26191 PTPN22 222100,600716 within within NM_001232 270 845 AMPD1 CASQ2 102770 114251 within within NM_000549 7252 TSHB 188540 within NM_006623 26227 PHGDH 9 55 chr1 119,979,355 120,958,392 Sanger 2 2 NM_005518 3158 HMGCS2 606879 600234 spanOne within NM_213653 148738 NM_202004 148738 10 56 chr1 141,387,477 143,032,961 Both 1 4 NM_213652 148738 HFE2 HFE2 608374 608374 within within NM_145277 148738 HFE2 HFE2 608374 608374 within within 11 58 chr1 144,800,023 146,809,052 Both 1 1 NM_000566 2209 FCGR1A 146760 within NM_000298 5313 NM_000157 2629 NM_001005749 2629 12 61 chr1 151,908,051 152,127,880 Sanger 2 7 NM_001005741 2629 PKLR GBA 609712 606463 within within NM_001005750 2629 GBA GBA 606463 606463 within within NM_181871 5313 GBA PKLR 606463 609712 within within NM_001005742 2629 GBA 606463 within NM_001002275 2213 FCGR2B NM_001002273 2213 FCGR2B NM_021642 2212 FCGR2A 13 62 chr1 158,157,328 158,413,210 Both 3 6 NM_000569 2214 FCGR3A 604590 604590 within within NM_004001 2213 FCGR2B 146790 146740 within within NM_001002274 2213 FCGR2B 604590 604590 within within 14 68 chr1 170,542,299 170,687,600 Sanger 1 1 NM_000488 462 SERPINC1 107300 within NM_018136 259266 NM_000186 3075 15 80 chr1 193,322,494 193,901,429 Both 3 4 NM_001014975 3075 ASPM CFH 605481 134370 within within NM_001994 2165 CFH F13B 134370 134580 within within NM_000651 1378 16 84 chr1 203,946,290 204,313,462 Sanger 1 2 NM_000573 1378 CR1 CR1 120620 120620 within within NM_001012957 27185 NM_001012958 27185 17 95 chr1 227,931,495 228,222,731 Both 1 4 NM_018662 27185 DISC1 DISC1 605210 605210 spanOne within NM_001012959 27185 DISC1 DISC1 605210 605210 spanOne spanOne 18 99 chr1 234,267,835 235,094,143 Both 1 1 NM_001035 6262 RYR2 180902,600996 spanOne NM_000547 7173 spanBothExon NM_175722 7173 spanBothExon 19 108 chr2 1,410,597 1,484,084 Affy 1 5 NM_175720 7173 TPO TPO 606765 606765 spanBothExon NM_175719 7173 TPO TPO 606765 606765 spanBothExon NM_175721 7173 TPO 606765 spanBothExon NM_018062 55120 20 145 chr2 58,306,194 61,252,101 Both 2 2 NM_002618 5194 FANCL PEX13 608111 601789 spanOne within 21 151 chr2 73,628,687 73,990,247 Sanger 1 1 NM_015120 7840 ALMS1 606844 spanOne NM_023019 1639 22 152 chr2 74,391,579 74,674,080 Sanger 2 3 NM_004082 1639 DCTN1 DCTN1 601143 601143 within within NM_006302 7841 GCS1 601336 within 23 168 chr2 96,992,983 97,795,025 Both 1 1 NM_001079 7535 ZAP70 176947 spanOne NM_000272 4867 213300,607100 24 173 chr2 110,050,731 110,558,272 Both 1 2 NM_207181 4867 NPHP1 NPHP1 213300,607100 within within 25 174 chr2 111,616,014 112,463,168 Sanger 1 1 NM_006343 10461 MERTK 604705 spanOne 26 183 chr2 130,063,068 133,031,735 Both 1 1 NM_032545 55997 CFC1 605194 within NM_133378 7273 spanBothExon NM_003319 7273 spanBothExon 27 194 chr2 179,234,579 179,433,748 Sanger 1 4 NM_133437 7273 TTN TTN 188840 188840 spanBothExon NM_133432 7273 TTN TTN 188840 188840 spanBothExon 28 195 chr2 183,263,206 183,660,590 Both 1 1 NM_001463 2487 FRZB 165720,605083 within NM_212475 2335 NM_054034 2335 NM_212478 2335 29 205 chr2 216,116,776 216,276,027 Both 1 7 NM_002026 2335 FN1 FN1 135600 135600 spanOne spanOne NM_212482 2335 FN1 FN1 135600 135600 spanOne spanOne NM_212476 2335 FN1 FN1 135600 135600 spanOne spanOne NM_212474 2335 FN1 135600 spanOne NM_023089 11132 CAPN10 NM_023085 11132 CAPN10 30 210 chr2 241,085,111 241,308,861 Both 1 4 NM_021251 11132 CAPN10 605286 605286 within within NM_023083 11132 CAPN10 605286 605286 within within 31 212 chr2 242,415,890 242,787,722 Both 1 1 NM_152783 257054 D2HGDH 609186 spanOne 32 217 chr3 4,113,369 4,395,357 Both 1 1 NM_182760 285362 SUMF1 607939 spanOne NM_007338 9940 NM_007336 9940 33 231 chr3 37,806,487 38,079,228 Sanger 1 5 NM_007337 9940 DLEC1 DLEC1 604050 604050 spanOne spanOne NM_005106 9940 DLEC1 DLEC1 604050 604050 spanOne spanOne NM_007335 9940 DLEC1 604050 spanOne NM_147196 259236 34 238 chr3 46,655,456 46,947,493 Sanger 3 3 NM_000316 5745 TMIE PTHR1 607237 168468 within within NM_000258 4634 MYL3 160790 within

