Table S1. Outlier loci detected by DeepGenomeScan using geographic coordinates. Loci highlighted in red are detected by DeepGenomeScan but are not listed in Yang et al. (2012; Supplementary Table 4). RsID is annotated according to the dbSNP database released on 21st April, 2020.

CHR BP (Grch37) BP (Grch38) rsID p.value Genes 1 1:4208918 1:4148858 rs9426495 3.8582E-104 1 1:175738168 1:175769032 rs6425357 2.0088E-105 2 2:20310668 2:20110907 rs11679737 1.2002E-111 LAPTM4A-DT 2 2:40289267 2:40062127 rs759361 5.5658E-104 SLC8A1-AS1 2 2:82495127 2:82268003 rs6726401 3.9451E-103 2 2:96660300 2:95994552 rs2579520 1.8176E-127 2 2:96672001 2:96006253 rs1917890 3.7698E-104 2 2:134333012 2:133575441 rs17816830 9.702E-105 NCKAP5 2 2:134350570 2:133592999 rs6715224 5.8745E-111 NCKAP5 2 2:134912243 2:134154672 rs2139309 1.7418E-191 MGAT5 2 2:134917005 2:134159434 rs11692586 9.2121E-151 MGAT5 2 2:134972732 2:134215161 rs11679218 0 MGAT5 2 2:134979966 2:134222395 rs1965183 5.3171E-107 MGAT5 2 2:135260071 2:134502500 rs503562 2.057E-153 TMEM163 2 2:135280039 2:134522468 rs579670 3.1477E-118 TMEM163 2 2:135285279 2:134527708 rs512375 0 TMEM163 2 2:135290221 2:134532650 rs655472 0 TMEM163 2 2:135290453 2:134532882 rs666614 0 TMEM163 2 2:135340840 2:134583270 rs842361 5.6717E-237 TMEM163 2 2:135393110 2:134635540 rs11684785 2.2164E-276 TMEM163 2 2:135430709 2:134673139 rs6745983 0 TMEM163 2 2:135469769 2:134712199 rs6747870 9.6117E-114 TMEM163 2 2:135483381 2:134725811 rs3739034 5.0357E-154 2 2:135483534 2:134725964 rs3739036 3.7269E-156 2 2:135539967 2:134782397 rs6430538 0 2 2:135602601 2:134845031 rs6430545 0 ACMSD 2 2:135606879 2:134849309 rs1530557 0 ACMSD 2 2:135612422 2:134854852 rs6430547 0 ACMSD 2 2:135618982 2:134861412 rs6706537 0 ACMSD 2 2:135623517 2:134865947 rs7593370 0 ACMSD 2 2:135629927 2:134872357 rs12469941 0 ACMSD, CCNT2-AS1 2 2:135637338 2:134879768 rs2166480 0 ACMSD, CCNT2-AS1 2 2:135657471 2:134899901 rs10176573 0 ACMSD, CCNT2-AS1 2 2:135693537 2:134935967 rs6743206 2.0048E-214 CCNT2 2 2:135694379 2:134936809 rs1374289 0 CCNT2 2 2:135694848 2:134937278 rs4953938 0 CCNT2 2 2:135737908 2:134980338 rs4954209 4.6215E-270 MAP3K19 2 2:135762344 2:135004774 rs16831243 2.8757E-253 MAP3K19