NM_153282 3373 NM_144499 2779 NM_153285 3373 NM_153283 3373 NM_002070 2771 35 239 chr3 50,173,482 50,346,381 Sanger 3 11 NM_153286 3373 HYAL1 GNAT1 607071 139330 within within NM_000172 2779 HYAL1 HYAL1 607071 607071 within within NM_153281 3373 GNAI2 HYAL1 139360 607071 within within NM_153284 3373 GNAT1 HYAL1 139330 607071 within within NM_033159 3373 HYAL1 HYAL1 607071 607071 within within NM_007312 3373 HYAL1 607071 within 36 268 chr3 131,142,165 131,422,680 Both 1 1 NM_007117 7200 TRH 275120 within NM_000893 3827 37 297 chr3 187,819,836 188,050,028 Both 3 3 NM_000412 3273 KNG1 HRG 228960 142640 within within NM_004797 9370 ADIPOQ 605441 spanOne # OMIM Region CNP_ID Chromosome Start End Info # Genes Accessions GeneID Gene Symbol OMIM ID Class Transcripts NM_130835 4976 NM_130833 4976 NM_130836 4976 NM_130831 4976 38 303 chr3 194,716,602 194,886,348 Sanger 1 8 NM_130834 4976 OPA1 OPA1 605290 605290 spanOne spanOne NM_130837 4976 OPA1 OPA1 605290 605290 spanOne spanOne NM_015560 4976 OPA1 OPA1 605290 605290 spanOne spanOne NM_130832 4976 OPA1 OPA1 605290 605290 spanOne spanOne 39 308 chr4 593,208 921,184 Sanger 1 1 NM_000283 5158 PDE6B 180072 within NM_000142 2261 40 309 chr4 1,592,784 1,782,006 Sanger 1 2 NM_022965 2261 FGFR3 FGFR3 134934 134934 within within 41 310 chr4 3,431,313 4,469,058 Both 1 1 NM_000683 152 ADRA2C 104250 within 42 313 chr4 8,640,244 9,952,736 Both 1 1 NM_000798 1816 DRD5 126453 within NM_138982 5602 MAPK10 spanBothExon 43 354 chr4 87,432,938 87,495,944 Affy 1 3 NM_002753 5602 MAPK10 602897 602897 spanBothExon NM_138980 5602 MAPK10 602897 spanBothExon 44 357 chr4 89,275,730 89,570,298 Both 1 1 NM_000297 5311 PKD2 173910 within 45 363 chr4 109,298,778 109,305,695 Affy 1 1 NM_005327 3033 HADHSC 601609 spanBothExon 46 370 chr4 118,836,451 120,032,345 Both 1 1 NM_003619 8492 PRSS12 606709 within NM_002100 2994 47 379 chr4 144,705,898 145,489,197 Both 2 2 NM_002099 2993 GYPB GYPA 111740 111300 within within 48 395 chr4 178,540,618 178,780,523 Both 1 1 NM_000027 175 AGA 208400 within 49 406 chr5 70,263 648,955 Sanger 1 1 NM_004168 6389 SDHA 600857 within 50 429 chr5 32,281,118 32,774,401 Sanger 1 1 NM_000908 4883 NPR3 108962 spanOne 51 432 chr5 40,909,835 41,045,039 Affy 1 1 NM_000587 730 C7 217070 within NM_000344 6606 52 439 chr5 69,109,876 70,831,640 Sanger 1 2 NM_022874 6606 SMN1 SMN1 600354 600354 within within 53 471 chr5 135,193,500 135,502,898 Both 1 1 NM_000358 7045 TGFBI 601692,602082 within NM_181676 5521 PPP2R2B NM_181674 5521 PPP2R2B 54 476 chr5 146,410,036 146,519,693 Affy 1 4 NM_181677 5521 PPP2R2B 604325 604325 spanOne spanOne NM_181678 5521 PPP2R2B 604325 604325 spanOne spanOne 55 480 chr5 156,930,186 157,165,622 Sanger 1 1 NM_014666 9685 ENTH 607265 spanOne NM_172349 64324 56 487 chr5 176,550,923 176,735,050 Sanger 1 2 NM_022455 64324 NSD1 NSD1 606681 606681 spanOne spanOne NM_021599 9509 ADAMTS2 57 488 chr5 178,593,872 178,970,135 Both 1 2 NM_014244 9509 ADAMTS2 604539 604539 spanOne spanOne 58 492 chr6 5,001 720,274 Both 1 1 NM_002460 3662 IRF4 601900 within NM_001491 2651 59 497 chr6 10,551,783 10,751,118 Both 1 3 NM_145655 2651 GCNT2 GCNT2 600429 600429 within within NM_145649 2651 GCNT2 600429 within 60 503 chr6 29,900,413 30,083,123 Both 1 1 NM_002127 3135 HLA-G 142871,600807 within NM_001264 1041 NM_005514 3106 146520,602593 61 505 chr6 31,136,269 31,650,287 Both 4 4 NM_000595 4049 CDSN HLA-B 142830 153440 within within NM_005007 4795 LTA NFKBIL1 601022 within within NM_000500 NM_000063 NM_007293 62 506 chr6 31,979,491 32,317,091 Sanger 5 6 NM_019105 1589 717 CYP21A2 C2 201910 217000 within within NM_032470 720 7148 C4A TNXB 120810 600985 within within NM_001002029 7148 721 TNXB C4B 600985 120820 within within NM_002124 3123 HLA-DRB1 63 507 chr6 32,479,731 32,813,412 Sanger 2 2 NM_019602 56244 BTNL2 142857 606000 within spanOne NM_004117 2289 64 511 chr6 35,571,719 35,914,482 Sanger 2 2 NM_003322 7287 FKBP5 TULP1 602623 602280 within within 65 512 chr6 38,696,947 38,819,063 Sanger 1 1 NM_006708 2739 GLO1 138750,209850 within 147050,600807,6010 66 516 chr6 46,808,141 47,036,030 Sanger 1 1 NM_005084 7941 PLA2G7 00 spanOne 67 560 chr6 129,315,361 129,484,648 Sanger 1 1 NM_000426 3908 LAMA2 156225 spanBothExon NM_172105 2070 NM_004100 2070 68 561 chr6 133,486,412 133,669,057 Sanger 1 4 NM_172103 2070 EYA4 EYA4 603550 603550 spanOne spanOne NM_172104 2070 EYA4 EYA4 603550 603550 spanOne spanOne 69 564 chr6 137,501,221 137,615,031 Sanger 1 1 NM_000416 3459 IFNGR1 107470 within 70 574 chr6 159,974,242 160,185,562 Sanger 1 1 NM_005891 39 ACAT2 100678 within NM_000301 5340 71 575 chr6 160,342,655 161,205,076 Both 3 3 NM_005577 4018 PLG LPA 173350 152200 within within NM_000876 3482 IGF2R 147280 within NM_013987 5071 602544,607572 spanBothIntron 72 576 chr6 161,906,087 161,907,120 Affy 1 3 NM_004562 5071 PARK2 PARK2 602544,607572 spanBothIntron NM_013988 5071 PARK2 602544,607572 spanBothIntron NM_013987 5071 602544,607572 spanBothExon 73 577 chr6 162,161,167 162,381,661 Sanger 1 3 NM_004562 5071 PARK2 PARK2 602544,607572 spanBothExon NM_013988 5071 PARK2 602544,607572 spanBothExon NM_013987 5071 602544,607572 spanBothIntron 74 578 chr6 162,461,349 162,478,101 Affy 1 3 NM_004562 5071 PARK2 PARK2 602544,607572 spanBothIntron NM_013988 5071 PARK2 602544,607572 spanBothIntron NM_013987 5071 602544,607572 spanBothIntron 75 579 chr6 162,706,292 162,710,176 Affy 1 3 NM_004562 5071 PARK2 PARK2 602544,607572 spanBothIntron NM_013988 5071 PARK2 602544,607572 spanBothIntron NM_013987 5071 602544,607572 76 580 chr6 162,811,333 163,203,672 Both 1 3 NM_004562 5071 PARK2 PARK2 602544,607572 spanOne spanOne NM_013988 5071 PARK2 602544,607572 spanOne 77 588 chr6 170,499,383 170,927,551 Sanger 1 1 NM_003194 6908 TBP 600075 within 78 609 chr7 22,528,824 22,694,150 Sanger 1 1 NM_000600 3569 IL6 147620 within 79 611 chr7 27,566,856 27,746,109 Sanger 1 1 NM_175061 221895 JAZF1 606246 spanOne 80 616 chr7 39,833,420 40,042,823 Affy 1 1 NM_138701 136647 C7orf11 609188 within 81 626 chr7 65,845,580 66,303,403 Sanger 1 1 NM_016038 51119 SBDS 607444 within NM_000265 4687 NM_000941 5447 82 629 chr7 73,439,084 76,494,030 Both 4 4 NM_005338 3092 NCF1 POR 608512 124015 within within NM_001540 3315 HIP1 HSPB1 601767 602195 within within NM_000665 83 638 chr7 100,000,141 100,342,681 Sanger 1 2 NM_015831 43 43 ACHE ACHE 100740 100740 within within NM_002769 5644 84 660 chr7 141,610,138 142,240,984 Both 2 2 NM_000420 3792 PRSS1 KEL 276000 110900 within within NM_172056 3757 85 665 chr7 149,976,469 150,101,345 Sanger 1 3 NM_172057 3757 KCNH2 KCNH2 152427 152427 spanOne within NM_000238 3757 KCNH2 152427 spanOne 86 682 chr8 8,745,049 8,785,304 Affy 1 1 NM_004225 9258 MFHAS1 605352 spanBothExon NM_178234 7991 87 689 chr8 14,670,571 15,809,077 Both 1 2 NM_006765 7991 TUSC3 TUSC3 601385 601385 within within 88 691 chr8 17,335,551 17,685,810 Both 1 1 NM_006207 5157 PDGFRL 604584 within NM_005144 55806 NM_147187 8795 HR 89 695 chr8 20,577,324 23,167,554 Both 3 5 NM_018411 55806 TNFRSF10B 602302 603612 within within NM_003018 6440 HR SFTPC 602302 178620 within within NM_003842 8795 TNFRSF10B 603612 within 90 697 chr8 25,324,942 25,478,051 Sanger 1 1 NM_000825 2796 GNRH1 152760 within 91 702 chr8 48,950,846 49,170,567 Sanger 1 1 NM_006904 5591 PRKDC 600899 spanOne 92 719 chr8 91,069,962 91,398,845 Both 1 1 NM_001359 1666 DECR1 222745 within NM_017890 157680 VPS13B spanBothExon NM_152564 157680 VPS13B spanBothExon 93 723 chr8 100,098,024 100,265,857 Sanger 1 4 NM_015243 157680 VPS13B 607817 607817 spanBothExon NM_181661 157680 VPS13B 607817 607817 spanOne # OMIM Region CNP_ID Chromosome Start End Info # Genes Accessions GeneID Gene Symbol OMIM ID Class Transcripts NM_017890 157680 VPS13B spanBothExon 94 724 chr8 100,473,327 100,907,800 Sanger 1 2 NM_152564 157680 VPS13B 607817 607817 spanBothExon 95 726 chr8 102,678,650 102,718,857 Affy 1 1 NM_024915 79977 GRHL2 608576 spanBothExon 96 730 chr8 120,012,490 120,344,931 Sanger 1 1 NM_002546 4982 TNFRSF11B 602643 spanOne 97 733 chr8 133,470,532 133,754,071 Sanger 1 1 NM_004519 3786 KCNQ3 602232 spanOne NM_017767 55630 SLC39A4 98 743 chr8 145,494,501 145,668,486 Sanger 1 2 NM_130849 55630 SLC39A4 607059 607059 within within 99 746 chr9 514,413 843,033 Both 1 1 NM_021951 1761 DMRT1 602424 spanOne 100 750 chr9 4,517,262 4,518,816 Affy 1 1 NM_004170 6505 SLC1A1 133550 spanBothIntron 101 752 chr9 6,566,991 6,835,561 Both 1 1 NM_000170 2731 GLDC 238300 spanOne 102 762 chr9 12,225,048 12,774,092 Both 1 1 NM_000550 7306 TYRP1 115501 within 103 804 chr9 120,727,751 120,922,549 Sanger 1 1 NM_001735 727 C5 120900 within NM_007313 104 808 chr9 130,767,120 131,058,115 Sanger 2 3 NM_005157 25 25 ABL1 ABL1 189980 189980 spanOne spanOne NM_005085 8021 NUP214 114350 spanOne 105 809 chr9 131,300,676 131,508,504 Both 1 1 NM_007171 10585 POMT1 607423 within NM_006412 10555 AGPAT2 106 811 chr9 136,526,666 137,102,322 Sanger 2 3 NM_001012727 10555 AGPAT2 603100 603100 within within NM_017617 4851 NOTCH1 190198 within 107 840 chr10 50,641,980 51,595,172 Sanger 1 1 NM_005437 8031 NCOA4 601984 within 108 844 chr10 55,027,142 55,256,936 Both 1 1 NM_033056 65217 PCDH15 605514 spanOne 109 845 chr10 56,078,033 56,236,143 Both 1 1 NM_033056 65217 PCDH15 605514 spanOne 110 855 chr10 70,127,725 70,301,318 Sanger 1 1 NM_152709 219736 STOX1 189800,609397 spanOne NM_033500 3098 spanBothExon 111 856 chr10 70,708,723 70,722,894 Affy 1 3 NM_033497 3098 HK1 HK1 142600 142600 spanBothExon NM_033498 3098 HK1 142600 spanBothExon NM_022124 64072 spanBothExon 112 857 chr10 72,907,909 72,956,161 Affy 1 2 NM_052836 64072 CDH23 CDH23 605516 605516 spanBothExon NM_002247 3778 113 860 chr10 78,781,397 79,263,477 Both 2 3 NM_004747 9231 KCNMA1 DLG5 600150 604090 spanOne spanOne NM_001014797 3778 KCNMA1 600150 spanOne 114 861 chr10 80,945,468 81,810,835 Both 1 1 NM_005411 6435 SFTPA1 178630 within NM_004897 MINPP1 115 865 chr10 88,505,038 89,299,742 Both 3 3 NM_004329 9562 657 BMPR1A 605391 601299 spanOne within NM_005271 2746 GLUD1 138130 within 116 866 chr10 90,825,044 91,007,466 Sanger 1 1 NM_000235 3988 LIPA 278000 within NM_003990 5076 NM_003988 5076 117 870 chr10 102,141,840 102,555,726 Both 1 5 NM_003989 5076 PAX2 PAX2 167409 167409 spanOne spanOne NM_003987 5076 PAX2 PAX2 167409 167409 spanOne spanOne NM_000278 5076 PAX2 167409 spanOne NM_018117 55717 BRWD2 118 875 chr10 122,625,702 122,891,863 Sanger 2 1 NM_022971 2263 FGFR2 606417 101200 spanOne spanOne NM_007329 1755 119 877 chr10 124,253,065 124,444,805 Sanger 1 3 NM_017579 1755 DMBT1 DMBT1 601969 601969 within within NM_004406 1755 DMBT1 601969 within 120 879 chr10 127,443,890 127,776,692 Sanger 1 1 NM_000375 7390 UROS 606938 within NM_001039490 NM_139029 NM_006755 NM_000797 977 977 121 885 chr11 399,846 1,313,968 Sanger 5 9 NM_004357 6888 CD151 CD151 602243 602243 within within NM_139030 1815 977 TALDO1 DRD4 602063 126452 within within NM_176795 977 3265 CD151 CD151 602243 602243 within within NM_005343 3265 HRAS HRAS 190020 190020 within within NM_024698 79751 SLC25A22 609302 within NM_181797 3784 KCNQ1 NM_002555 5002 SLC22A18 NM_181798 3784 KCNQ1 122 886 chr11 2,745,620 2,920,188 Sanger 3 6 NM_183233 5002 SLC22A18 607542 602631 spanOne within NM_000076 1028 CDKN1C 607542 602631 spanOne within NM_000218 3784 KCNQ1 600856 607542 within spanOne NM_139132 4928 NM_005387 4928 123 887 chr11 3,193,088 3,758,005 Both 1 4 NM_139131 4928 NUP98 NUP98 601021 601021 spanOne spanOne NM_016320 4928 NUP98 NUP98 601021 601021 spanOne spanOne 124 908 chr11 34,869,891 34,920,304 Affy 1 1 NM_003477 8050 PDHX 608769 spanOne NM_001001392 NM_001001390 125 909 chr11 34,986,509 35,195,154 Both 1 5 NM_000610 960 960 CD44 CD44 107269 107269 spanOne spanOne NM_001001391 960 960 CD44 CD44 107269 107269 spanOne spanOne NM_001001389 960 CD44 107269 spanOne 126 922 chr11 60,671,936 60,837,233 Sanger 1 1 NM_001923 1642 DDB1 600045 spanOne NM_006053 10312 TCIRG1 127 926 chr11 67,229,481 67,647,865 Both 2 3 NM_002496 4728 NDUFS8 604592 602141 within within NM_006019 10312 TCIRG1 604592 within 128 928 chr11 73,520,257 74,235,245 Both 1 1 NM_005472 10008 KCNE3 604433 within NM_213655 378465 608620 129 966 chr12 205,271 860,805 Both 2 2 NM_018979 65125 HSN2 WNK1 145260,605232 within spanOne 130 967 chr12 6,324,145 6,534,096 Both 1 1 NM_001038 6337 SCNN1A 600228 within 131 989 chr12 46,715,969 47,111,766 Both 1 1 NM_000289 5213 PFKM 232800 within NM_002281 KRTHB1 132 990 chr12 50,849,531 51,071,786 Both 3 2 NM_002282 3887 KRTHB3 602153 158000 within within NM_002284 3889 3892 KRTHB6 601928 within NM_004984 3798 133 992 chr12 56,116,000 56,288,135 Sanger 2 2 NM_004083 1649 KIF5A DDIT3 602821 126337 within within NM_002562 5027 602566 134 1008 chr12 119,878,565 120,047,533 Sanger 2 3 NM_000545 6927 P2RX7 TCF1 142410,222100 spanOne within NM_177427 5027 P2RX7 602566 spanOne 135 1009 chr12 122,635,002 122,720,736 Affy 1 1 NM_001414 1967 EIF2B1 606686 spanOne 136 1051 chr13 101,459,508 101,483,261 Affy 1 1 NM_175929 2259 FGF14 601515 spanBothIntron NM_001024858 6710 spanBothExon 137 1085 chr14 64,324,218 64,341,533 Affy 1 2 NM_000347 6710 SPTB SPTB 182870 182870 spanBothExon 138 1088 chr14 73,620,134 73,676,171 Affy 1 1 NM_005589 4329 ALDH6A1 603178 spanOne NM_001037525 2581 139 1099 chr14 87,460,869 87,500,047 Affy 1 2 NM_000153 2581 GALC GALC 606890 606890 spanOne spanOne 140 1104 chr14 103,217,278 103,482,566 Sanger 1 1 NM_005432 7517 XRCC3 600675 within 141 1107 chr15 18,263,733 21,365,850 Both 1 1 NM_144599 123606 NIPA1 608145 within NM_022807 6638 176270,182279 NM_022805 6638 176270,182279 142 1110 chr15 22,606,371 22,689,056 Affy 1 4 NM_022808 6638 SNRPN SNRPN 176270,182279 spanOne spanOne NM_022806 6638 SNRPN SNRPN 176270,182279 spanOne spanOne 143 1114 chr15 29,553,592 30,773,871 Both 1 1 NM_000746 1139 CHRNA7 118511 within 144 1115 chr15 32,330,313 32,775,539 Both 1 1 NM_005135 9990 SLC12A6 604878 spanOne NM_002875 5888 145 1117 chr15 38,619,837 38,782,403 Sanger 1 2 NM_133487 5888 RAD51 RAD51 179617 179617 spanOne spanOne 146 1119 chr15 41,610,450 41,935,933 Both 1 1 NM_153700 161497 STRC 606440 within NM_014080 147 1120 chr15 42,756,160 43,210,134 Both 3 3 NM_003104 50506 DUOX2 SORD 606759 182500 within within NM_004048 6652 567 B2M 109700 within 148 1121 chr15 46,296,330 46,451,070 Sanger 1 1 NM_000338 6557 SLC12A1 600839 spanOne NM_031226 1588 CYP19A1 149 1122 chr15 49,069,549 49,617,631 Both 1 2 NM_000103 1588 CYP19A1 107910 107910 within within 150 1130 chr15 70,606,839 70,907,613 Sanger 1 1 NM_033028 585 BBS4 600374 within # OMIM Region CNP_ID Chromosome Start End Info # Genes Accessions GeneID Gene Symbol OMIM ID Class Transcripts NM_033247 5371 NM_033245 5371 NM_002675 5371 NM_033239 5371 NM_033250 5371 151 1131 chr15 72,002,167 72,251,969 Sanger 1 11 NM_033246 5371 PML PML 102578 102578 within within NM_033244 5371 PML PML 102578 102578 within within NM_033242 5371 PML PML 102578 102578 within within NM_033249 5371 PML PML 102578 102578 within within NM_033238 5371 PML PML 102578 102578 within within NM_033240 5371 PML 102578 within 152 1132 chr15 74,957,605 75,160,503 Sanger 1 1 NM_003978 9051 PSTPIP1 604416,606347 within NM_018445 55829 153 1154 chr15 99,537,666 99,872,978 Both 1 2 NM_203472 55829 SELS SELS 607918 607918 within within NM_181050 8312 154 1157 chr16 266,993 1,111,069 Sanger 2 3 NM_001053 6755 AXIN1 SSTR5 603816 182455 within within NM_003502 8312 AXIN1 603816 within 155 1160 chr16 4,912,851 5,364,830 Both 1 1 NM_019109 56052 ALG1 605907 within 156 1171 chr16 16,092,718 16,831,289 Both 1 1 NM_001171 368 ABCC6 603234 within NM_001014444 1428 157 1174 chr16 21,212,772 21,856,623 Both 2 3 NM_170664 146183 CRYM OTOA 123740 607038 spanOne within NM_144672 146183 OTOA 607038 within NM_004320 158 1178 chr16 28,082,639 29,058,054 Sanger 2 3 NM_000086 487 1201 ATP2A1 CLN3 108730 607042 within within NM_173201 487 ATP2A1 108730 within NM_184043 159 1180 chr16 29,981,456 30,290,781 Sanger 1 3 NM_184041 226 226 ALDOA ALDOA 103850 103850 within within NM_000034 226 ALDOA 103850 spanOne NM_001031835 5257 160 1182 chr16 45,819,013 46,163,788 Both 1 2 NM_000293 5257 PHKB PHKB 172490 172490 spanOne spanOne NM_001025194 1066 NM_001266 1066 161 1187 chr16 54,226,897 54,541,091 Sanger 2 4 NM_001025195 1066 CES1 CES1 114835 114835 within within NM_001043 6530 CES1 SLC6A2 114835 163970 within within 162 1192 chr16 70,533,845 70,831,848 Sanger 1 1 NM_005143 3240 HP 140100 within 163 1195 chr16 73,977,115 74,134,472 Sanger 1 1 NM_021615 4166 CHST6 605294 within NM_130791 51741 spanOne 164 1198 chr16 76,811,430 76,974,815 Both 1 2 NM_016373 51741 WWOX WWOX 605131 605131 spanBothIntron 165 1199 chr16 77,607,617 77,626,238 Affy 1 1 NM_016373 51741 WWOX 605131 spanBothIntron NM_199367 6687 166 1208 chr16 87,970,408 88,179,649 Sanger 1 2 NM_003119 6687 SPG7 SPG7 602783 602783 within within NM_000135 2175 167 1209 chr16 88,398,233 88,495,450 Sanger 1 2 NM_001018112 2175 FANCA FANCA 607139 607139 spanOne spanOne 168 1213 chr17 13,821,966 14,069,281 Both 1 1 NM_001303 1352 COX10 602125 within NM_000382 ALDH3A2 169 1217 chr17 19,426,327 19,504,358 Affy 1 2 NM_001031806 224 224 ALDH3A2 609523 609523 spanOne spanOne NM_153292 4843 163730,248310 170 1221 chr17 22,902,614 23,201,246 Sanger 1 2 NM_000625 4843 NOS2A NOS2A 163730,248310 within within 171 1222 chr17 27,245,834 27,562,095 Sanger 1 1 NM_015355 23512 SUZ12 606245 within NM_198837 NM_198838 172 1225 chr17 32,642,843 32,848,430 Sanger 1 5 NM_198836 31 31 ACACA ACACA 200350 200350 spanOne spanOne NM_198834 31 31 ACACA ACACA 200350 200350 spanOne spanOne NM_198839 31 ACACA 200350 spanOne NM_000458 6928 173 1226 chr17 33,140,728 34,010,545 Sanger 1 2 NM_006481 6928 TCF2 TCF2 189907 189907 spanOne within NM_000422 3872 NM_000526 3861 NM_005557 3868 174 1228 chr17 36,554,901 37,150,369 Both 5 6 NM_002274 3860 KRT17 KRT14 148069 148066 within within NM_000226 3857 KRT16 KRT13 148067 148065 within within NM_153490 3860 KRT9 KRT13 607606 148065 within within NM_016834 4137 157140,168610 NM_016841 4137 157140,168610 175 1230 chr17 41,439,751 42,632,332 Both 2 5 NM_016835 4137 MAPT MAPT 157140,168610 spanOne spanOne NM_005910 4137 MAPT MAPT 157140,168610 spanOne spanOne NM_030753 7473 WNT3 165330 within NM_015294 4591 TRIM37 176 1237 chr17 54,437,361 54,780,416 Sanger 1 2 NM_001005207 4591 TRIM37 605073 605073 spanOne spanOne NM_000455 6794 NM_024407 374291 STK11 177 1281 chr19 902,641 1,495,933 Sanger 3 4 NM_138924 2593 NDUFS7 GAMT 602216 601825 within within NM_000156 2593 GAMT 601240 601240 within within NM_004364 1050 178 1293 chr19 38,468,914 39,273,401 Both 2 2 NM_000285 5184 CEBPA PEPD 116897 170100 within within 179 1296 chr19 40,402,918 40,578,953 Sanger 1 1 NM_021175 57817 HAMP 606464 within 180 1299 chr19 45,304,260 45,531,360 Sanger 1 1 NM_001626 208 AKT2 164731 within 181 1300 chr19 45,983,467 46,237,908 Both 1 1 NM_000762 1548 CYP2A6 122720 within NM_139176 199713 182 1309 chr19 59,359,391 60,158,136 Both 2 3 NM_206828 199713 NALP7 NALP7 609661 609661 within within NM_013289 3811 KIR3DL1 604946 within 183 1310 chr19 60,229,274 60,342,499 Affy 1 1 NM_003283 7138 TNNT1 191041 spanOne 184 1327 chr20 22,977,404 23,127,604 Both 1 NM_000361 7056 THBD 188040 spanOne NM_152854 185 1334 chr20 44,126,322 44,398,283 Sanger 1 2 NM_001250 958 958 CD40 CD40 109535 109535 within within 186 1338 chr20 49,756,024 49,852,802 Affy 1 1 NM_020436 57167 SALL4 607343 within NM_172109 3785 NM_004518 3785 187 1344 chr20 61,572,793 61,846,811 Sanger 1 5 NM_172107 3785 KCNQ2 KCNQ2 602235 602235 spanOne spanOne NM_172108 3785 KCNQ2 KCNQ2 602235 602235 spanOne spanOne NM_172106 3785 KCNQ2 602235 spanOne 188 1345 chr20 62,108,666 62,435,964 Sanger 1 1 NM_018419 54345 SOX18 601618 within NM_002058 2679 189 1362 chr22 16,926,349 17,436,267 Both 3 3 NM_016335 5625 GGT2 PRODH 137181 606810 within within NM_017929 55670 PEX26 608666 within 190 1363 chr22 18,401,047 18,684,001 Sanger 1 1 NM_023004 65078 RTN4R 605566 within NM_000496 1415 CRYBB2 191 1367 chr22 23,691,355 24,371,067 Both 2 2 NM_004076 1417 CRYBB3 123620 123630 within within 192 1369 chr22 25,223,053 25,354,450 Sanger 1 1 NM_001887 1414 CRYBB1 600929 within NM_133642 9215 spanBothIntron 193 1370 chr22 32,193,499 32,234,100 Sanger 1 2 NM_004737 9215 LARGE LARGE 603590 603590 spanBothIntron NM_133642 9215 spanBothIntron 194 1371 chr22 32,494,349 32,528,033 Sanger 1 2 NM_004737 9215 LARGE LARGE 603590 603590 spanBothIntron 195 1375 chr22 35,499,654 35,685,405 Sanger 1 1 NM_000395 1439 CSF2RB 138981 within NM_138632 11078 TRIOBP 196 1376 chr22 36,328,377 36,590,378 Sanger 1 3 NM_001039141 11078 TRIOBP 609761 609761 within within NM_007032 11078 TRIOBP 609761 within NM_000398 1727 CYB5R3 197 1377 chr22 41,091,699 41,407,804 Both 1 2 NM_007326 1727 CYB5R3 250800 250800 within within NM_006485 2192 NM_006486 2192 198 1381 chr22 43,894,761 44,245,703 Both 1 4 NM_001996 2192 FBLN1 FBLN1 135820 135820 spanOne spanOne NM_006487 2192 FBLN1 FBLN1 135820 135820 spanOne spanOne NM_001953 1890 199 1390 chr22 49,219,663 49,307,552 Sanger 2 2 NM_005138 9997 ECGF1 SCO2 131222 604272 within within 200 1391 chr22 49,392,382 49,495,206 Sanger 1 1 NM_001097 49 ACR 102480 within # OMIM Region CNP_ID Chromosome Start End Info # Genes Accessions GeneID Gene Symbol OMIM ID Class Transcripts NM_000047 201 1393 chrX 1,865,728 3,187,726 Both 2 2 NM_175569 415 7499 ARSE XG 300180 314700 within within 202 1396 chrX 7,061,134 7,483,618 Both 1 1 NM_000351 412 STS 308100 spanOne

1756 NM_004006 1756 NM_004015 1756 NM_004010 1756 NM_004007 2710 NM_203391 1756 190 NM_004016 1756 NM_000475 1756 NM_004011 11141 203 1403 chrX 27,751,188 31,356,624 Both 4 22 NM_004020 1756 NM_014271 1756 DMD DMD 300377 300377 spanOne within NM_004017 1756 DMD DMD 300377 300377 spanOne spanOne NM_004012 1756 GK DMD 300474 300377 within within NM_004021 1756 NR0B1 DMD 300473 300377 within spanOne NM_004009 2710 DMD IL1RAPL1 300377 300206 spanOne within NM_004018 1756 DMD DMD 300377 300377 within spanOne NM_000167 1756 DMD DMD 300377 300377 spanOne spanOne NM_004013 1756 DMD GK 300377 300474 within within NM_000109 1756 DMD DMD 300377 300377 spanOne spanOne NM_004022 1756 DMD DMD 300377 300377 spanOne within NM_00401 1756 DMD DMD 300377 300377 within spanOne NM_007137 347344 204 1404 chrX 47,523,164 47,902,964 Both 2 2 NM_005635 6756 ZNF81 SSX1 314998 312820 spanOne within NM_001011645 205 1409 chrX 66,282,690 67,102,115 Both 2 3 NM_000044 367 367 AR AR 313700 313700 within within NM_002547 4983 OPHN1 300127 spanOne 206 1412 chrX 77,031,055 77,115,217 Sanger 1 1 NM_000052 538 ATP7A 300011 spanOne NM_022977 2182 207 1421 chrX 108,585,146 108,787,037 Sanger 1 2 NM_004458 2182 ACSL4 ACSL4 300157 300157 within within 208 1424 chrX 115,037,017 115,175,870 Affy 1 1 NM_000686 186 AGTR2 300034 within NM_013995 3920 209 1427 chrX 119,183,307 119,364,831 Sanger 1 2 NM_002294 3920 LAMP2 LAMP2 309060 309060 spanOne spanOne NM_000276 4952 OCRL 210 1431 chrX 128,423,110 128,689,620 Sanger 2 3 NM_003399 7512 XPNPEP2 300535 300145 spanOne within NM_001587 4952 OCRL 300535 spanOne 211 1437 chrX 146,718,150 146,857,358 Affy 1 1 NM_002024 2332 FMR1 309550 spanOne 212 1439 chrX 151,572,622 151,688,320 Affy 1 1 NM_015922 50814 NSDHL 300275 spanOne 213 1447 chrY 22,936,103 26,838,610 Sanger 1 1 NM_004081 1617 DAZ1 400003 within Supplementary Table 17: Overlap of Genomic Disorder Breakpoints (LCRs) with CNVs Inheritance Chromosomal LCR Disorders OMIM LCRs WGPT 500K EA General comments Pattern location Size (Kb)

CNV_ID=61 LCR1: chr1:151,993,247-152,003,828 10.58 No CNVs detected (Gain only) Gaucher disease 230800 AR 1q22 CNV_ID=61 LCR2: chr1:152,013,841-152,026,330 12.5 No CNVs detected (Gain only)

CNV_ID=173 No CNVs detected LCR1: chr2:110,000,806-110,179,715 178.91 (Gain and Loss) (no SNP coverage) Familial juvenile 500k EA CNV (1 Gain, JPT) is seen overlapping 256100 AR 2q13 nephronophthisis NPHP1 in between LCR1 and LCR2 CNV_ID=173 No CNVs detected LCR2: chr2:110,498,738-110,682,662 183.92 (Gain and Loss) (no SNP coverage)

CNV_ID=439 No CNVs detected LCR1: chr5:69,125,144-69,461,320 336.18 (Gain and Loss) (no SNP coverage) Extremely complex region. Merged CNV spans entire Spinal muscular atrophy 253300 AR 5q13.2 regions (121 Gain, 11 Loss; in all populations) CNV_ID=439 No CNVs detected LCR2: chr5:70,000,002-70,336,743 336.74 (Gain and Loss) (no SNP coverage)

CNV_ID=486 CNV_ID=486 LCR1: chr5:175,262,066-175,661,584 399.52 (Gain only) (Gain only) 54 Gains overlap the NSD1 gene (9 CEU, 2 CHB, 5 Sotos Syndrome 117550 AD 5q35.2 - 5q35.3 JPT, 38 YRI) in between the LCRs No CNVs detected No CNVs detected LCR2: chr5:176,980,401-177,414,661 434.26 (gap in BAC coverage) (gap in SNP coverage)

CNV_ID=506 No CNVs detected LCR1: chr6:32,056,289-32,089,024 32.74 Congenital adrenal (Gain and Loss) (no SNP coverage) 20% of patiets with this disease have deletions of the hyperplasia III/21 201910 AR 6p21.32 entire gene hydroxylase deficiency CNV_ID=506 No CNVs detected LCR2: chr6:32,089,026-32,121,878 32.85 (Gain and Loss) (no SNP coverage)

CNV_ID=628 CNV_ID=628 Deletion, duplication and inversion have all been LCR1: chr7:71,923,541-72,139,109 215.57 (Gain and Loss) (Gain only) reported at this locus; A Merged CNV (3 Gains, 1 Williams-Beuren 194050 AD 7q11.23 Loss) is seen overlapping GTF2I between LCR1 and Syndrome 6097571 CNV_ID=629 No CNVs detected LCR2; genome assembly in this region may be LCR2: chr7:73,934,638-74,160,375 225.74 (Gain and Loss) (no SNP coverage) incorrect

CNV_ID=1107 CNV_ID=1107 LCR1: chr15:18,456,197-19,107,462 651.27 (Gain and Loss) (Gain and Loss) Prader-Willi syndrome 176270 AD CNV_ID=1107 CNV_ID=1107 Extremely complex region. Merged CNV spans LCR1 & 15q11.2-15q13.1 LCR2: chr15:20,643,734-21,234,436 590.7 (Gain and Loss) (Gain and Loss) to LCR2 Angelman syndrome 105830 AD

CNV_ID=1112 LCR3: chr15:26,205,079-26,896,311 691.23 No CNVs detected (Gain and Loss)

CNV_ID=1107 CNV_ID=1107 LCR1: chr15:18,456,197-19,107,462 651.27 (Gain and Loss) (Gain and Loss)

CNV_ID=1107 CNV_ID=1107 LCR2: chr15:20,643,734-21,234,436 590.7 (Gain and Loss) (Gain and Loss) dup(15)(q11.2q13) & 15q11.2- CNV_ID=1112 Extremely complex region. Many large and frequent trip(15)(q11.2q13) -- LCR3: chr15:26,205,079-26,896,311 691.23 No CNVs detected 15q4 (Gain and Loss) merged CNVs & inv dup(15)(q11q13) CNV_ID=1113 CNV_ID=1113 LCR4: chr15:28,157,403-28,722,451 565.05 (Gain and Loss) (Loss only)

CNV_ID=1115 CNV_ID=1115 LCR5: chr15:32,458,295-32,663,061 204.77 (Gain and Loss) (Gain and Loss)

Charcot-Marie-Tooth CNV_ID=1213 No CNVs detected (CMT1A) LCR1: chr17:14,014,755-14,038,639 23.88 118220 AD (Loss only) (no SNP coverage) & 17p12 Hereditary neuopathy with 162500 AD liability to pressure palsies (HNPP) LCR2: chr17:15,411,629-15,435,499 23.87 No CNVs detected No CNVs detected

Smith-Magenis syndrome/ CNV_ID=1214 CNV_ID=1214 LCR1: chr17:16,523,189-16,717,303 194.11 dup(17)(p11.2-p11.2) 182290 AD (Loss only) (Gain and Loss) Several merged CNVs present (with multiple gains & 17p11.2 and losses in all populations) between LCRs (overlaps dup(17)(p11.2p11.2) - AD CNV_ID=1218 seg. dup. cluster) LCR2: chr17:20,160,584-20,418,643 258.06 No CNVs detected syndrome (Gain only)

No CNVs detected LCR1: chr17:25,973,023-26,023,995 50.97 No CNVs detected (no SNP coverage) Neurofibromatosis type 1 162200 AD 17q11.2 (NF1) CNV_ID=1222 No CNVs detected LCR2: chr17:27,389,103-27,440,083 50.98 (Gain only) (no SNP coverage)

CNV_ID=1362 CNV_ID=1362 LCR1: chr22:17,017,175-17,338,797 321.62 (Gain and Loss) (Gain only) DiGeorge syndrome and 188400 AD 192430 No CNVs detected No CNVs detected velocardiofacial syndrome LCR2: chr22:18,933,986-19,056,412 122.43 (gap in BAC coverage) (gap in SNP coverage) & LCR1 has complex CNV; CNV (2 Loss) also seen 22q11.2-22q11.21 dup(22)(q11.2q11.2) between LCR1 and LCR2 - - & LCR3: chr22:19,366,625-19,398,625 32.00 No CNVs detected No CNVs detected trip(22)(q11.2q11.2) - - No CNVs detected No CNVs detected LCR4: chr22:19,790,228-20,163,938 373.71 (No BAC coverage) (gap in SNP coverage)

CNV_ID=1395 LCR1: chrX:6,305,340-6,314,296 8.96 No CNVs detected (Gain only) CNV (1 Loss) seen between LCR1 and LCR2; Ichthyosis 308100 X-Linked Xp22.32 overlaps causative STS gene LCR2: chrX:7,618,632-7,628,650 10.02 No CNVs detected No CNVs detected

CNV_ID=1447 No CNVs detected LCR1: chrY:22,977,582-23,211,266 233.68 (Gain and Loss) (no SNP coverage)

CNV_ID=1447 No CNVs detected LCR2: chrY:23,210,666-23,546,051 335.39 (Gain and Loss) (no SNP coverage) Male infertility AZFc Extremely complex region. Merged CNV spans entire 415000 Y-Linked Yq11.23 microdeletion region 2 regions CNV_ID=1447 No CNVs detected LCR3: chrY:24,864,420-25,179,796 315.38 (Gain and Loss) (no SNP coverage)

CNV_ID=1447 No CNVs detected LCR4: chrY:26,451,434-26,681,378 229.94 (Gain and Loss) (no SNP coverage)