1

2 2:135762656 2:135005086 rs10197646 3.3948E-218 MAP3K19 2 2:135775130 2:135017560 rs7581382 0 MAP3K19 2 2:135803425 2:135045855 rs4954218 0 MAP3K19 2 2:135907088 2:135149518 rs6730157 0 RAB3GAP1 2 2:136388473 2:135630903 rs10187054 0 R3HDM1 2 2:136419961 2:135662391 rs1446584 0 R3HDM1 2 2:136420690 2:135663120 rs4954280 0 R3HDM1 2 2:136462661 2:135705091 rs2117511 3.0786E-143 R3HDM1 2 2:136499166 2:135741596 rs1438307 0 UBXN4, LOC107985946 2 2:136506927 2:135749357 rs6430585 0 UBXN4 2 2:136545844 2:135788274 rs1042712 0 LCT 2 2:136555525 2:135797955 rs2015532 0 LCT 2 2:136556182 2:135798612 rs3769013 2.3001E-307 LCT 2 2:136556480 2:135798910 rs3769012 0 LCT 2 2:136556805 2:135799235 rs872151 6.4599E-149 LCT 2 2:136557319 2:135799749 rs2322660 0 LCT 2 2:136561557 2:135803987 rs2304371 0 LCT 2 2:136571982 2:135814412 rs4954445 3.6282E-117 LCT 2 2:136614255 2:135856685 rs309180 0 MCM6 2 2:136628121 2:135870551 rs4988163 4.0179E-286 MCM6 2 2:136637350 2:135879780 rs16832138 1.5766E-116 2 2:136641593 2:135884023 rs7581814 0 2 2:136694905 2:135937335 rs7573555 0 DARS1 2 2:136702601 2:135945031 rs6743537 0 DARS1 2 2:136719173 2:135961603 rs6430594 0 DARS1 2 2:136765951 2:136008381 rs309137 0 2 2:136770509 2:136012939 rs12471781 0 2 2:136786651 2:136029081 rs12475139 0 2 2:136806774 2:136049204 rs7371606 0 2 2:136808949 2:136051379 rs11693502 0 2 2:136910273 2:136152703 rs6715785 0 2 2:136921703 2:136164133 rs10180515 2.2455E-281 2 2:136956733 2:136199163 rs7578292 3.7209E-216 2 2:136963794 2:136206224 rs12691876 1.3461E-265 2 2:136973781 2:136216211 rs1519528 9.1417E-244 LOC107985947 2 2:137037386 2:136279816 rs4954599 1.0298E-196 2 2:137057148 2:136299578 rs13008975 1.6878E-135 2 2:137058248 2:136300678 rs4296479 4.9792E-133 2 2:137058433 2:136300863 rs4599171 4.0031E-214 2 2:137197151 2:136439581 rs7561441 5.3311E-173 2 2:137300091 2:136542521 rs10205768 5.1224E-276 2 2:137341944 2:136584374 rs12691894 1.1911E-163

2

2 2:137433213 2:136675643 rs11681380 1.5164E-192 2 2:137475070 2:136717500 rs7582192 5.155E-212 2 2:137496806 2:136739236 rs10199153 8.9959E-130 2 2:137512698 2:136755128 rs7564005 2.1506E-128 2 2:137514418 2:136756848 rs1427591 1.253E-146 2 2:137610518 2:136852948 rs778207 2.4208E-196 THSD7B 2 2:137612229 2:136854659 rs778202 2.0497E-109 THSD7B 2 2:137614786 2:136857216 rs1429978 3.9634E-206 THSD7B 2 2:160867553 2:160011042 rs2667012 1.0935E-118 PLA2R1 2 2:160891688 2:160035177 rs17830904 6.4076E-116 PLA2R1 2 2:160906931 2:160050420 rs10929965 7.3545E-120 PLA2R1 2 2:160912652 2:160056141 rs925410 2.3118E-126 PLA2R1, LOC105373717 2 2:160914156 2:160057645 rs17831251 3.7725E-121 PLA2R1, LOC105373717 2 2:160914540 2:160058029 rs6707458 5.846E-116 PLA2R1, LOC105373717 2 2:160915106 2:160058595 rs16844715 4.6953E-126 PLA2R1, LOC105373717 2 2:166924472 2:166067962 rs1461197 2.2877E-104 SCN1A 2 2:174486590 2:173621862 rs6722856 2.9251E-127 LOC107985961 2 2:177977545 2:177112817 rs2588865 3.7631E-139 LOC105373760 2 2:177991618 2:177126890 rs2706137 3.1043E-172 LOC105373760 3 3:45846769 3:45805277 rs17763742 1.8336E-162 LOC107986082 3 3:81427818 3:81378667 rs275360 3.1048E-120 3 3:127416142 3:127697299 rs782440 1.8735E-121 MGLL 3 3:127417202 3:127698359 rs782437 9.6119E-114 MGLL 3 3:127426929 3:127708086 rs1071912 2.7892E-104 MGLL 3 3:178429939 3:178712151 rs9290663 4.5367E-112 KCNMB2, KCNMB2-AS1 3 3:178995657 3:179277869 rs9813206 3.7674E-125 4 4:14093170 4:14091546 rs7673306 4.0281E-109 4 4:38768533 4:38766912 rs10470854 4.5861E-114 4 4:38776303 4:38774682 rs11466652 5.0508E-141 TLR10 4 4:38776491 4:38774870 rs11096957 8.3115E-109 TLR10 4 4:38783964 4:38782343 rs4321646 1.4399E-155 TLR10 4 4:38787216 4:38785595 rs12233670 4.7111E-144 4 4:38894380 4:38892759 rs6835514 4.1487E-200 FAM114A1 4 4:38908038 4:38906417 rs4832790 7.1817E-108 FAM114A1 4 4:84909466 4:83988313 rs4693665 5.537E-127 LOC101928978 4 4:100260274 4:99339117 rs1693476 2.4983E-155 ADH1C 4 4:100262041 4:99340884 rs1789903 2.3041E-165 ADH1C 4 4:100263778 4:99342621 rs1789911 5.5025E-158 ADH1C 4 4:100285148 4:99363991 rs1154435 9.4022E-145 4 4:103243101 4:102321944 rs17278473 2.2816E-103 SLC39A8 4 4:112051824 4:111130668 rs294942 1.1955E-129 5 5:36368967 5:36368865 rs4602650 3.9055E-113