1 Somerville, M. J. et al. Severe expressive-language delay related to duplication of the Williams-Beuren locus. New Eng J Med 353, 1694-1701 (2005). Supplemental Table 17: List of genomic disorders adapted from *Genomic Disorders: The Genomic Basis of Disease */James R. Lupski, Pawel T. Stankiewicz, /Totowa, NJ:Humana Press, 2006. Each region was manually curated to identify overlap with CNVs. Supplemental Table 18. SNP genotyping errors in WGTP and 500K CNV gains and losses 500K EA + WGTP GainsANDLosses Significant After BF Chromosome Population Type SNP class Direction Observed # Expected # p-value Significant correction chr1 All gains+loses QCMinus Enrichment 1630 837 0.0000 * * chr2 All gains+loses QCMinus Enrichment 1789 999 0.0000 * * chr3 All gains+loses QCMinus Enrichment 1289 1003 0.0080 * chr4 All gains+loses QCMinus Enrichment 1859 568 0.0000 * * chr5 All gains+loses QCMinus Enrichment 998 603 0.0000 * * chr6 All gains+loses QCMinus Enrichment 931 516 0.0000 * * chr7 All gains+loses QCMinus Enrichment 1450 635 0.0000 * * chr8 All gains+loses QCMinus Enrichment 1372 1060 0.0370 * chr9 All gains+loses QCMinus Enrichment 1426 590 0.0000 * * chr10 All gains+loses QCMinus Enrichment 752 512 0.0000 * * chr11 All gains+loses QCMinus Enrichment 1069 516 0.0000 * * chr12 All gains+loses QCMinus Enrichment 520 274 0.0000 * * chr13 All gains+loses QCMinus Enrichment 365 186 0.0000 * * chr14 All gains+loses QCMinus Enrichment 406 182 0.0000 * * chr15 All gains+loses QCMinus Enrichment 1310 429 0.0000 * * chr16 All gains+loses QCMinus Enrichment 939 549 0.0020 * * chr17 All gains+loses QCMinus Enrichment 536 332 0.0030 * * chr18 All gains+loses QCMinus Enrichment 545 203 0.0000 * * chr19 All gains+loses QCMinus Enrichment 918 427 0.0000 * * chr20 All gains+loses QCMinus Enrichment 236 123 0.0000 * * chr21 All gains+loses QCMinus Enrichment 496 196 0.0000 * * chr22 All gains+loses QCMinus Enrichment 791 310 0.0030 * * chrX All gains+loses QCMinus Enrichment 742 544 0.0440 * chr1 All gains+loses QCPlus Impoverishment 7622 7735 0.3656 chr2 All gains+loses QCPlus Impoverishment 7803 9267 0.0030 * * chr3 All gains+loses QCPlus Enrichment 5738 5642 0.3437 chr4 All gains+loses QCPlus Enrichment 7571 7102 0.1359 chr5 All gains+loses QCPlus Impoverishment 4655 5199 0.0010 * * chr6 All gains+loses QCPlus Impoverishment 6019 6086 0.3237 chr7 All gains+loses QCPlus Impoverishment 6038 6934 0.0539 chr8 All gains+loses QCPlus Impoverishment 7640 8725 0.0829 chr9 All gains+loses QCPlus Impoverishment 5745 7642 0.0250 * chr10 All gains+loses QCPlus Impoverishment 4411 5126 0.0150 * chr11 All gains+loses QCPlus Impoverishment 3847 4092 0.1289 chr12 All gains+loses QCPlus Impoverishment 4559 4798 0.2458 chr13 All gains+loses QCPlus Enrichment 2474 2055 0.0020 * * chr14 All gains+loses QCPlus Enrichment 1824 1553 0.0260 * chr15 All gains+loses QCPlus Impoverishment 2780 3445 0.1159 chr16 All gains+loses QCPlus Impoverishment 2989 3932 0.0110 * chr17 All gains+loses QCPlus Impoverishment 1976 2516 0.0020 * * chr18 All gains+loses QCPlus Impoverishment 2743 3002 0.1948 chr19 All gains+loses QCPlus Enrichment 2710 2568 0.3636 chr20 All gains+loses QCPlus Enrichment 1666 1649 0.4855 chr21 All gains+loses QCPlus Enrichment 1407 1123 0.1449 chr22 All gains+loses QCPlus Enrichment 2061 1712 0.1748 chrX All gains+loses QCPlus Impoverishment 2651 3064 0.0679 chr1 All gains+loses QC-d Enrichment 79 9 0.0000 * * chr3 All gains+loses QC-d Impoverishment 1 1 0.3497 chr4 All gains+loses QC-d Enrichment 5 3 0.1289 chr5 All gains+loses QC-d Enrichment 1 0 0.3546 chr6 All gains+loses QC-d Enrichment 78 8 0.0000 * * chr7 All gains+loses QC-d Enrichment 7 4 0.0879 chr8 All gains+loses QC-d Enrichment 8 1 0.0000 * * chr9 All gains+loses QC-d Impoverishment 1 1 0.2987 chr10 All gains+loses QC-d Enrichment 42 9 0.0000 * * chr12 All gains+loses QC-d Impoverishment 120 194 0.0030 * * chr13 All gains+loses QC-d Enrichment 31 2 0.0000 * * chr15 All gains+loses QC-d Enrichment 1 0 0.0999 chr16 All gains+loses QC-d Enrichment 1 0 0.0000 * * chr17 All gains+loses QC-d Enrichment 1 0 0.2637 chr19 All gains+loses QC-d Enrichment 5 1 0.0040 * * chr20 All gains+loses QC-d Enrichment 13 3 0.0000 * * chr22 All gains+loses QC-d Enrichment 2 1 0.0809 chrX All gains+loses QC-d Enrichment 1 0 0.0000 * * chr1 All gains+loses QC-h Enrichment 292 67 0.0000 * * chr2 All gains+loses QC-h Enrichment 12 6 0.0829 chr3 All gains+loses QC-h Enrichment 88 40 0.0000 * * chr4 All gains+loses QC-h Enrichment 172 33 0.0000 * * chr5 All gains+loses QC-h Enrichment 10 3 0.0010 * * chr6 All gains+loses QC-h Enrichment 180 42 0.0000 * * chr7 All gains+loses QC-h Enrichment 294 39 0.0000 * * chr8 All gains+loses QC-h Enrichment 69 22 0.0000 * * chr9 All gains+loses QC-h Enrichment 10 4 0.0280 * chr10 All gains+loses QC-h Enrichment 99 37 0.0000 * * chr11 All gains+loses QC-h Enrichment 5 5 0.3207 chr12 All gains+loses QC-h Enrichment 82 8 0.0000 * * chr13 All gains+loses QC-h Enrichment 61 12 0.0000 * * chr14 All gains+loses QC-h Impoverishment 1 1 0.3167 chr15 All gains+loses QC-h Enrichment 15 3 0.0000 * * chr16 All gains+loses QC-h Enrichment 12 4 0.0080 * chr17 All gains+loses QC-h Enrichment 4 2 0.1928 chr18 All gains+loses QC-h Enrichment 108 13 0.0000 * * chr19 All gains+loses QC-h Enrichment 10 6 0.1099 chr20 All gains+loses QC-h Enrichment 21 17 0.2478 chr21 All gains+loses QC-h Enrichment 58 5 0.0000 * * chr22 All gains+loses QC-h Enrichment 9 4 0.0130 * chrX All gains+loses QC-h Enrichment 40 1 0.0000 * * chr1 All gains+loses QC-m Enrichment 235 112 0.0000 * * chr2 All gains+loses QC-m Enrichment 37 10 0.0000 * * chr3 All gains+loses QC-m Enrichment 82 37 0.0000 * * chr4 All gains+loses QC-m Enrichment 92 19 0.0000 * * chr5 All gains+loses QC-m Enrichment 21 9 0.0010 * * chr6 All gains+loses QC-m Enrichment 121 81 0.0000 * * chr7 All gains+loses QC-m Enrichment 79 17 0.0000 * * chr8 All gains+loses QC-m Enrichment 89 28 0.0000 * * chr9 All gains+loses QC-m Enrichment 12 6 0.0270 * chr10 All gains+loses QC-m Enrichment 114 69 0.0010 * * chr11 All gains+loses QC-m Enrichment 30 8 0.0000 * * chr12 All gains+loses QC-m Enrichment 102 24 0.0000 * * chr13 All gains+loses QC-m Enrichment 44 20 0.0000 * * chr14 All gains+loses QC-m Enrichment 6 2 0.0280 * chr15 All gains+loses QC-m Enrichment 8 4 0.0799 chr16 All gains+loses QC-m Enrichment 20 9 0.0130 * chr17 All gains+loses QC-m Enrichment 9 6 0.1369 chr18 All gains+loses QC-m Enrichment 10 3 0.0100 * chr19 All gains+loses QC-m Enrichment 22 10 0.0000 * * chr20 All gains+loses QC-m Enrichment 39 27 0.0579 chr21 All gains+loses QC-m Enrichment 8 2 0.0030 * * chr22 All gains+loses QC-m Enrichment 5 6 0.4745 chrX All gains+loses QC-m Enrichment 2 3 0.3886 chr1 All gains+loses QC-p Impoverishment 270 362 0.0729 chr2 All gains+loses QC-p Enrichment 1718 958 0.0000 * * chr3 All gains+loses QC-p Impoverishment 661 667 0.4655 chr4 All gains+loses QC-p Enrichment 1276 363 0.0000 * * chr5 All gains+loses QC-p Enrichment 906 559 0.0000 * * chr6 All gains+loses QC-p Enrichment 177 176 0.4715 chr7 All gains+loses QC-p Enrichment 789 425 0.0000 * * chr8 All gains+loses QC-p Impoverishment 621 733 0.2148 chr9 All gains+loses QC-p Enrichment 1239 420 0.0000 * * chr10 All gains+loses QC-p Impoverishment 114 191 0.0050 * * chr11 All gains+loses QC-p Enrichment 943 453 0.0000 * * chr12 All gains+loses QC-p Enrichment 131 29 0.0000 * * chr13 All gains+loses QC-p Impoverishment 66 91 0.0599 chr14 All gains+loses QC-p Enrichment 377 170 0.0000 * * chr15 All gains+loses QC-p Enrichment 1242 400 0.0000 * * chr16 All gains+loses QC-p Enrichment 855 508 0.0020 * * chr17 All gains+loses QC-p Enrichment 500 305 0.0040 * * chr18 All gains+loses QC-p Enrichment 311 106 0.0000 * * chr19 All gains+loses QC-p Enrichment 834 381 0.0000 * * chr20 All gains+loses QC-p Enrichment 17 2 0.0000 * * chr21 All gains+loses QC-p Enrichment 244 137 0.0100 * chr22 All gains+loses QC-p Enrichment 695 253 0.0030 * * chrX All gains+loses QC-p Enrichment 576 490 0.1439 chr1 All gains+loses QC-s Enrichment 523 147 0.0000 * * chr2 All gains+loses QC-s Impoverishment 11 19 0.0280 * chr3 All gains+loses QC-s Enrichment 368 157 0.0000 * * chr4 All gains+loses QC-s Enrichment 225 129 0.0000 * * chr5 All gains+loses QC-s Enrichment 55 30 0.0000 * * chr6 All gains+loses QC-s Enrichment 241 102 0.0000 * * chr7 All gains+loses QC-s Enrichment 200 124 0.0000 * * chr8 All gains+loses QC-s Enrichment 529 254 0.0000 * * chr9 All gains+loses QC-s Enrichment 155 156 0.4805 chr10 All gains+loses QC-s Enrichment 240 99 0.0000 * * chr11 All gains+loses QC-s Enrichment 79 44 0.0000 * * chr12 All gains+loses QC-s Enrichment 65 13 0.0000 * * chr13 All gains+loses QC-s Enrichment 107 34 0.0000 * * chr14 All gains+loses QC-s Enrichment 20 7 0.0000 * * chr15 All gains+loses QC-s Enrichment 42 19 0.0000 * * chr16 All gains+loses QC-s Enrichment 34 19 0.0110 * chr17 All gains+loses QC-s Enrichment 18 13 0.1269 chr18 All gains+loses QC-s Enrichment 103 78 0.1678 chr19 All gains+loses QC-s Enrichment 41 19 0.0000 * * chr20 All gains+loses QC-s Enrichment 93 30 0.0000 * * chr21 All gains+loses QC-s Enrichment 181 51 0.0000 * * chr22 All gains+loses QC-s Enrichment 72 44 0.1229 chrX All gains+loses QC-s Enrichment 13 11 0.3167 500K EA + WGTP Gains Significant After BF Chromosome Population Type SNP class Direction Observed # Expected # p-value Significant correction chr1 All gains QCMinus Enrichment 1016 485 0.0000 * * chr2 All gains QCMinus Enrichment 1306 707 0.0000 * * chr2 All gains QCMinus Enrichment 1306 707 0.0000 * * chr3 All gains QCMinus Enrichment 544 493 0.2527 chr4 All gains QCMinus Enrichment 1330 352 0.0000 * * chr5 All gains QCMinus Enrichment 405 261 0.0010 * * chr6 All gains QCMinus Enrichment 619 305 0.0000 * * chr7 All gains QCMinus Enrichment 916 381 0.0000 * * chr8 All gains QCMinus Enrichment 668 538 0.0969 chr9 All gains QCMinus Enrichment 842 290 0.0000 * * chr10 All gains QCMinus Enrichment 428 284 0.0140 * chr11 All gains QCMinus Enrichment 434 236 0.0000 * * chr12 All gains QCMinus Enrichment 395 205 0.0000 * * chr13 All gains QCMinus Enrichment 120 53 0.0000 * * chr14 All gains QCMinus Enrichment 208 56 0.0000 * * chr15 All gains QCMinus Enrichment 989 295 0.0000 * * chr16 All gains QCMinus Enrichment 719 427 0.0070 * * chr17 All gains QCMinus Enrichment 423 266 0.0060 * * chr18 All gains QCMinus Enrichment 406 124 0.0000 * * chr19 All gains QCMinus Enrichment 601 257 0.0000 * * chr20 All gains QCMinus Enrichment 93 65 0.0859 chr21 All gains QCMinus Enrichment 243 86 0.0000 * * chr22 All gains QCMinus Enrichment 451 180 0.0250 * chrX All gains QCMinus Enrichment 560 369 0.0270 * chr1 All gains QCPlus Impoverishment 3796 4464 0.0649 chr2 All gains QCPlus Impoverishment 5155 6538 0.0030 * * chr3 All gains QCPlus Impoverishment 2764 2800 0.3546 chr4 All gains QCPlus Enrichment 4867 4412 0.1189 chr5 All gains QCPlus Impoverishment 1746 2281 0.0010 * * chr6 All gains QCPlus Impoverishment 3377 3608 0.0889 chr7 All gains QCPlus Impoverishment 3106 4167 0.0020 * * chr8 All gains QCPlus Impoverishment 3678 4455 0.0909 chr9 All gains QCPlus Impoverishment 1572 3814 0.0030 * * chr10 All gains QCPlus Impoverishment 2115 2859 0.0130 * chr11 All gains QCPlus Impoverishment 1517 1859 0.0210 * chr12 All gains QCPlus Impoverishment 3270 3578 0.1159 chr13 All gains QCPlus Enrichment 734 589 0.0250 * chr14 All gains QCPlus Enrichment 541 482 0.2527 chr15 All gains QCPlus Impoverishment 1668 2331 0.1479 chr16 All gains QCPlus Impoverishment 2026 3046 0.0040 * * chr17 All gains QCPlus Impoverishment 1475 1978 0.0020 * * chr18 All gains QCPlus Impoverishment 1580 1871 0.1479 chr19 All gains QCPlus Impoverishment 1558 1551 0.4685 chr20 All gains QCPlus Impoverishment 848 870 0.3057 chr21 All gains QCPlus Enrichment 555 496 0.3337 chr22 All gains QCPlus Impoverishment 876 1007 0.3397 chrX All gains QCPlus Impoverishment 1504 2093 0.0120 * chr1 All gains QC-d Enrichment 56 6 0.0000 * * chr4 All gains QC-d Enrichment 5 2 0.0240 * chr5 All gains QC-d Enrichment 1 0 0.1838 chr6 All gains QC-d Enrichment 45 5 0.0000 * * chr7 All gains QC-d Enrichment 6 2 0.0320 * chr8 All gains QC-d Enrichment 6 1 0.0000 * * chr9 All gains QC-d Enrichment 1 1 0.4056 chr10 All gains QC-d Enrichment 21 5 0.0000 * * chr12 All gains QC-d Impoverishment 105 146 0.0509 chr13 All gains QC-d Enrichment 10 1 0.0000 * * chr15 All gains QC-d Enrichment 1 0 0.0719 chr17 All gains QC-d Enrichment 1 0 0.2098 chr19 All gains QC-d Enrichment 1 1 0.4935 chr20 All gains QC-d Enrichment 4 1 0.0739 chrX All gains QC-d Enrichment 1 0 0.0000 * * chr1 All gains QC-h Enrichment 195 39 0.0000 * * chr2 All gains QC-h Enrichment 10 4 0.0789 chr2 All gains QC-h Enrichment 10 4 0.0789 chr3 All gains QC-h Enrichment 59 20 0.0000 * * chr4 All gains QC-h Enrichment 131 21 0.0000 * * chr5 All gains QC-h Enrichment 4 1 0.0709 chr6 All gains QC-h Enrichment 150 25 0.0000 * * chr7 All gains QC-h Enrichment 237 23 0.0000 * * chr8 All gains QC-h Enrichment 48 11 0.0000 * * chr9 All gains QC-h Enrichment 5 2 0.1109 chr10 All gains QC-h Enrichment 63 21 0.0000 * * chr11 All gains QC-h Enrichment 4 2 0.1099 chr12 All gains QC-h Enrichment 70 6 0.0000 * * chr13 All gains QC-h Enrichment 24 4 0.0000 * * chr14 All gains QC-h Enrichment 1 0 0.2867 chr15 All gains QC-h Enrichment 13 2 0.0010 * * chr16 All gains QC-h Enrichment 10 3 0.0140 * chr17 All gains QC-h Enrichment 4 2 0.1229 chr18 All gains QC-h Enrichment 102 7 0.0000 * * chr19 All gains QC-h Enrichment 4 4 0.4825 chr20 All gains QC-h Impoverishment 7 9 0.3506 chr21 All gains QC-h Enrichment 34 2 0.0000 * * chr22 All gains QC-h Enrichment 5 2 0.0829 chrX All gains QC-h Enrichment 40 0 0.0000 * * chr1 All gains QC-m Enrichment 136 65 0.0000 * * chr2 All gains QC-m Enrichment 21 7 0.0000 * * chr2 All gains QC-m Enrichment 21 7 0.0000 * * chr3 All gains QC-m Enrichment 41 18 0.0000 * * chr4 All gains QC-m Enrichment 55 12 0.0000 * * chr5 All gains QC-m Enrichment 5 4 0.3566 chr6 All gains QC-m Enrichment 55 48 0.2278 chr7 All gains QC-m Enrichment 40 10 0.0000 * * chr8 All gains QC-m Enrichment 24 14 0.1149 chr9 All gains QC-m Impoverishment 2 3 0.3117 chr10 All gains QC-m Enrichment 65 39 0.0180 * chr11 All gains QC-m Impoverishment 2 4 0.1269 chr12 All gains QC-m Enrichment 66 17 0.0000 * * chr13 All gains QC-m Enrichment 13 6 0.0120 * chr14 All gains QC-m Enrichment 5 1 0.0010 * * chr15 All gains QC-m Enrichment 3 3 0.4985 chr16 All gains QC-m Impoverishment 4 7 0.1379 chr17 All gains QC-m Impoverishment 1 4 0.0140 * chr18 All gains QC-m Enrichment 8 2 0.0140 * chr19 All gains QC-m Enrichment 14 6 0.0010 * * chr20 All gains QC-m Impoverishment 14 15 0.4525 chr21 All gains QC-m Enrichment 3 1 0.0599 chr22 All gains QC-m Enrichment 5 3 0.1868 chr1 All gains QC-p Impoverishment 144 210 0.0579 chr2 All gains QC-p Enrichment 1263 678 0.0000 * * chr2 All gains QC-p Enrichment 1263 678 0.0000 * * chr3 All gains QC-p Impoverishment 231 327 0.0879 chr4 All gains QC-p Enrichment 925 225 0.0000 * * chr5 All gains QC-p Enrichment 376 242 0.0020 * * chr6 All gains QC-p Enrichment 112 105 0.3407 chr7 All gains QC-p Enrichment 476 256 0.0000 * * chr8 All gains QC-p Impoverishment 325 373 0.3347 chr9 All gains QC-p Enrichment 774 206 0.0000 * * chr10 All gains QC-p Impoverishment 59 106 0.0420 * chr11 All gains QC-p Enrichment 411 207 0.0000 * * chr12 All gains QC-p Enrichment 93 22 0.0000 * * chr13 All gains QC-p Impoverishment 23 26 0.3726 chr14 All gains QC-p Enrichment 189 53 0.0000 * * chr15 All gains QC-p Enrichment 944 276 0.0000 * * chr16 All gains QC-p Enrichment 682 396 0.0060 * * chr17 All gains QC-p Enrichment 402 244 0.0070 * * chr18 All gains QC-p Enrichment 204 65 0.0000 * * chr19 All gains QC-p Enrichment 556 229 0.0000 * * chr20 All gains QC-p Enrichment 8 1 0.0000 * * chr21 All gains QC-p Enrichment 125 60 0.0050 * * chr22 All gains QC-p Enrichment 407 146 0.0180 * chrX All gains QC-p Enrichment 405 334 0.1389 chr1 All gains QC-s Enrichment 355 85 0.0000 * * chr2 All gains QC-s Impoverishment 5 13 0.0030 * * chr2 All gains QC-s Impoverishment 5 13 0.0030 * * chr3 All gains QC-s Enrichment 176 78 0.0000 * * chr4 All gains QC-s Enrichment 146 79 0.0000 * * chr5 All gains QC-s Enrichment 17 13 0.1958 chr6 All gains QC-s Enrichment 164 60 0.0000 * * chr7 All gains QC-s Enrichment 110 74 0.0230 * chr8 All gains QC-s Enrichment 250 129 0.0000 * * chr9 All gains QC-s Impoverishment 58 77 0.2458 chr10 All gains QC-s Enrichment 144 55 0.0000 * * chr11 All gains QC-s Impoverishment 16 20 0.2488 chr12 All gains QC-s Enrichment 43 10 0.0000 * * chr13 All gains QC-s Enrichment 41 10 0.0000 * * chr14 All gains QC-s Enrichment 11 2 0.0000 * * chr15 All gains QC-s Enrichment 27 12 0.0050 * * chr16 All gains QC-s Impoverishment 13 15 0.3487 chr17 All gains QC-s Enrichment 12 10 0.3407 chr18 All gains QC-s Enrichment 82 48 0.0979 chr19 All gains QC-s Enrichment 23 12 0.0040 * * chr20 All gains QC-s Enrichment 42 16 0.0080 * chr21 All gains QC-s Enrichment 79 22 0.0000 * * chr22 All gains QC-s Enrichment 31 26 0.2787 chrX All gains QC-s Enrichment 9 7 0.3167 500K EA + WGTP Losses Significant After BF chromosome population Type SNP class Direction Observed # Expected # p-value Significant correction chr1 All loses QCMinus Enrichment 1201 576 0.0000 * * chr2 All loses QCMinus Enrichment 801 440 0.0030 * * chr3 All loses QCMinus Enrichment 884 556 0.0000 * * chr4 All loses QCMinus Enrichment 940 291 0.0000 * * chr5 All loses QCMinus Enrichment 685 354 0.0000 * * chr6 All loses QCMinus Enrichment 374 221 0.0000 * * chr7 All loses QCMinus Enrichment 701 282 0.0000 * * chr8 All loses QCMinus Enrichment 927 702 0.0420 * chr9 All loses QCMinus Enrichment 995 435 0.0000 * * chr10 All loses QCMinus Enrichment 474 319 0.0120 * chr11 All loses QCMinus Enrichment 732 333 0.0000 * * chr12 All loses QCMinus Enrichment 173 99 0.0000 * * chr13 All loses QCMinus Enrichment 281 142 0.0000 * * chr14 All loses QCMinus Enrichment 214 129 0.0060 * * chr15 All loses QCMinus Enrichment 994 262 0.0000 * * chr16 All loses QCMinus Enrichment 502 228 0.0000 * * chr17 All loses QCMinus Enrichment 232 121 0.0130 * chr18 All loses QCMinus Enrichment 143 78 0.0140 * chr19 All loses QCMinus Enrichment 552 232 0.0000 * * chr20 All loses QCMinus Enrichment 143 58 0.0000 * * chr21 All loses QCMinus Enrichment 439 153 0.0000 * * chr22 All loses QCMinus Enrichment 628 242 0.0110 * chrX All loses QCMinus Enrichment 184 179 0.4016 chr1 All loses QCPlus Impoverishment 5107 5289 0.3217 chr2 All loses QCPlus Impoverishment 2950 4080 0.0010 * * chr3 All loses QCPlus Enrichment 3231 3146 0.3247 chr4 All loses QCPlus Impoverishment 3186 3620 0.0340 * chr5 All loses QCPlus Impoverishment 3000 3051 0.3357 chr6 All loses QCPlus Enrichment 2797 2625 0.0160 * chr7 All loses QCPlus Enrichment 3103 3084 0.3007 chr8 All loses QCPlus Impoverishment 4656 5783 0.0430 * chr9 All loses QCPlus Impoverishment 4344 5565 0.0330 * chr10 All loses QCPlus Impoverishment 2635 3224 0.0180 * chr11 All loses QCPlus Impoverishment 2501 2631 0.2008 chr12 All loses QCPlus Impoverishment 1640 1716 0.3267 chr13 All loses QCPlus Enrichment 1902 1572 0.0010 * * chr14 All loses QCPlus Enrichment 1322 1105 0.0470 * chr15 All loses QCPlus Impoverishment 1507 2099 0.1588 chr16 All loses QCPlus Impoverishment 1095 1664 0.0270 * chr17 All loses QCPlus Impoverishment 710 903 0.0250 * chr18 All loses QCPlus Enrichment 1186 1152 0.3267 chr19 All loses QCPlus Enrichment 1423 1384 0.4995 chr20 All loses QCPlus Enrichment 818 775 0.2737 chr21 All loses QCPlus Enrichment 1009 880 0.4006 chr22 All loses QCPlus Enrichment 1548 1316 0.2547 chrX All loses QCPlus Enrichment 1155 1016 0.1489 chr1 All loses QC-d Enrichment 38 6 0.0000 * * chr3 All loses QC-d Enrichment 1 1 0.4505 chr6 All loses QC-d Enrichment 36 4 0.0000 * * chr7 All loses QC-d Enrichment 2 2 0.4775 chr8 All loses QC-d Enrichment 5 1 0.0000 * * chr10 All loses QC-d Enrichment 26 6 0.0000 * * chr12 All loses QC-d Impoverishment 15 71 0.0010 * * chr13 All loses QC-d Enrichment 23 2 0.0000 * * chr16 All loses QC-d Enrichment 1 0 0.0000 * * chr17 All loses QC-d Enrichment 1 0 0.1139 chr19 All loses QC-d Enrichment 4 1 0.0020 * * chr20 All loses QC-d Enrichment 9 1 0.0000 * * chr22 All loses QC-d Enrichment 2 0 0.0629 chr1 All loses QC-h Enrichment 231 47 0.0000 * * chr2 All loses QC-h Enrichment 3 3 0.4116 chr3 All loses QC-h Enrichment 53 22 0.0010 * * chr4 All loses QC-h Enrichment 96 17 0.0000 * * chr5 All loses QC-h Enrichment 9 1 0.0010 * * chr6 All loses QC-h Enrichment 46 17 0.0290 * chr7 All loses QC-h Enrichment 140 17 0.0000 * * chr8 All loses QC-h Enrichment 50 15 0.0000 * * chr9 All loses QC-h Enrichment 6 3 0.1409 chr10 All loses QC-h Enrichment 62 23 0.0000 * * chr11 All loses QC-h Impoverishment 2 3 0.3516 chr12 All loses QC-h Enrichment 35 3 0.0000 * * chr13 All loses QC-h Enrichment 41 10 0.0000 * * chr14 All loses QC-h Enrichment 2 1 0.2128 chr15 All loses QC-h Enrichment 11 2 0.0020 * * chr16 All loses QC-h Enrichment 2 2 0.4975 chr18 All loses QC-h Enrichment 6 5 0.2827 chr19 All loses QC-h Enrichment 6 3 0.1289 chr20 All loses QC-h Enrichment 14 8 0.0809 chr21 All loses QC-h Enrichment 54 4 0.0000 * * chr22 All loses QC-h Enrichment 4 3 0.2847 chr1 All loses QC-m Enrichment 186 78 0.0000 * * chr2 All loses QC-m Enrichment 28 5 0.0000 * * chr3 All loses QC-m Enrichment 50 20 0.0000 * * chr4 All loses QC-m Enrichment 64 10 0.0000 * * chr5 All loses QC-m Enrichment 19 5 0.0000 * * chr6 All loses QC-m Enrichment 72 35 0.0000 * * chr7 All loses QC-m Enrichment 41 8 0.0000 * * chr8 All loses QC-m Enrichment 91 18 0.0000 * * chr9 All loses QC-m Enrichment 11 4 0.0120 * chr10 All loses QC-m Enrichment 68 44 0.0220 * chr11 All loses QC-m Enrichment 28 5 0.0000 * * chr12 All loses QC-m Enrichment 45 8 0.0000 * * chr13 All loses QC-m Enrichment 37 15 0.0000 * * chr14 All loses QC-m Impoverishment 1 2 0.2448 chr15 All loses QC-m Enrichment 7 2 0.0270 * chr16 All loses QC-m Enrichment 16 4 0.0030 * * chr17 All loses QC-m Enrichment 9 2 0.0000 * * chr18 All loses QC-m Enrichment 2 1 0.3367 chr19 All loses QC-m Enrichment 16 6 0.0010 * * chr20 All loses QC-m Enrichment 25 13 0.0100 * chr21 All loses QC-m Enrichment 8 1 0.0040 * * chr22 All loses QC-m Enrichment 4 4 0.4515 chrX All loses QC-m Enrichment 2 1 0.0809 chr1 All loses QC-p Impoverishment 200 248 0.2298 chr2 All loses QC-p Enrichment 759 422 0.0040 * * chr3 All loses QC-p Enrichment 464 369 0.1029 chr4 All loses QC-p Enrichment 612 187 0.0000 * * chr5 All loses QC-p Enrichment 613 328 0.0000 * * chr6 All loses QC-p Enrichment 76 76 0.4745 chr7 All loses QC-p Enrichment 369 188 0.0010 * * chr8 All loses QC-p Impoverishment 347 485 0.0789 chr9 All loses QC-p Enrichment 854 312 0.0000 * * chr10 All loses QC-p Impoverishment 80 117 0.0589 chr11 All loses QC-p Enrichment 624 292 0.0000 * * chr12 All loses QC-p Enrichment 46 10 0.0000 * * chr13 All loses QC-p Impoverishment 49 69 0.0549 chr14 All loses QC-p Enrichment 201 121 0.0050 * * chr15 All loses QC-p Enrichment 943 245 0.0000 * * chr16 All loses QC-p Enrichment 455 210 0.0040 * * chr17 All loses QC-p Enrichment 213 111 0.0140 * chr18 All loses QC-p Enrichment 111 40 0.0000 * * chr19 All loses QC-p Enrichment 491 206 0.0000 * * chr20 All loses QC-p Enrichment 9 1 0.0000 * * chr21 All loses QC-p Enrichment 200 108 0.0130 * chr22 All loses QC-p Enrichment 556 198 0.0120 * chrX All loses QC-p Enrichment 173 161 0.3397 chr1 All loses QC-s Enrichment 381 102 0.0000 * * chr2 All loses QC-s Impoverishment 6 8 0.1808 chr3 All loses QC-s Enrichment 257 87 0.0000 * * chr4 All loses QC-s Enrichment 111 65 0.0020 * * chr5 All loses QC-s Enrichment 40 17 0.0000 * * chr6 All loses QC-s Enrichment 95 44 0.0000 * * chr7 All loses QC-s Enrichment 111 56 0.0000 * * chr8 All loses QC-s Enrichment 384 168 0.0000 * * chr9 All loses QC-s Enrichment 115 113 0.4635 chr10 All loses QC-s Enrichment 146 62 0.0000 * * chr11 All loses QC-s Enrichment 67 28 0.0000 * * chr12 All loses QC-s Enrichment 28 5 0.0000 * * chr13 All loses QC-s Enrichment 81 26 0.0000 * * chr14 All loses QC-s Enrichment 10 5 0.0400 * chr15 All loses QC-s Enrichment 32 11 0.0010 * * chr16 All loses QC-s Enrichment 21 8 0.0040 * * chr17 All loses QC-s Enrichment 8 5 0.1109 chr18 All loses QC-s Impoverishment 21 30 0.3267 chr19 All loses QC-s Enrichment 31 10 0.0000 * * chr20 All loses QC-s Enrichment 51 14 0.0000 * * chr21 All loses QC-s Enrichment 172 40 0.0000 * * chr22 All loses QC-s Enrichment 55 34 0.1439 chrX All loses QC-s Enrichment 4 4 0.4805 500K EA Gains Significant After BF Chromosome Population Type SNP class Direction Observed # Expected # p-value Significant correction chr1 All gains QCMinus Enrichment 729 320 0.0000 * * chr2 All gains QCMinus Enrichment 937 489 0.0030 * * chr3 All gains QCMinus Enrichment 342 204 0.0040 * * chr4 All gains QCMinus Enrichment 858 217 0.0000 * * chr5 All gains QCMinus Enrichment 197 105 0.0050 * * chr6 All gains QCMinus Enrichment 201 139 0.0370 * chr7 All gains QCMinus Enrichment 558 205 0.0000 * * chr8 All gains QCMinus Enrichment 519 410 0.0919 chr9 All gains QCMinus Enrichment 690 222 0.0000 * * chr10 All gains QCMinus Enrichment 337 220 0.0250 * chr11 All gains QCMinus Enrichment 183 93 0.0130 * chr12 All gains QCMinus Enrichment 256 121 0.0000 * * chr13 All gains QCMinus Enrichment 80 33 0.0000 * * chr14 All gains QCMinus Enrichment 132 24 0.0000 * * chr15 All gains QCMinus Enrichment 882 223 0.0000 * * chr16 All gains QCMinus Enrichment 473 269 0.0350 * chr17 All gains QCMinus Enrichment 204 118 0.0320 * chr18 All gains QCMinus Enrichment 129 44 0.0010 * * chr19 All gains QCMinus Enrichment 444 153 0.0000 * * chr20 All gains QCMinus Impoverishment 25 38 0.1548 chr21 All gains QCMinus Enrichment 209 61 0.0000 * * chr22 All gains QCMinus Enrichment 336 147 0.0440 * chr1 All gains QCPlus Impoverishment 2184 2941 0.0360 * chr2 All gains QCPlus Impoverishment 3308 4519 0.0110 * chr3 All gains QCPlus Impoverishment 1104 1159 0.2328 chr4 All gains QCPlus Enrichment 2995 2693 0.0709 chr5 All gains QCPlus Impoverishment 721 911 0.0070 * * chr6 All gains QCPlus Impoverishment 1449 1637 0.0579 chr7 All gains QCPlus Impoverishment 1689 2240 0.0340 * chr8 All gains QCPlus Impoverishment 2598 3364 0.0779 chr9 All gains QCPlus Impoverishment 880 2881 0.0060 * * chr10 All gains QCPlus Impoverishment 1381 2170 0.0120 * chr11 All gains QCPlus Impoverishment 636 740 0.1279 chr12 All gains QCPlus Impoverishment 1879 2123 0.0969 chr13 All gains QCPlus Enrichment 478 370 0.0080 * chr14 All gains QCPlus Enrichment 236 210 0.4046 chr15 All gains QCPlus Impoverishment 1063 1753 0.1289 chr16 All gains QCPlus Impoverishment 1032 1983 0.0050 * * chr17 All gains QCPlus Impoverishment 536 885 0.0030 * * chr18 All gains QCPlus Impoverishment 531 667 0.1039 chr19 All gains QCPlus Impoverishment 891 930 0.3836 chr20 All gains QCPlus Impoverishment 484 505 0.2647 chr21 All gains QCPlus Impoverishment 314 363 0.2997 chr22 All gains QCPlus Impoverishment 554 792 0.2368 chr1 All gains QC-d Enrichment 32 4 0.0000 * * chr4 All gains QC-d Enrichment 4 1 0.0350 * chr6 All gains QC-d Enrichment 15 2 0.0000 * * chr7 All gains QC-d Enrichment 3 1 0.1259 chr8 All gains QC-d Enrichment 6 1 0.0000 * * chr9 All gains QC-d Enrichment 1 0 0.3287 chr10 All gains QC-d Enrichment 17 4 0.0000 * * chr12 All gains QC-d Impoverishment 73 85 0.2787 chr13 All gains QC-d Enrichment 5 0 0.0000 * * chr17 All gains QC-d Enrichment 1 0 0.0939 chr20 All gains QC-d Enrichment 2 1 0.2208 chr1 All gains QC-h Enrichment 142 26 0.0000 * * chr2 All gains QC-h Enrichment 10 3 0.0320 * chr3 All gains QC-h Enrichment 46 8 0.0000 * * chr4 All gains QC-h Enrichment 105 13 0.0000 * * chr5 All gains QC-h Enrichment 1 0 0.3057 chr6 All gains QC-h Enrichment 34 12 0.0400 * chr7 All gains QC-h Enrichment 169 13 0.0000 * * chr8 All gains QC-h Enrichment 43 8 0.0000 * * chr9 All gains QC-h Enrichment 4 2 0.1339 chr10 All gains QC-h Enrichment 53 16 0.0010 * * chr12 All gains QC-h Enrichment 51 3 0.0000 * * chr13 All gains QC-h Enrichment 16 2 0.0010 * * chr14 All gains QC-h Enrichment 1 0 0.1439 chr15 All gains QC-h Enrichment 11 2 0.0020 * * chr16 All gains QC-h Enrichment 9 2 0.0010 * * chr17 All gains QC-h Enrichment 2 1 0.2178 chr18 All gains QC-h Enrichment 31 3 0.0020 * * chr19 All gains QC-h Impoverishment 1 2 0.1349 chr20 All gains QC-h Impoverishment 2 5 0.1099 chr21 All gains QC-h Enrichment 31 2 0.0000 * * chr22 All gains QC-h Enrichment 4 2 0.1259 chr1 All gains QC-m Enrichment 103 43 0.0000 * * chr2 All gains QC-m Enrichment 18 5 0.0000 * * chr3 All gains QC-m Enrichment 25 7 0.0000 * * chr4 All gains QC-m Enrichment 42 8 0.0000 * * chr5 All gains QC-m Enrichment 3 2 0.2228 chr6 All gains QC-m Enrichment 22 22 0.4815 chr7 All gains QC-m Enrichment 21 6 0.0000 * * chr8 All gains QC-m Enrichment 21 11 0.0889 chr9 All gains QC-m Impoverishment 2 2 0.4655 chr10 All gains QC-m Enrichment 45 30 0.0519 chr12 All gains QC-m Enrichment 38 11 0.0050 * * chr13 All gains QC-m Enrichment 10 4 0.0030 * * chr14 All gains QC-m Enrichment 3 0 0.0080 * chr15 All gains QC-m Impoverishment 2 2 0.4456 chr16 All gains QC-m Impoverishment 2 5 0.1139 chr18 All gains QC-m Enrichment 5 1 0.0020 * * chr19 All gains QC-m Enrichment 12 4 0.0010 * * chr20 All gains QC-m Impoverishment 6 8 0.2458 chr21 All gains QC-m Enrichment 3 1 0.0310 * chr22 All gains QC-m Enrichment 5 3 0.1469 chr1 All gains QC-p Impoverishment 101 138 0.1359 chr2 All gains QC-p Enrichment 902 469 0.0030 * * chr3 All gains QC-p Enrichment 134 136 0.4975 chr4 All gains QC-p Enrichment 554 139 0.0000 * * chr5 All gains QC-p Enrichment 189 98 0.0040 * * chr6 All gains QC-p Impoverishment 41 47 0.3307 chr7 All gains QC-p Enrichment 278 137 0.0080 * chr8 All gains QC-p Impoverishment 215 284 0.2228 chr9 All gains QC-p Enrichment 644 158 0.0000 * * chr10 All gains QC-p Impoverishment 50 82 0.1369 chr11 All gains QC-p Enrichment 179 82 0.0070 * * chr12 All gains QC-p Enrichment 56 13 0.0000 * * chr13 All gains QC-p Impoverishment 15 16 0.4226 chr14 All gains QC-p Enrichment 117 23 0.0000 * * chr15 All gains QC-p Enrichment 841 209 0.0000 * * chr16 All gains QC-p Enrichment 454 249 0.0340 * chr17 All gains QC-p Enrichment 195 108 0.0320 * chr18 All gains QC-p Enrichment 67 23 0.0000 * * chr19 All gains QC-p Enrichment 409 136 0.0000 * * chr20 All gains QC-p Enrichment 3 1 0.0270 * chr21 All gains QC-p Enrichment 99 42 0.0020 * * chr22 All gains QC-p Enrichment 303 120 0.0390 * chr1 All gains QC-s Enrichment 261 56 0.0000 * * chr2 All gains QC-s Impoverishment 5 9 0.0579 chr3 All gains QC-s Enrichment 113 32 0.0000 * * chr4 All gains QC-s Enrichment 102 49 0.0020 * * chr5 All gains QC-s Impoverishment 4 5 0.2947 chr6 All gains QC-s Enrichment 55 27 0.0030 * * chr7 All gains QC-s Enrichment 58 40 0.0719 chr8 All gains QC-s Enrichment 219 98 0.0000 * * chr9 All gains QC-s Impoverishment 37 59 0.1918 chr10 All gains QC-s Enrichment 120 42 0.0000 * * chr11 All gains QC-s Impoverishment 4 8 0.1159 chr12 All gains QC-s Enrichment 30 6 0.0000 * * chr13 All gains QC-s Enrichment 28 6 0.0000 * * chr14 All gains QC-s Enrichment 9 1 0.0000 * * chr15 All gains QC-s Enrichment 27 9 0.0000 * * chr16 All gains QC-s Impoverishment 6 10 0.1648 chr17 All gains QC-s Enrichment 5 5 0.4945 chr18 All gains QC-s Enrichment 22 18 0.2667 chr19 All gains QC-s Enrichment 20 7 0.0000 * * chr20 All gains QC-s Impoverishment 9 9 0.4925 chr21 All gains QC-s Enrichment 74 16 0.0000 * * chr22 All gains QC-s Enrichment 21 21 0.3596 500K EA Losses Significant After BF Chromosome Population Type SNP class Direction Observed # Expected # p-value Significant correction chr1 All loses QCMinus Enrichment 850 387 0.0000 * * chr2 All loses QCMinus Enrichment 553 270 0.0070 * * chr3 All loses QCMinus Enrichment 389 206 0.0000 * * chr4 All loses QCMinus Enrichment 599 133 0.0000 * * chr5 All loses QCMinus Enrichment 367 121 0.0000 * * chr6 All loses QCMinus Enrichment 211 84 0.0000 * * chr7 All loses QCMinus Enrichment 358 129 0.0010 * * chr8 All loses QCMinus Enrichment 594 380 0.0220 * chr9 All loses QCMinus Enrichment 498 184 0.0000 * * chr10 All loses QCMinus Enrichment 261 185 0.0380 * chr11 All loses QCMinus Enrichment 584 246 0.0000 * * chr12 All loses QCMinus Enrichment 84 39 0.0000 * * chr13 All loses QCMinus Enrichment 148 57 0.0000 * * chr14 All loses QCMinus Enrichment 116 51 0.0020 * * chr15 All loses QCMinus Enrichment 870 181 0.0000 * * chr16 All loses QCMinus Enrichment 369 138 0.0090 * chr17 All loses QCMinus Enrichment 154 57 0.0000 * * chr18 All loses QCMinus Enrichment 60 36 0.0689 chr19 All loses QCMinus Enrichment 360 152 0.0000 * * chr20 All loses QCMinus Enrichment 46 18 0.0010 * * chr21 All loses QCMinus Enrichment 406 119 0.0000 * * chr22 All loses QCMinus Enrichment 371 128 0.0230 * chr1 All loses QCPlus Impoverishment 3352 3593 0.2547 chr2 All loses QCPlus Impoverishment 1522 2526 0.0010 * * chr3 All loses QCPlus Impoverishment 1173 1158 0.4975 chr4 All loses QCPlus Impoverishment 1263 1672 0.0090 * chr5 All loses QCPlus Impoverishment 969 1052 0.0969 chr6 All loses QCPlus Enrichment 1091 999 0.0120 * chr7 All loses QCPlus Impoverishment 1135 1424 0.0539 chr8 All loses QCPlus Impoverishment 2229 3116 0.0170 * chr9 All loses QCPlus Impoverishment 1795 2384 0.1508 chr10 All loses QCPlus Impoverishment 1287 1840 0.0290 * chr11 All loses QCPlus Impoverishment 1679 1934 0.0549 chr12 All loses QCPlus Impoverishment 625 691 0.1648 chr13 All loses QCPlus Enrichment 767 626 0.0100 * chr14 All loses QCPlus Enrichment 511 436 0.0879 chr15 All loses QCPlus Impoverishment 662 1412 0.1019 chr16 All loses QCPlus Impoverishment 371 992 0.0060 * * chr17 All loses QCPlus Impoverishment 202 427 0.0010 * * chr18 All loses QCPlus Enrichment 620 526 0.0899 chr19 All loses QCPlus Impoverishment 873 934 0.2987 chr20 All loses QCPlus Impoverishment 241 238 0.4945 chr21 All loses QCPlus Impoverishment 743 692 0.4166 chr22 All loses QCPlus Impoverishment 556 727 0.3237 chr1 All loses QC-d Enrichment 25 4 0.0000 * * chr3 All loses QC-d Enrichment 1 0 0.2218 chr6 All loses QC-d Enrichment 21 1 0.0000 * * chr7 All loses QC-d Enrichment 2 1 0.1828 chr8 All loses QC-d Enrichment 3 0 0.0110 * chr10 All loses QC-d Enrichment 10 3 0.0150 * chr12 All loses QC-d Impoverishment 7 28 0.0010 * * chr13 All loses QC-d Enrichment 17 1 0.0000 * * chr19 All loses QC-d Enrichment 1 0 0.3237 chr20 All loses QC-d Enrichment 1 0 0.3137 chr1 All loses QC-h Enrichment 176 31 0.0000 * * chr2 All loses QC-h Impoverishment 1 2 0.2308 chr3 All loses QC-h Enrichment 34 8 0.0000 * * chr4 All loses QC-h Enrichment 76 8 0.0000 * * chr5 All loses QC-h Enrichment 1 1 0.3746 chr6 All loses QC-h Enrichment 28 7 0.0100 * chr7 All loses QC-h Enrichment 107 8 0.0000 * * chr8 All loses QC-h Enrichment 42 8 0.0000 * * chr9 All loses QC-h Enrichment 4 1 0.0909 chr10 All loses QC-h Enrichment 39 14 0.0010 * * chr11 All loses QC-h Enrichment 3 2 0.2617 chr12 All loses QC-h Enrichment 28 1 0.0000 * * chr13 All loses QC-h Enrichment 22 4 0.0000 * * chr14 All loses QC-h Enrichment 2 0 0.0619 chr15 All loses QC-h Enrichment 10 1 0.0010 * * chr18 All loses QC-h Enrichment 2 2 0.4446 chr19 All loses QC-h Impoverishment 1 2 0.1499 chr20 All loses QC-h Enrichment 5 2 0.1159 chr21 All loses QC-h Enrichment 54 3 0.0000 * * chr22 All loses QC-h Enrichment 2 1 0.3946 chr1 All loses QC-m Enrichment 140 52 0.0000 * * chr2 All loses QC-m Enrichment 23 3 0.0000 * * chr3 All loses QC-m Enrichment 31 8 0.0000 * * chr4 All loses QC-m Enrichment 40 5 0.0000 * * chr5 All loses QC-m Enrichment 12 2 0.0000 * * chr6 All loses QC-m Enrichment 42 13 0.0000 * * chr7 All loses QC-m Enrichment 20 4 0.0000 * * chr8 All loses QC-m Enrichment 78 10 0.0000 * * chr9 All loses QC-m Enrichment 2 2 0.4835 chr10 All loses QC-m Enrichment 36 25 0.0659 chr11 All loses QC-m Enrichment 24 4 0.0000 * * chr12 All loses QC-m Enrichment 20 3 0.0000 * * chr13 All loses QC-m Enrichment 17 6 0.0000 * * chr15 All loses QC-m Enrichment 7 2 0.0110 * chr16 All loses QC-m Enrichment 7 2 0.0519 chr17 All loses QC-m Enrichment 3 1 0.0879 chr18 All loses QC-m Enrichment 1 1 0.3936 chr19 All loses QC-m Enrichment 9 4 0.0190 * chr20 All loses QC-m Enrichment 10 4 0.0230 * chr21 All loses QC-m Enrichment 6 1 0.0080 * chr22 All loses QC-m Enrichment 3 2 0.3387 chr1 All loses QC-p Impoverishment 127 168 0.2527 chr2 All loses QC-p Enrichment 527 259 0.0080 * chr3 All loses QC-p Enrichment 158 137 0.3207 chr4 All loses QC-p Enrichment 379 84 0.0000 * * chr5 All loses QC-p Enrichment 318 112 0.0000 * * chr6 All loses QC-p Enrichment 40 29 0.0789 chr7 All loses QC-p Enrichment 165 87 0.0200 * chr8 All loses QC-p Impoverishment 183 261 0.1249 chr9 All loses QC-p Enrichment 418 132 0.0000 * * chr10 All loses QC-p Impoverishment 39 68 0.0859 chr11 All loses QC-p Enrichment 493 217 0.0000 * * chr12 All loses QC-p Enrichment 16 4 0.0050 * * chr13 All loses QC-p Impoverishment 12 28 0.0220 * chr14 All loses QC-p Enrichment 106 47 0.0030 * * chr15 All loses QC-p Enrichment 822 169 0.0000 * * chr16 All loses QC-p Enrichment 343 128 0.0100 * chr17 All loses QC-p Enrichment 144 52 0.0020 * * chr18 All loses QC-p Enrichment 50 19 0.0010 * * chr19 All loses QC-p Enrichment 325 136 0.0000 * * chr21 All loses QC-p Enrichment 177 84 0.0050 * * chr22 All loses QC-p Enrichment 343 104 0.0210 * chr1 All loses QC-s Enrichment 285 68 0.0000 * * chr2 All loses QC-s Impoverishment 1 5 0.0100 * chr3 All loses QC-s Enrichment 141 32 0.0000 * * chr4 All loses QC-s Enrichment 62 30 0.0040 * * chr5 All loses QC-s Enrichment 35 6 0.0000 * * chr6 All loses QC-s Enrichment 52 17 0.0000 * * chr7 All loses QC-s Enrichment 49 25 0.0170 * chr8 All loses QC-s Enrichment 248 92 0.0000 * * chr9 All loses QC-s Enrichment 70 48 0.1389 chr10 All loses QC-s Enrichment 89 36 0.0000 * * chr11 All loses QC-s Enrichment 58 21 0.0000 * * chr12 All loses QC-s Enrichment 11 2 0.0030 * * chr13 All loses QC-s Enrichment 50 11 0.0000 * * chr14 All loses QC-s Enrichment 8 2 0.0030 * * chr15 All loses QC-s Enrichment 30 7 0.0000 * * chr16 All loses QC-s Enrichment 18 5 0.0060 * * chr17 All loses QC-s Enrichment 6 2 0.0300 * chr18 All loses QC-s Impoverishment 6 14 0.1349 chr19 All loses QC-s Enrichment 22 7 0.0000 * * chr20 All loses QC-s Enrichment 21 4 0.0000 * * chr21 All loses QC-s Enrichment 164 31 0.0000 * * chr22 All loses QC-s Enrichment 21 18 0.2767 WGTP Losses Significant After BF Chromosome Population Type SNP class Direction Observed # Expected # p-value Significant correction chr1 All loses QCMinus Enrichment 683 378 0.0000 * * chr2 All loses QCMinus Enrichment 446 287 0.0260 * chr3 All loses QCMinus Enrichment 678 469 0.0050 * * chr4 All loses QCMinus Enrichment 623 221 0.0000 * * chr5 All loses QCMinus Enrichment 400 264 0.0010 * * chr6 All loses QCMinus Enrichment 238 161 0.0080 * chr7 All loses QCMinus Enrichment 435 203 0.0000 * * chr8 All loses QCMinus Enrichment 564 509 0.2468 chr9 All loses QCMinus Enrichment 653 328 0.0000 * * chr10 All loses QCMinus Enrichment 266 185 0.0170 * chr11 All loses QCMinus Enrichment 406 177 0.0000 * * chr12 All loses QCMinus Enrichment 111 69 0.0000 * * chr13 All loses QCMinus Enrichment 173 105 0.0000 * * chr14 All loses QCMinus Enrichment 126 98 0.1069 chr15 All loses QCMinus Enrichment 160 121 0.1828 chr16 All loses QCMinus Enrichment 149 99 0.1229 chr17 All loses QCMinus Enrichment 97 74 0.1868 chr18 All loses QCMinus Enrichment 119 62 0.0220 * chr19 All loses QCMinus Enrichment 308 155 0.0140 * chr20 All loses QCMinus Enrichment 98 44 0.0000 * * chr21 All loses QCMinus Enrichment 86 48 0.1019 chr22 All loses QCMinus Enrichment 280 115 0.0100 * chrX All loses QCMinus Enrichment 184 177 0.3836 chr1 All loses QCPlus Enrichment 3742 3500 0.3836 chr2 All loses QCPlus Impoverishment 2334 2681 0.0500 * chr3 All loses QCPlus Enrichment 2693 2651 0.4016 chr4 All loses QCPlus Impoverishment 2414 2778 0.0539 chr5 All loses QCPlus Enrichment 2311 2287 0.4565 chr6 All loses QCPlus Enrichment 2008 1905 0.1099 chr7 All loses QCPlus Enrichment 2480 2221 0.1748 chr8 All loses QCPlus Impoverishment 3747 4190 0.1878 chr9 All loses QCPlus Impoverishment 3686 4264 0.1299 chr10 All loses QCPlus Enrichment 1921 1868 0.3287 chr11 All loses QCPlus Enrichment 1442 1404 0.4146 chr12 All loses QCPlus Impoverishment 1170 1217 0.4266 chr13 All loses QCPlus Enrichment 1413 1173 0.0210 * chr14 All loses QCPlus Enrichment 1030 837 0.0509 chr15 All loses QCPlus Impoverishment 903 922 0.4216 chr16 All loses QCPlus Enrichment 766 699 0.3656 chr17 All loses QCPlus Impoverishment 545 568 0.3147 chr18 All loses QCPlus Impoverishment 900 917 0.4995 chr19 All loses QCPlus Enrichment 1002 931 0.4086 chr20 All loses QCPlus Enrichment 630 586 0.2507 chr21 All loses QCPlus Enrichment 388 282 0.2188 chr22 All loses QCPlus Enrichment 1120 626 0.0000 * * chrX All loses QCPlus Enrichment 1155 1004 0.1299 chr1 All loses QC-d Enrichment 25 4 0.0000 * * chr6 All loses QC-d Enrichment 18 3 0.0000 * * chr8 All loses QC-d Enrichment 2 1 0.1229 chr10 All loses QC-d Enrichment 23 3 0.0000 * * chr12 All loses QC-d Impoverishment 10 49 0.0010 * * chr13 All loses QC-d Enrichment 12 1 0.0000 * * chr16 All loses QC-d Enrichment 1 0 0.0000 * * chr17 All loses QC-d Enrichment 1 0 0.0589 chr19 All loses QC-d Enrichment 4 0 0.0000 * * chr20 All loses QC-d Enrichment 8 1 0.0000 * * chr22 All loses QC-d Enrichment 2 0 0.0120 * chr1 All loses QC-h Enrichment 120 30 0.0000 * * chr2 All loses QC-h Enrichment 2 2 0.4605 chr3 All loses QC-h Enrichment 40 19 0.0030 * * chr4 All loses QC-h Enrichment 46 13 0.0000 * * chr5 All loses QC-h Enrichment 8 1 0.0020 * * chr6 All loses QC-h Enrichment 25 13 0.0669 chr7 All loses QC-h Enrichment 42 12 0.0020 * * chr8 All loses QC-h Enrichment 21 10 0.0450 * chr9 All loses QC-h Enrichment 4 2 0.2318 chr10 All loses QC-h Enrichment 27 13 0.0300 * chr12 All loses QC-h Enrichment 20 2 0.0000 * * chr13 All loses QC-h Enrichment 31 7 0.0000 * * chr15 All loses QC-h Enrichment 2 1 0.2048 chr16 All loses QC-h Enrichment 2 1 0.1918 chr18 All loses QC-h Enrichment 4 4 0.3696 chr19 All loses QC-h Enrichment 5 2 0.0999 chr20 All loses QC-h Enrichment 9 6 0.2168 chr21 All loses QC-h Enrichment 4 1 0.0899 chr22 All loses QC-h Enrichment 2 1 0.3626 chr1 All loses QC-m Enrichment 102 50 0.0000 * * chr2 All loses QC-m Enrichment 7 3 0.0599 chr3 All loses QC-m Enrichment 29 17 0.0180 * chr4 All loses QC-m Enrichment 44 8 0.0000 * * chr5 All loses QC-m Enrichment 9 4 0.0250 * chr6 All loses QC-m Enrichment 50 25 0.0000 * * chr7 All loses QC-m Enrichment 28 6 0.0000 * * chr8 All loses QC-m Enrichment 36 13 0.0040 * * chr9 All loses QC-m Enrichment 10 3 0.0060 * * chr10 All loses QC-m Enrichment 37 25 0.0450 * chr11 All loses QC-m Enrichment 13 3 0.0000 * * chr12 All loses QC-m Enrichment 28 6 0.0000 * * chr13 All loses QC-m Enrichment 20 11 0.0230 * chr14 All loses QC-m Impoverishment 1 1 0.3696 chr16 All loses QC-m Enrichment 9 2 0.0080 * chr17 All loses QC-m Enrichment 6 1 0.0030 * * chr18 All loses QC-m Impoverishment 1 1 0.4126 chr19 All loses QC-m Enrichment 7 4 0.1029 chr20 All loses QC-m Enrichment 15 10 0.1209 chr21 All loses QC-m Enrichment 2 0 0.1029 chr22 All loses QC-m Impoverishment 1 2 0.2627 chrX All loses QC-m Enrichment 2 1 0.0809 chr1 All loses QC-p Impoverishment 114 164 0.1818 chr2 All loses QC-p Enrichment 428 275 0.0300 * chr3 All loses QC-p Enrichment 377 311 0.1788 chr4 All loses QC-p Enrichment 410 141 0.0000 * * chr5 All loses QC-p Enrichment 366 245 0.0040 * * chr6 All loses QC-p Impoverishment 50 55 0.3417 chr7 All loses QC-p Enrichment 260 136 0.0040 * * chr8 All loses QC-p Impoverishment 242 352 0.1159 chr9 All loses QC-p Enrichment 557 233 0.0000 * * chr10 All loses QC-p Impoverishment 45 69 0.0380 * chr11 All loses QC-p Enrichment 352 156 0.0000 * * chr12 All loses QC-p Enrichment 33 7 0.0000 * * chr13 All loses QC-p Impoverishment 41 51 0.1828 chr14 All loses QC-p Enrichment 123 91 0.0789 chr15 All loses QC-p Enrichment 155 113 0.1708 chr16 All loses QC-p Enrichment 118 91 0.1998 chr17 All loses QC-p Enrichment 88 68 0.2058 chr18 All loses QC-p Enrichment 93 33 0.0000 * * chr19 All loses QC-p Enrichment 274 139 0.0190 * chr20 All loses QC-p Enrichment 9 1 0.0000 * * chr21 All loses QC-p Enrichment 56 34 0.1409 chr22 All loses QC-p Enrichment 234 94 0.0160 * chrX All loses QC-p Enrichment 173 160 0.3277 chr1 All loses QC-s Enrichment 203 66 0.0000 * * chr2 All loses QC-s Impoverishment 5 6 0.3666 chr3 All loses QC-s Enrichment 184 73 0.0000 * * chr4 All loses QC-s Enrichment 77 51 0.0270 * chr5 All loses QC-s Enrichment 14 13 0.4226 chr6 All loses QC-s Enrichment 65 32 0.0000 * * chr7 All loses QC-s Enrichment 76 40 0.0010 * * chr8 All loses QC-s Enrichment 227 122 0.0040 * * chr9 All loses QC-s Impoverishment 75 87 0.3467 chr10 All loses QC-s Enrichment 81 36 0.0000 * * chr11 All loses QC-s Enrichment 32 15 0.0060 * * chr12 All loses QC-s Enrichment 18 3 0.0000 * * chr13 All loses QC-s Enrichment 44 20 0.0000 * * chr14 All loses QC-s Impoverishment 2 4 0.1518 chr15 All loses QC-s Impoverishment 3 5 0.1578 chr16 All loses QC-s Enrichment 13 3 0.0010 * * chr17 All loses QC-s Impoverishment 2 3 0.1938 chr18 All loses QC-s Impoverishment 19 23 0.4705 chr19 All loses QC-s Enrichment 14 7 0.0290 * chr20 All loses QC-s Enrichment 30 11 0.0030 * * chr21 All loses QC-s Enrichment 24 12 0.1349 chr22 All loses QC-s Enrichment 36 17 0.0949 chrX All loses QC-s Enrichment 4 4 0.4545 WGTP Gains Significant After BF Chromosome Population Type SNP class Direction Observed # Expected # p-value Significant correction chr1 All gains QCMinus Enrichment 423 277 0.0020 * * chr2 All gains QCMinus Enrichment 779 484 0.0130 * chr3 All gains QCMinus Impoverishment 276 373 0.0779 chr4 All gains QCMinus Enrichment 855 259 0.0000 * * chr5 All gains QCMinus Enrichment 264 214 0.0789 chr6 All gains QCMinus Enrichment 534 262 0.0000 * * chr7 All gains QCMinus Enrichment 605 299 0.0000 * * chr8 All gains QCMinus Impoverishment 355 377 0.4266 chr9 All gains QCMinus Enrichment 232 96 0.0030 * * chr10 All gains QCMinus Enrichment 208 144 0.0220 * chr11 All gains QCMinus Enrichment 357 197 0.0020 * * chr12 All gains QCMinus Enrichment 264 153 0.0000 * * chr13 All gains QCMinus Enrichment 95 44 0.0000 * * chr14 All gains QCMinus Enrichment 79 35 0.0040 * * chr15 All gains QCMinus Enrichment 216 148 0.1249 chr16 All gains QCMinus Enrichment 337 227 0.0639 chr17 All gains QCMinus Enrichment 247 166 0.0380 * chr18 All gains QCMinus Enrichment 379 124 0.0000 * * chr19 All gains QCMinus Enrichment 261 186 0.0919 chr20 All gains QCMinus Enrichment 88 59 0.0669 chr21 All gains QCMinus Enrichment 34 25 0.2937 chr22 All gains QCMinus Enrichment 155 53 0.0260 * chrX All gains QCMinus Enrichment 560 366 0.0320 * chr1 All gains QCPlus Enrichment 2654 2553 0.3616 chr2 All gains QCPlus Impoverishment 4153 4500 0.1309 chr3 All gains QCPlus Enrichment 2167 2121 0.4136 chr4 All gains QCPlus Enrichment 4137 3250 0.0450 * chr5 All gains QCPlus Impoverishment 1409 1857 0.0010 * * chr6 All gains QCPlus Impoverishment 2919 3126 0.0859 chr7 All gains QCPlus Impoverishment 2196 3259 0.0030 * * chr8 All gains QCPlus Impoverishment 2959 3106 0.3497 chr9 All gains QCPlus Impoverishment 985 1244 0.1748 chr10 All gains QCPlus Impoverishment 1445 1440 0.4885 chr11 All gains QCPlus Impoverishment 1281 1575 0.0300 * chr12 All gains QCPlus Impoverishment 2468 2686 0.1558 chr13 All gains QCPlus Enrichment 577 489 0.1968 chr14 All gains QCPlus Enrichment 343 299 0.2837 chr15 All gains QCPlus Enrichment 1226 1132 0.3117 chr16 All gains QCPlus Impoverishment 1514 1639 0.2438 chr17 All gains QCPlus Impoverishment 1071 1246 0.0529 chr18 All gains QCPlus Impoverishment 1508 1811 0.1399 chr19 All gains QCPlus Enrichment 1183 1125 0.4645 chr20 All gains QCPlus Impoverishment 804 822 0.3107 chr21 All gains QCPlus Enrichment 241 141 0.0140 * chr22 All gains QCPlus Enrichment 482 305 0.1049 chrX All gains QCPlus Impoverishment 1504 2076 0.0230 * chr1 All gains QC-d Enrichment 43 3 0.0000 * * chr4 All gains QC-d Enrichment 4 1 0.0280 * chr5 All gains QC-d Enrichment 1 0 0.1299 chr6 All gains QC-d Enrichment 38 4 0.0000 * * chr7 All gains QC-d Enrichment 4 2 0.1289 chr8 All gains QC-d Enrichment 2 0 0.0809 chr9 All gains QC-d Enrichment 1 0 0.1798 chr10 All gains QC-d Enrichment 11 2 0.0000 * * chr12 All gains QC-d Impoverishment 80 109 0.0809 chr13 All gains QC-d Enrichment 9 0 0.0000 * * chr15 All gains QC-d Enrichment 1 0 0.0380 * chr18 All gains QC-d Enrichment 1 0 0.0959 chr19 All gains QC-d Enrichment 1 1 0.4216 chr20 All gains QC-d Enrichment 4 1 0.0639 chrX All gains QC-d Enrichment 1 0 0.0000 * * chr1 All gains QC-h Enrichment 68 22 0.0000 * * chr2 All gains QC-h Enrichment 8 3 0.0589 chr3 All gains QC-h Enrichment 15 15 0.4855 chr4 All gains QC-h Enrichment 67 15 0.0000 * * chr5 All gains QC-h Enrichment 3 1 0.1029 chr6 All gains QC-h Enrichment 135 21 0.0000 * * chr7 All gains QC-h Enrichment 131 19 0.0000 * * chr8 All gains QC-h Enrichment 23 8 0.0210 * chr9 All gains QC-h Enrichment 3 1 0.0669 chr10 All gains QC-h Enrichment 29 11 0.0040 * * chr11 All gains QC-h Enrichment 4 2 0.0889 chr12 All gains QC-h Enrichment 33 4 0.0000 * * chr13 All gains QC-h Enrichment 22 3 0.0010 * * chr15 All gains QC-h Enrichment 3 1 0.1319 chr16 All gains QC-h Enrichment 10 2 0.0000 * * chr17 All gains QC-h Enrichment 2 1 0.3177 chr18 All gains QC-h Enrichment 95 9 0.0000 * * chr19 All gains QC-h Enrichment 4 3 0.2777 chr20 All gains QC-h Impoverishment 7 8 0.4356 chr21 All gains QC-h Enrichment 3 1 0.0779 chr22 All gains QC-h Enrichment 5 1 0.0010 * * chrX All gains QC-h Enrichment 40 0 0.0000 * * chr1 All gains QC-m Enrichment 42 37 0.2977 chr2 All gains QC-m Enrichment 6 5 0.3726 chr3 All gains QC-m Enrichment 22 14 0.0490 * chr4 All gains QC-m Enrichment 37 9 0.0000 * * chr5 All gains QC-m Impoverishment 2 3 0.2208 chr6 All gains QC-m Enrichment 47 42 0.2567 chr7 All gains QC-m Enrichment 27 8 0.0000 * * chr8 All gains QC-m Impoverishment 8 10 0.4036 chr9 All gains QC-m Impoverishment 1 1 0.4216 chr10 All gains QC-m Enrichment 40 19 0.0040 * * chr11 All gains QC-m Impoverishment 2 3 0.2018 chr12 All gains QC-m Enrichment 43 13 0.0030 * * chr13 All gains QC-m Enrichment 7 5 0.2298 chr14 All gains QC-m Enrichment 3 0 0.0250 * chr15 All gains QC-m Impoverishment 1 1 0.2687 chr16 All gains QC-m Impoverishment 3 4 0.3017 chr17 All gains QC-m Impoverishment 1 3 0.0569 chr18 All gains QC-m Enrichment 5 2 0.1139 chr19 All gains QC-m Enrichment 6 4 0.2927 chr20 All gains QC-m Impoverishment 13 13 0.4875 chr1 All gains QC-p Impoverishment 61 120 0.0110 * chr2 All gains QC-p Enrichment 757 464 0.0130 * chr3 All gains QC-p Impoverishment 138 247 0.0250 * chr4 All gains QC-p Enrichment 609 165 0.0000 * * chr5 All gains QC-p Enrichment 241 198 0.1189 chr6 All gains QC-p Enrichment 95 89 0.3796 chr7 All gains QC-p Enrichment 328 200 0.0170 * chr8 All gains QC-p Impoverishment 194 261 0.2288 chr9 All gains QC-p Enrichment 193 68 0.0020 * * chr10 All gains QC-p Impoverishment 26 53 0.0130 * chr11 All gains QC-p Enrichment 337 173 0.0020 * * chr12 All gains QC-p Enrichment 68 16 0.0000 * * chr13 All gains QC-p Impoverishment 17 22 0.3077 chr14 All gains QC-p Enrichment 73 33 0.0040 * * chr15 All gains QC-p Enrichment 202 138 0.1319 chr16 All gains QC-p Enrichment 306 210 0.0889 chr17 All gains QC-p Enrichment 234 152 0.0380 * chr18 All gains QC-p Enrichment 198 65 0.0000 * * chr19 All gains QC-p Enrichment 242 166 0.0839 chr20 All gains QC-p Enrichment 8 1 0.0000 * * chr21 All gains QC-p Enrichment 26 17 0.2418 chr22 All gains QC-p Enrichment 133 43 0.0230 * chrX All gains QC-p Enrichment 405 331 0.1349 chr1 All gains QC-s Enrichment 147 48 0.0000 * * chr2 All gains QC-s Impoverishment 3 9 0.0060 * * chr3 All gains QC-s Enrichment 83 60 0.0849 chr4 All gains QC-s Enrichment 102 59 0.0050 * * chr5 All gains QC-s Enrichment 15 11 0.1489 chr6 All gains QC-s Enrichment 138 52 0.0000 * * chr7 All gains QC-s Enrichment 84 58 0.0470 * chr8 All gains QC-s Enrichment 116 90 0.1578 chr9 All gains QC-s Enrichment 34 25 0.2198 chr10 All gains QC-s Enrichment 53 28 0.0010 * * chr11 All gains QC-s Impoverishment 13 17 0.2468 chr12 All gains QC-s Enrichment 26 7 0.0030 * * chr13 All gains QC-s Enrichment 34 8 0.0000 * * chr14 All gains QC-s Enrichment 3 1 0.1479 chr15 All gains QC-s Enrichment 8 6 0.3007 chr16 All gains QC-s Enrichment 9 8 0.3996 chr17 All gains QC-s Enrichment 8 7 0.3327 chr18 All gains QC-s Enrichment 71 46 0.1219 chr19 All gains QC-s Impoverishment 6 8 0.2038 chr20 All gains QC-s Enrichment 40 15 0.0110 * chr21 All gains QC-s Enrichment 5 7 0.4795 chr22 All gains QC-s Enrichment 16 8 0.0989 chrX All gains QC-s Enrichment 9 7 0.3067 SupplementaryTable 19: Tagging SNPs for common CNVs CNVID Platform CEU tag SNP YRI tag SNP JPT+CHB tag SNP 37 500K EA rs4240531 rs4240531 418 500K EA rs9447791 rs11757291 421 500K EA rs13220198 rs10485287 491 500K EA rs193807 519 500K EA rs7460394 rs10093913 542 500K EA rs11203531 555 500K EA rs2979813 rs2950291 rs2056705 641 500K EA rs1342114 rs1935384 727 500K EA rs4372479 rs1453415 rs4372479 752 500K EA rs2077851 rs6486020 780 500K EA rs10501812 70 500K EA rs1037388 rs1037388 785 500K EA rs4350331 789 500K EA rs7117758 891 500K EA rs1780906 rs2792146 901 500K EA rs1779540 rs1779540 1015 500K EA rs8057434 rs3803648 1034 500K EA rs9921348 rs718954 1082 500K EA rs12455301 rs716669 1084 500K EA rs10503141 1100 500K EA rs10405246 rs4806131 rs1633921 1104 500K EA rs4803593 rs8113109 1122 500K EA rs3760858 1153 500K EA rs2827417 214 500K EA rs9757129 rs10934906 rs9758051 228 500K EA rs4413326 268 500K EA rs10155079 rs16990341 293 500K EA rs10002047 rs1112531 302 500K EA rs1559698 391 500K EA rs2394180 rs29234 rs4078116 Chr10tp-1H10 (Chr10_6) WGTP rs2359536 rs10764249 Chr11tp-13E10 (Chr11_25) WGTP rs1048374 rs1048374 Chr11tp-5D4 (Chr11_27) WGTP rs1118333 rs12274356 rs2202839 Chr12tp-19A11 (Chr12_16) WGTP rs2543217 rs2575260 Chr12tp-19H4 (Chr12_14) WGTP rs4763630 rs11829861 rs10771789 Chr15tp-11F12 (Chr15_5) WGTP rs678217 rs16959394 rs750904 Chr15tp-9C6 (Chr15_36) WGTP rs4779683 rs12904872 rs7173960 Chr16tp-3C5 (Chr16_38) WGTP rs1424241 Chr1tp-13A8 (Chr1_38) WGTP rs1339867 rs10863690 rs11118949 Chr1tp-15A9 (Chr1_45) WGTP rs4916176 rs11204613 rs12569285 Chr1tp-21E1 (Chr1_55) WGTP rs3818361 rs6701713 rs9429944 Chr1tp-23H1 (Chr1_66) WGTP rs10494095 rs11804847 rs2454327 Chr1tp-31C8 (Chr1_13) WGTP rs6700158 rs6700158 rs4845459 Chr1tp-32E9 (Chr1_17) WGTP rs2986127 rs3766404 rs457950 Chr1tp-4C10 (Chr1_27) WGTP rs1460943 rs2815752 rs1460943 Chr1tp-7D2 (Chr1_33) WGTP rs7516133 rs1620351 rs12082225 Chr1tp-7H5 (Chr1_68) WGTP rs11581756 rs4950701 rs4347261 Chr20tp-4A10 (Chr20_5) WGTP rs11697985 rs2746609 rs11697985 Chr22tp-8C6 (Chr22_26) WGTP rs136989 rs1812240 rs7287384 Chr3tp-10A3 (Chr3_32) WGTP rs6763025 Chr3tp-15F5 (Chr3_6) WGTP rs9841435 rs192671 Chr3tp-23C12 (Chr3_22) WGTP rs206276 rs206276 Chr4tp-10F11 (Chr4_47) WGTP rs4863215 rs2739585 rs12649488 Chr4tp-18E9 (Chr4_57) WGTP rs4457014 rs11249532 rs4643883 Chr4tp-1H7 (Chr4_23) WGTP rs1553911 rs16990341 Chr4tp-23H10 (Chr4_57) WGTP rs3100645 rs10471154 rs3100645 Chr4tp-6G5 (-) WGTP rs7686995 rs7686403 Chr5tp-22E4 (Chr5_11) WGTP rs1816256 rs4554200 rs1820682 Chr6tp-11A11 (Chr6_45) WGTP rs12213776 rs9361364 rs1338321 Chr6tp-18F9 (Chr6_14) WGTP rs4945830 rs4945830 rs1008965 Chr6tp-2C12 (Chr6_63) WGTP rs11753874 rs11753874 Chr6tp-5C11 (Chr6_19) WGTP rs2516049 rs2516049 rs2516049 Chr6tp-5C12 (Chr6_6) WGTP rs3129763 rs3130320 rs9268541 Chr8tp-17E9 (Chr8_11) WGTP rs10958546 rs1451736 rs7461443 Chr9tp-2A1 (Chr9_3) WGTP rs7020324 rs11559484