3

5 5:110472967 5:111137269 rs464275 2.278E-141 6 6:27987776 6:28019998 rs149976 5.1992E-136 6 6:28100640 6:28132862 rs1225710 5.0364E-157 ZSCAN16-AS1 6 6:28113373 6:28145595 rs1225715 1.3359E-139 ZKSCAN8 6 6:28391465 6:28423688 rs2859365 3.2334E-133 LOC105374997 6 6:28415572 6:28447795 rs13215804 1.458E-224 6 6:28417222 6:28449445 rs6903535 1.1153E-191 6 6:28542520 6:28574743 rs370520 7.3625E-166 ZBED9 6 6:28665362 6:28697585 rs7382146 5.3108E-300 LOC101929006, 6 6:29256420 6:29288643 rs1884123 2.2056E-105 LOC105375005 6 6:30103360 6:30135583 rs1541269 1.1572E-107 TRIM40 6 6:30152467 6:30184690 rs11158 4.2464E-119 TRIM26 6 6:30328192 6:30360415 rs3130351 1.0679E-104 6 6:30363351 6:30395574 rs3094034 2.9109E-102 6 6:30739972 6:30772195 rs3132605 2.572E-102 HCG20 6 6:31025713 6:31057936 rs2517524 7.1036E-144 HCG22 6 6:31030122 6:31062345 rs2517510 2.4694E-197 6 6:31030283 6:31062506 rs2523841 2.188E-123 6 6:31030425 6:31062648 rs2523840 4.7541E-127 6 6:31042070 6:31074293 rs2523883 4.2821E-181 6 6:31042306 6:31074529 rs2517489 2.4633E-192 6 6:31042608 6:31074831 rs2523881 6.9967E-188 6 6:31042769 6:31074992 rs2523880 2.4424E-165 6 6:31051388 6:31083611 rs2535318 1.4176E-189 6 6:31052098 6:31084321 rs2517471 9.6266E-197 6 6:31053867 6:31086090 rs2535306 5.342E-202 6 6:31172655 6:31204878 rs2894180 8.1758E-109 6 6:31255500 6:31287723 rs2524051 2.4487E-163 6 6:31265554 6:31297777 rs2524115 3.9166E-141 LINC02571, LOC112267902 6 6:31277686 6:31309909 rs1634788 6.1552E-102 LOC112267902 6 6:31333939 6:31366162 rs7761068 1.6372E-158 6 6:31336649 6:31368872 rs2523533 5.5187E-127 6 6:31379931 6:31412154 rs1063635 2.1436E-251 MICA 6 6:31777946 6:31810169 rs2075800 4.1936E-126 HSPA1L 6 6:31856070 6:31888293 rs486416 0 EHMT2 6 6:31883957 6:31916180 rs644045 7.5006E-221 C2 6 6:31919578 6:31951801 rs2072633 0 CFB, NELFE 6 6:32179896 6:32212119 rs2071286 2.5495E-111 NOTCH4 6 6:32200147 6:32232370 rs3134926 2.8449E-106 6 6:32216850 6:32249073 rs3115576 4.511E-241 6 6:32217367 6:32249590 rs3130311 2.0337E-237 6 6:32288190 6:32320413 rs574710 1.366E-230 TSBP1, TSBP1-AS1