Supplementary Table 19: List of tagging SNPs for common CNVs This table lists the SNP in highest pairwise LD with each genotyped CNV in each of the three analysis classes. SNPs are not listed for a CNV if the minor allele frequency in that population was less than 5%, or if there was more than 1 Mendelian incompatibility. SNPs listed in red are in high pairwise LD with their respective CNV, with r^2>0.8. For CNVs genotyped from WGTP data, the genotyping is performed on log2 ratios from individual clones (Methods). For these clones the CNVID of a CNV containing that clone is given in brackets, after the clone ID. One of the WGTP genotyped clones was not called as a CNV using the final analysis calling parameters, and so does not have an associated CNV ID. Supplementary Table 20: CNVs exhibiting highest (VST>0.45) population differentiation

Starting Ending Population a Chromosome Genes in region VST Positiona Positiona Comparisonb

1 7,567,410 7,617,039 CEU-YRI CAMTA1 0.47 1 81,599,438 81,608,767 CEU-YRI no genes 0.70 1 111,503,176 111,504,937 CEU-YRI no genes 0.74 1 142,391,276 142,548,088 YRI-CHB+JPT NOTCH2NL 0.49 2 66,041,145 66,060,953 CEU-YRI no genes 0.62 2 81,671,346 81,727,952 CEU-YRI Q8NBL2 0.47 TMIE, TESSP2, MYL3, PTHR1, 3 46,770,243 46,947,493 YRI-CHB+JPT 0.55 CCDC12 3 122,747,576 122,806,127 YRI-CHB+JPT FBXO40 0.59 3 164,054,860 164,221,008 CEU-CHB+JPT no genes 0.45 4 22,969,909 22,984,031 CEU-YRI no genes 0.50 4 69,126,468 69,296,476 YRI-CHB+JPT UGT2B17 0.57 5 15,362,984 15,386,338 CEU-YRI no genes 0.49 5 150,080,197 150,239,374 CEU-YRI DCTN4 0.47 5 159,269,486 159,462,776 YRI-CHB+JPT TTC1, ADRA1B 0.52 6 2,570,100 2,577,107 CEU-YRI no genes 0.47 6 41,727,028 41,734,726 CEU-YRI MDFI 0.54 6 143,862,472 143,866,797 YRI-CHB+JPT FUCA2 0.57 7 110,707,542 110,824,769 CEU-YRI IMMP2L 0.45 8 96,892,887 96,916,149 CEU-YRI no genes 0.65 8 121,834,882 121,898,100 CEU-YRI SNTB1 0.53 10 37,974,972 37,997,426 YRI-CHB+JPT no genes 0.57 11 122,339,246 122,371,312 YRI-CHB+JPT ENSG00000188909 0.57 12 10,961,112 11,122,296 YRI-CHB+JPT PRH1, TAS2R 0.49 MBD6, INHBC/E, GLI1, MARS, 12 56,116,000 56,288,135 CEU-YRI DDIT3, DCTN2, KIF5A, 0.59 PIP5K2C, DTX3 14 106,223,861 106,231,735 YRI-CHB+JPT no genes 0.46 17 18,175,250 18,350,351 CEU-YRI SHMT1 0.47 17 31,583,743 31,651,855 CEU-YRI CCL3L1 0.67* 17 41,635,804 41,722,491 CEU-CHB+JPT LRRC37A, MAPT 0.49* 18 26,068,546 26,069,966 YRI-CHB+JPT no genes 0.46 18 68,579,533 68,582,952 CEU-YRI NETO1 0.49 20 17,306,430 17,338,095 CEU-YRI PCSK2 0.50 22 43,439,702 43,531,066 CEU-YRI PRR5, ARHGAP8 0.46 Y 9,997,065 10,072,259 CEU-YRI TSPY 0.55 a Chromosomal coordinates refer to clones (WGTP) or CNVs (500K EA) that exhibit VST values above a threshold of 0.45.

Where multiple clones responding to the same CNV have high VST values, only the clone with the highest VST is given. b The pairwise population comparison in which this VST value is obtained

*CNVs that overlap regions of positive selection identified by Voight et al 2006 Supplementary Table 21A: Overlap between CNV regions and regions of positive selection

CNVs Voight et al. selected regions CNV / Voight-region Gene information CNV ID Chromosome Start End CNV size Platform Chromosome Start Endoverlap GeneSymb Description Source Access Zinc finger protein Rlf (Rearranged L-myc fusion RLF Uniprot/SWISSPROT Q13129 Chr_1_23 1 39894236 40329525 435289 WGTP 1 4025579940355799 73726 gene protein) U6 U6 spliceosomal RNA RFAM RF00026 Chr_1_32 1 73325120 73487705 162585 WGTP 1 73442105 73542105 45600 NULL 1 75689428 75789428 90503 NULL Chr_1_33 1 75698925 75899769 200844 WGTP 1 75789428 75889428 Full NULL Membrane-associated guanylate kinase-related 3 1 113613315 113713315 Full MAGI3 RefSeq_peptide NP_066016 isoform 1 Membrane-associated guanylate kinase-related 3 1 113913315 114013315 Full MAGI3 RefSeq_peptide NP_066016 Chr_1_52 1 112869177 116453414 3584237 WGTP isoform 1 PHTF1 Putative homeodomain transcription factor 1. Uniprot/SWISSPROT Q9UMS5 1 114013315 114113315 Full Tyrosine-protein phosphatase non-receptor type PTPN22 Uniprot/SWISSPROT Q9Y2R2 22. MTX1 Metaxin 1. Uniprot/SWISSPROT Q13505 GBA Glucosylceramidase precursor. Uniprot/SWISSPROT P04062 COTE1 COTE1 protein. Uniprot/SWISSPROT P81408

SCAMP3 Secretory carrier-associated membrane protein 3. Uniprot/SWISSPROT O14828 1 151996281 152096281 Full CLK2 Dual specificity protein kinase CLK2. Uniprot/SWISSPROT P49760 Potassium/sodium hyperpolarization-activated HCN3 Uniprot/SWISSPROT Q9P1Z3 cyclic nucleotide-gated channel 3. PKLR Pyruvate kinase, isozymes R/L. Uniprot/SWISSPROT P30613 Chr_1_61 1 151908051 152127880 219829 WGTP FDPS Farnesyl pyrophosphate synthetase. Uniprot/SWISSPROT P14324 Y Y RNA RFAM RF00019 EFNA1 Ephrin-A1 precursor. Uniprot/SWISSPROT P20827 RAG1AP1 Stromal cell protein RefSeq_peptide NP_061333

Uniprot/SWISSPROT Q9P2X0 1 151896281 151996281 88230 DPM3 Dolichol-phosphate mannosyltransferase subunit 3 KRTCAP2 Keratinocyte associated protein 2 RefSeq_peptide NP_776251 TRIM46 Tripartite motif protein 46. Uniprot/SWISSPROT Q7Z4K8 THBS3 Thrombospondin-3 precursor. Uniprot/SWISSPROT P49746 MTX1 Metaxin 1. Uniprot/SWISSPROT Q13505 Carboxyl-terminal PDZ ligand of neuronal nitric Chr_1_63 1 158796126 159235014 438888 Both 1 158744281 158844281 48155 NOS1AP Uniprot/SWISSPROT O75052 oxide synthase protein. Chr_1_76 1 190363185 190441853 78668 500K EA 1 190343398 190443398 Full ENSG00000194267 Chr_1_92 1 221394659 221560009 165350 WGTP 1 221432104 221532104 Full Q5VU34_HUMAN Novel protein (MGC27277). Uniprot/SPTREMBL Q5VU34

OR2L8 Olfactory receptor, family 2, subfamily L, member Uniprot/SWISSPROT Q8NGY9

Olfactory receptor,family 2, subfamilyAK, member Chr_1_105 1 244040626 244648357 607731Both 1 244428448 244528448 Full OR2AK2 Uniprot/SWISSPROT Q8NG84 2. Olfactory receptor, family 2, subfamily L, member OR2L2 Uniprot/SWISSPROT Q8NG80 2 Chr_2_40 2 64164656 64451207 286551 WGTP 2 64237117 64337117 Full PELI1 Pellino protein homolog 1. Uniprot/SWISSPROT Q96FA3

Chr_2_45 2 73628687 73990247 361560 WGTP 2 73837117 73937117 Full DUSP11 RNA/RNP complex-1 intereracting phosphatase. Uniprot/SWISSPROT O75319

PCGF1 polycomb group ring finger 1 RefSeq_peptide NP_116062 TLX2 T-cell leukemia homeobox protein 2 Uniprot/SWISSPROT O43763 DQX1 DEAQ box polypeptide 1 RefSeq_peptide NP_598376 Chr_2_46 2 74391579 74674080 282501 WGTP 2 74637117 74737117 36963 AUP1 Ancient ubiquitous protein 1 precursor. Uniprot/SWISSPROT Q9Y679

HTRA2 Serine protease HTRA2, mitochondrial precursor Uniprot/SWISSPROT O43464

LOXL3 Lysyl oxidase homolog 3 precursor. Uniprot/SWISSPROT P58215 2 78337118 78437118 Full NULL Chr_2_53 2 78038044 78622687 584643 WGTP 2 78437118 78537118 Full NULL CTNNA2 Alpha-2 catenin. Uniprot/SWISSPROT P26232 Chr_2_54 2 80312976 80754119 441143 WGTP 2 80437118 80537118 Full Leucine-rich repeat transmembrane neuronal LRRTM1 Uniprot/SWISSPROT Q86UE6 protein 1 precursor. 2 83337118 83437118 Full NULL Chr_2_56 2 83160508 83876420 715912 WGTP 2 83437118 83537118 Full NULL 2 108137118 108237118 Full NULL 2 108337118 108437118 Full SULT1C1 Sulfotransferase 1C1. Uniprot/SWISSPROT O00338 2 108437118 108537118 Full GCC2 Ran-binding protein 2-like 4. Uniprot/SWISSPROT Q4ZG46 Chr_2_66 2 107908395 108681855 773460 Both GCC2 Ran-binding protein 2-like 4. Uniprot/SWISSPROT Q4ZG46 2 108537118 108637118 Full SULT1C2 Sulfotransferase 1C2. Uniprot/SWISSPROT O75897 LIMS1 Protein PINCH. Uniprot/SWISSPROT P48059 Chr_2_73 2 122037995 122198553 160558 WGTP 2 122021085 122121085 83090 CLASP1 CLIP-associating protein 1. Uniprot/SWISSPROT Q7Z460 Chr_2_79 2 137031522 137074036 42514 500K EA 2 137022963 137122963 Full NULL Chr_2_94 2 194745343 194782381 37038 500K EA 2 194722963 194822963 Full ENSG00000183013 Amyotrophic lateral sclerosis 2 chromosome Chr_2_96 2 205365338 205666680 301342 WGTP 2 205322963 205422963 57625 ALS2CR19 Uniprot/SWISSPROT Q8TEW8 region candidate gene 19 protein. Chr_3_15 3 26021365 26194166 172801 Both 3 26000039 26100039 78674 ENSG00000179807 No_description Chr_3_24 3 45991468 46095404 103936 500K EA 3 46014412 46114412 80992 XCR1 Chemokine XC receptor 1. Uniprot/SWISSPROT P46094 WNT5A Wnt-5a protein precursor. Uniprot/SWISSPROT P41221 Chr_3_29 3 55465669 55640833 175164 WGTP 3 55417692 55517692 52023 ERC2_HUMAN ERC protein 2. Uniprot/SWISSPROT O15083 Limbic system-associated membrane protein Chr_3_49 3 117568368 117604638 36270 500K EA 3 117561789 117661789 Full LSAMP Uniprot/SWISSPROT Q13449 precursor. Limbic system-associated membrane protein Chr_3_50 3 117624820 117790232 165412 WGTP 3 117561789 117661789 36969 LSAMP Uniprot/SWISSPROT Q13449 precursor. 3 165261789 165361789 Full NULL Chr_3_78 3 165085151 165392762 307611 WGTP 3 165161789 165261789 Full NULL Chr_3_81 3 174622697 174928079 305382 WGTP 3 174661789 174761789 Full NULL Chr_3_94 3 199260725 199450740 190015 WGTP 3 199161690 199261690 965 NULL Chr_4_16 4 21549473 21656828 107355 WGTP 4 21525386 21625386 75913 KCNIP4 Kv channel-interacting protein 4. Uniprot/SWISSPROT Q6PIL6 Chr_4_24 4 28220227 28515706 295479 WGTP 4 28325386 28425386 Full ENSG00000193806 Chr_4_28 4 29805053 29963713 158660 WGTP 4 29925386 30025386 38327 NULL 4 34125386 34225386 Full NULL Chr_4_31 4 33971807 34297097 325290 Both 4 34225386 34325386 71711 NULL Chr_4_32 4 34459337 34779109 319772 WGTP 4 34425386 34525386 66049 NULL Chr_4_36 4 48890029 49501045 611016 Both 4 48825386 48925386 35357 NP_079363.1 No_description Chr_4_39 4 60959924 61146015 186091 WGTP 4 60925386 61025386 65462 NULL Chr_4_39 4 60959924 61146015 186091 WGTP 4 61025386 61125386 Full NULL Chr_4_55 4 104137960 104414925 276965 WGTP 4 104198784 104298784 Full ENSG00000164037 RefSeq_dna NM_139173 Chr_4_64 4 118836451 120032345 1195894 WGTP 4 118998784 119098784 Full NULL Chr_4_68 4 133511465 133655754 144289 WGTP 4 133498784 133598784 87319 NULL Chr_4_79 4 162141027 162312760 171733 500K EA 4 162279978 162379978 32782 NULL Chr_5_17 5 21184910 21748947 564037 WGTP 5 21690256 21790256 58691 NULL Chr_5_18 5 21814498 22199675 385177 WGTP 5 21790256 21890256 75758 NULL 5 21890256 21990256 Full CDH12 Brain-cadherin precursor. Uniprot/SWISSPROT P55289 Chr_5_18 5 21814498 22199675 385177 WGTP 5 21990256 22090256 Full CDH12 Brain-cadherin precursor. Uniprot/SWISSPROT P55289 Chr_5_29 5 55016652 55094749 78097 500K EA 5 54919872 55019872 3220 NP_775785.1 No_description 5 109751683 109851683 Full NULL 5 109851683 109951683 Full Q6ZV23_HUMAN Chr_5_55 5 109669759 110180038 510279 Both 5 110051683 110151683 Full NP_620128.1 5 110151683 110251683 28355 NULL Chr_5_75 5 156930186 157165622 235436 WGTP 5 157151683 157251683 13939 EPN4_HUMAN Epsin-4. Uniprot/SWISSPROT Q14677 6 34661123 34761123 Full NP_073595.2 Chr_6_18 634490470 34822655 332185 WGTP 6 34761123 34861123 61532 NULL Chr_6_34 6 63764581 64043848 279267 WGTP 6 63761123 63861123 96542 NULL Chr_6_42 6 75018716 75218942 200226 Both 6 75161123 75261123 57819 NULL Chr_6_57 6 93634138 93728395 94257 500K EA 6 93661123 93761123 67272 NULL

Chr_6_82 6 158649279 158728910 79631 500K EA 6 158661123 158761123 67787 TULP4 Tubby-like protein 4 (Tubby superfamily protein). Uniprot/SWISSPROT Q9NRJ4

7 84732600 84832600 34627 NULL Chr_7_45 7 84797973 84962693 164720 WGTP 7 84832600 84932600 Full NULL

IMMP2L IMP2 inner mitochondrial membrane protease-like RefSeq_peptide NP_115938 Chr_7_57 7 110117249 110381800264551 WGTP 7 110333420 110433420 48380 LRRN3 leucine rich repeat neuronal 3 RefSeq_peptide NP_060804

Chr_7_58 7 110394862 110898776 503914 WGTP 7 110433420 110533420 Full IMMP2L IMP2 inner mitochondrial membrane protease-like RefSeq_peptide NP_115938 CNVs Voight et al. selected regions CNV / Voight-region Gene information CNV ID Chromosome Start End CNV size Platform Chromosome Start Endoverlap GeneSymb Description Source Access 7 133241128 133341128 39924 NP_653249.1 No_description Chr_7_68 7 133094440 133281052 186612 WGTP 7 133041126 133141128 46688 EXOC4 Exocyst complex component 4 Uniprot/SWISSPROT Q96A65 8 50712593 50812593 Full NULL Chr_8_32 8 50577786 50819905 242119 Both 8 50812593 50912593 7312 NULL 8 51912593 52012593 Full NULL Chr_8_34 8 51912593 52045960 133367 500K EA 8 52012593 52112593 33367 NULL Chr_8_55 8 102678650 102718857 40207 500K EA 8 102612593 102712593 33943 GRHL2 Transcription factor CP2-like 3 RefSeq_peptide NP_079191 Chr_8_61 8 129633607 129784954 151347 WGTP 8 129712593 129812593 72361 NULL 8 12500000 12600000 Full NULL Chr_9_18 9 12225048 12774092 549044 WGTP 5,6-dihydroxyindole-2-carboxylic acid oxidase 8 12600000 12700000 Full TYRP1 Uniprot/SWISSPROT P17643 precursor. Chr_9_29 9 24457996 24518103 60107 500K EA 9 24400000 24500000 42004 NULL Chr_9_37 9 33794006 33809555 15549 500K EA 9 33800000 33900000 9555 UBE2R2 Ubiquitin-conjugating enzyme UBC3B RefSeq_peptide NP_060281 Amyloid beta A4 precursor protein-binding family A Chr_9_41 9 69247800 69277652 29852 500K EA 9 69272435 69372435 5217 APBA1 Uniprot/SWISSPROT Q02410 member 1. Amyloid beta A4 precursor protein-binding family A Chr_9_42 9 69330123 69363930 33807 500K EA 9 69272435 69372435 Full APBA1 Uniprot/SWISSPROT Q02410 member 1. PHPT1 14 kDa phosphohistidine phosphatase. Uniprot/SWISSPROT Q9NRX4 MAMDC4 Apical early endosomal glycoprotein RefSeq_peptide NP_996803 Chr_9_67 9 136526666 137102322 575656 WGTP 9 137018544 137118544 83778 EDF1 Endothelial differentiation-related factor 1. Uniprot/SWISSPROT O60869 TRAF2 TNF receptor-associated factor 2. Uniprot/SWISSPROT Q12933 Chr_10_38 10 59214388 59489499 275111 WGTP 10 59225403 59325403 Full NULL Chr_10_45 10 74105644 74277126 171482 WGTP 10 74025403 74125403 19759 NP_612366.1 10 102125403 102225403 83563 NULL Chr_10_57 10 102141840 102555726 413886 WGTP 10 102225403 102325403 Full HIF1AN Hypoxia-inducible factor 1 alpha inhibitor. Uniprot/SWISSPROT Q9NWT6 11 24992267 25092267 46979 LUZP2 leucine zipper protein 2 RefSeq_peptide NP_001009909 Chr_11_17 11 25045288 25322096 276808 Both 11 25292267 25392267 29829 NULL Chr_11_28 11 38401344 38437928 36584 500K EA 11 38392267 38492267 Full NULL Olfactory receptor, family 4, subfamily C, member OR4C3 Uniprot/SWISSPROT Q8NH37 3. Chr_11_31 11 48260247 49141766 881519 WGTP 11 48292267 48392267 Full Olfactory receptor, family 4, subfamily C, member OR4C5 Uniprot/SWISSPROT Q8NGB2 5 Chr_11_38 11 60671936 60837233 165297 WGTP 11 60581216 60681216 9280 VPS37C Vacuolar protein sorting 37C RefSeq_peptide NP_060436 Chr_11_50 11 80996713 81508270 511557 Both 11 80951340 81051340 54627 NULL Chr_12_8 12 20833482 21009087 175605 WGTP 12 21000000 21100000 9087 NULL Chr_12_33 12 70388731 70594440 205709 WGTP 12 70400000 70500000 Full RAB21 Ras-related protein Rab-21. Uniprot/SWISSPROT Q9UL25 13 56500000 56600000 76375 NULL Chr_13_16 13 56523625 56824435 300810 Both 13 56700000 56800000 Full ENSG00000178196 13 56800000 56900000 24435 NULL LIM domain only protein 7 (LOMP) (F-box only Chr_13_27 13 75219611 75440004 220393 WGTP 13 75200000 75300000 80389 LMO7 Uniprot/SWISSPROT Q8WWI1 protein 20). Chr_13_44 13 110460034 110604912 144878 WGTP 13 110500000 110600000 Full ARHGEF7 Rho guanine nucleotide exchange factor 7. Uniprot/SWISSPROT Q14155 14 59479712 59579712 Full NP_940901.1 Chr_14_23 14 59477247 59652794 175547 WGTP 14 59579712 59679712 73082 NULL Chr_14_43 14 103217278 103482566 265288 WGTP 14 103479712 103579712 2854 NULL Chr_15_9 15 32330313 32775539 445226 WGTP 15 32271236 32371236 40923 SLC12A6 Solute carrier family 12 member 6 Uniprot/SWISSPROT Q9UHW9

Chr_15_11 15 38619837 38782403 162566 WGTP 15 38671236 38771236 Full CASC5 Cancer susceptibility candidate gene 5 protein. Uniprot/SWISSPROT Q8NG31

SLC12A1 Solute carrier family 12 member 1 Uniprot/SWISSPROT Q13621 Y Y RNA RFAM RF00019 Chr_15_15 15 46296330 46451070 154740 WGTP 15 46371236 46471236 79834 Deoxyuridine 5'-triphosphate nucleotidohydrolase, DUT Uniprot/SWISSPROT P33316 mitochondrial precursor

ATP6V0C Vacuolar ATP synthase 16 kDa proteolipid subunit. Uniprot/SWISSPROT P27449 Chr_16_3 16 2476826 2810537 333711 WGTP 16 2500444 2600450 Full PDPK1 3-phosphoinositide dependent protein kinase 1. Uniprot/SWISSPROT O15530

CHST6 Carbohydrate sulfotransferase 6 Uniprot/SWISSPROT Q9GZX3 Chr_16_40 16 73977115 74134472 157357WGTP 16 74077948 74177948 56524 CHST5 Carbohydrate sulfotransferase 5 Uniprot/SWISSPROT Q9GZS9 Chr_16_45 16 78452465 78480811 28346 500K EA 16 78377974 78477974 25509 NULL 17 41480361 41580361 Full KIAA1267 Uniprot/SWISSPROT Q7Z3B3 Chr_17_21 17 41439751 42632332 1192581 WGTP 17 41580361 41680361 Full LRRC37A Uniprot/SWISSPROT Homo sapiens leucine rich repeat containing 37A. Q8IWC7 Chr_18_6 18 11887023 12066102 179079 WGTP 18 11900000 12000000 Full IMPA2 Inositol monophosphatase 2. Uniprot/SWISSPROT O14732 Chr_18_10 18 24413258 24450849 37591 500K EA 18 24402011 24502011 Full NULL Chr_18_30 18 64888576 64912007 23431 500K EA 18 64802011 64902011 13435 U2 U2 spliceosomal RNA Q7Z3Q9_HUMAN No_description Chr_19_18 19 42486690 42743446256756 500K EA 19 42700000 42800000 43446 Q8N3U1_HUMAN No_description Protein tyrosine phosphatase non-receptor type PTPNS1L2 Uniprot/SWISSPROT Q9H106 Chr_20_2 20 1424781 1627256 202475 WGTP 20 1453000 1553000 Full substrate 1-like 2 precursor. SIRPB1 Signal-regulatory protein beta-1 precursor. Uniprot/SWISSPROT O00241 21 45968226 46068226 766 NULL NULL Chr_21_14 2146067460 46144196 76736 500K EA 21 46068226 46168226 75970 PCBP3 Poly(rC)-binding protein 3. Uniprot/SWISSPROT P57721 Chr_23_12 X 27751188 31356624 3605436 500K EA X 30098231 30198231 Full NULL Chr_23_18 X 66282690 67102115 819425 Both X 66916230 67016230 Full NULL X 126919912 127019912 99310 U1 No_description Chr_23_39 X 126868603 127019222 150619 WGTP X 126819912 126919912 51309 ACTRT1 Actin-related protein T1 RefSeq_peptide NP_612146 Chr_23_42 X 134328057 134880261 552204 WGTP X 134419913 134519913 Full DDX26B Protein DDX26B. Uniprot/SWISSPROT Q5JSJ4 Supplementary Table 21A: Overlap between the WGTP and the 500K EA CNV regions, and regions of positive selection reported in the genomewide survey of Voight et al. In the column 'overlap' the word "full" refers to either the CNV containing the entire selected region, or the selected region containing the entire CNV. The genes listed are those present in the selected region or in the portion overlapping with the CNV. Supplementary Table 21B: Selection Summary

>95th >99th Haplotype EHH REHH Population Region Chr CNV_start CNV_end EHH REHH Genes percentile percentile Frequency p_value p_value

Asia Downstream 1 149,320,000 149,500,000 X 0.326 0.242 4.682 0.027 0.031 LCE2, 3, 4 gene family

SYNPO, MYOZ3, RBM22, Asia Downstream 5 149,950,000 150,250,000 X 0.399 0.249 6.296 0.036 0.027 DCTN4

Asia Downstream 6 32,503,398 32,593,944 X 0.371 0.228 6.667 0.051 0.023 HLA-DRA, HLA-DRB9

Asia Downstream 7 105,179,617 105,181,392 X 0.028 0.600 9.831 0.021 0.110 NULL

Asia Downstream 11 5,734,586 5,774,897 X 0.146 0.338 6.561 0.054 0.049 OR52N5, OR52N1

Asia Downstream 11 98,679,357 98,691,890 X 0.039 0.333 8.621 0.114 0.132 NULL

Asia Downstream 14 19,402,695 19,435,240 X 0.562 0.133 3.553 0.075 0.043 OR4K2

Asia Downstream 18 63,111,650 63,119,574 X 0.236 0.338 7.661 0.021 0.015 NULL

Asia Downstream 21 22,577,771 22,586,139 X 0.433 0.198 4.692 0.067 0.053 NULL

Asia Upstream 4* 34,500,000 34,750,000 X 0.955 0.359 10.040 0.045 0.000 NULL

Asia Upstream 6 81,332,831 81,357,777 X 0.174 0.499 9.215 0.005 0.009 NULL

Asia Upstream 18 63,111,650 63,119,574 X 0.236 0.278 6.585 0.052 0.025 NULL

Asia Upstream 21 22,577,771 22,586,139 X 0.433 0.221 7.034 N.A. N.A. NULL

CEU Downstream 1 112,407,136 112,421,327 X 0.289 0.199 5.542 0.118 0.041 NULL

CEU Downstream 1 149,320,000 149,500,000 X 0.400 0.243 6.015 0.010 0.014 LCE2, 3, 4 gene family

CEU Downstream 1 192,669,983 192,672,977 X 0.261 0.273 6.371 0.031 0.025 NULL

CEU Downstream 6 150,000 360,000 X 0.867 0.063 1.583 0.119 0.022 DUSP22, IRF4

CEU Downstream 6 103,834,514 103,911,696 X 0.561 0.125 3.085 0.056 0.045 NULL

CEU Downstream 11 5,734,586 5,774,897 X 0.206 0.285 8.323 0.050 0.017 OR52N5, OR52N1

CEU Downstream 11 98,679,357 98,691,890 X 0.111 0.500 12.278 0.028 0.024 NULL

CEU Downstream 14 19,402,695 19,435,240 X 0.661 0.100 3.322 0.024 0.004 OR4K2

CEU Upstream 3 131,233,075 131,291,453 X 0.400 0.223 5.113 0.013 0.022 NULL

CEU Upstream 6 77,496,587 77,529,522 X 0.256 0.329 9.261 0.019 0.010 NULL

CEU Upstream 14 19,402,695 19,435,240 X 0.661 0.086 2.315 0.078 0.038 OR4K2

SERHL, SERHL2, 7SK, CEU Upstream 22 41,170,000 41,370,000 X 0.872 0.055 0.998 N.A. N.A. POLDIP3, CYB5R3

YRI Downstream 1 142,400,000 142,850,000 X 0.667 0.093 1.892 0.034 0.036 PDE4DIP, SEC22L1

YRI Downstream 1 193,424,505 193,544,439 X 0.589 0.124 3.763 0.026 0.014 CFH, CFHL3, CFHL1P

YRI Downstream 11 104,428,916 104,436,443 X 0.111 0.605 17.301 0.031 0.019 CASP1

YRI Downstream 12 9,420,000 9,680,000 X 0.661 0.099 2.775 0.020 0.009 KLRB1

KIR2DS1, KIR2DL1, YRI Downstream 19 59,944,016 60,040,503 X 0.111 0.721 17.844 0.016 0.017 KIR3DP1

YRI Upstream 6 29,967,224 29,982,554 X 0.122 0.827 20.227 0.008 0.010 HLA-J

*This region partially overlap with one of the Voight et al. selected regions described in supplementary table 21A N.A. = not available