4

6 6:32305690 6:32337913 rs926591 1.3828E-249 TSBP1, TSBP1-AS2 6 6:32313097 6:32345320 rs4959093 1.0302E-241 TSBP1, TSBP1-AS3 6 6:32389512 6:32421735 rs9268560 5.1383E-297 6 6:32408527 6:32440750 rs9268645 1.172E-227 HLA-DRA 6 6:32429758 6:32461981 rs9268858 2.0363E-156 6 6:32431147 6:32463370 rs9268877 0 6 6:32626272 6:32658495 rs9273363 5.5519E-129 HLA-DQB1-AS1 6 6:32635296 6:32667519 rs6908943 3.3296E-144 HLA-DQB1 6 6:32689529 6:32721752 rs9461799 2.3913E-199 6 6:32690001 6:32722224 rs9469240 2.4622E-170 6 6:32711782 6:32744005 rs2227127 9.9757E-175 HLA-DQA2 6 6:32712384 6:32744607 rs9276432 1.1768E-129 HLA-DQA2 6 6:32736144 6:32768367 rs9296044 6.0615E-120 6 6:32965942 6:32998165 rs176248 3.5831E-139 6 6:79190083 6:78480366 rs10943541 5.1113E-117 6 6:79212957 6:78503240 rs4632856 4.0872E-115 6 6:79232161 6:78522444 rs4706060 5.8085E-109 6 6:152942821 6:152621686 rs1744380 4.3781E-102 SYNE1 6 6:152950053 6:152628918 rs2057399 2.4192E-115 SYNE1 6 6:152966084 6:152644949 rs2758813 1.212E-121 6 6:153007917 6:152686782 rs2800629 8.0585E-128 LOC105378061 6 6:153047588 6:152726453 rs17782898 4.0948E-118 MYCT1 7 7:16581890 7:16542265 rs6945188 4.6453E-101 LRRC72 7 7:17827885 7:17788261 rs1830006 1.837E-109 7 7:17978129 7:17938506 rs6973480 1.5727E-113 SNX13 7 7:45247913 7:45208314 rs4724376 3.0209E-111 7 7:70705454 7:71240468 rs6974582 4.6209E-103 GALNT17 7 7:70706501 7:71241515 rs7811880 1.2501E-153 GALNT17 7 7:113954435 7:114314380 rs2690830 3.6717E-132 FOXP2 7 7:114122506 7:114482451 rs2106900 3.3647E-101 FOXP2 7 7:114374351 7:114734296 rs983483 2.1514E-105 7 7:140975246 7:141275446 rs10247172 1.8457E-123 TMEM178B 8 8:1359156 8:1410990 rs17680989 5.3562E-115 DLGAP2 8 8:40575914 8:40718395 rs10091954 1.6933E-105 ZMAT4 8 8:130269687 8:129257441 rs4451275 3.8653E-113 8 8:130269722 8:129257476 rs4451270 5.7863E-114 8 8:130289225 8:129276979 rs4373494 7.9365E-122 9 9:90135027 9:87520112 rs17399090 2.0581E-144 DAPK1 10 10:55958039 10:55958039 rs1296967295 2.6581E-106 10 10:60614717 10:58854957 rs7350384 2.0792E-226 11 11:8589648 11:8568101 rs9736791 1.2434E-118 STK33 11 11:18357270 11:18335723 rs4150581 3.2786E-109 GTF2H1

5

11 11:101235197 11:101364466 rs11224733 5.5218E-144 11 11:101262425 11:101391694 rs1938988 5.2617E-159 11 11:101300187 11:101429456 rs11224760 2.4771E-213 11 11:106318065 11:106447338 rs2513606 1.695E-108 11 11:106327768 11:106457041 rs12798744 3.4332E-175 11 11:106330162 11:106459435 rs10895959 1.0402E-116 12 12:1478570 12:1369404 rs11061714 1.8317E-102 ERC1 12 12:4228310 12:4119144 rs11063004 4.2892E-123 12 12:4237871 12:4128705 rs12579556 6.2258E-113 12 12:4240146 12:4130980 rs2160161 6.5504E-144 12 12:129905838 12:129421293 rs10773658 4.7388E-101 TMEM132D 12 12:129922249 12:129437704 rs11060347 5.2467E-117 TMEM132D 13 13:91070322 13:90418068 rs7997970 5.0695E-105 14 14:89901962 14:89435618 rs12885505 7.4002E-172 FOXN3 15 15:28080166 15:27835020 rs4778193 8.9648E-141 OCA2 15 15:28114289 15:27869143 rs4778201 1.105E-129 OCA2 15 15:28282741 15:28037595 rs1448485 3.3745E-200 OCA2 15 15:28283507 15:28038361 rs16950821 1.2125E-180 OCA2 15 15:28283689 15:28038543 rs8024968 8.2734E-184 OCA2 15 15:28443658 15:28198512 rs8041209 5.1245E-155 HERC2 15 15:28488888 15:28243742 rs8028689 3.0103E-163 HERC2 15 15:28496195 15:28251049 rs6497292 5.681E-172 HERC2 15 15:28510895 15:28265749 rs2240202 3.5215E-161 HERC2 15 15:28513364 15:28268218 rs916977 0 HERC2 15 15:28530359 15:28285213 rs12592730 8.478E-169 HERC2 15 15:84444878 15:83776126 rs11638104 3.9276E-176 ADAMTSL3 16 16:7081093 16:7031092 rs11645481 3.6133E-142 RBFOX1 PRM2, PRM3, 16 16:11369205 16:11275348 rs1559394 6.4488E-112 LOC105371082 16 16:11390728 16:11296871 rs11640295 2.3271E-101 LOC105371082 16 16:83896399 16:83862794 rs409861 7.3593E-104 17 17:60680468 17:62603107 rs6504112 5.4294E-110 TLK2 17 17:70097607 17:72101466 rs9894720 9.3284E-136 SOX9-AS1 18 18:63318342 18:65651106 rs10871590 3.2234E-121 18 18:63415573 18:65748337 rs10460125 3.7546E-161 CDH7 18 18:63435260 18:65768024 rs7237421 4.0738E-160 CDH7 18 18:63439141 18:65771905 rs8092259 4.3346E-161 CDH7 18 18:63443029 18:65775793 rs7228669 1.2715E-153 CDH7 18 18:63444000 18:65776764 rs1942831 2.7634E-170 CDH7 18 18:63444300 18:65777064 rs8093720 3.7572E-161 CDH7 Notes: p-values smaller than 2.225074e-308 are treated as 0 based on the algorithm of Cody's (1988) subroutine MACHAR in current implementations of R use 32-bit integers and use IEC 60559 floating-point (double precision) arithmetic.

6

Table S2. Outlier loci detected by DeepGenomeScan based on KLFDAPC reduced axes. Loci highlighted in red are detected by DeepGenomeScan but are not listed in Yang et al. (2012; Supplementary Table 4). SNP RsID is annotated according to the dbSNP database released on 21st April, 2020.

CHR BP (Grch37) BP (Grch38) rsID p.value Genes 1 1:59649116 1:59183444 rs9660067 4.6169E-106 1 1:76083408 1:75617723 rs2057519 6.8732E-166 SLC44A5 1 1:76083667 1:75617982 rs4949869 3.7033E-131 SLC44A5 1 1:77944732 1:77479047 rs11162351 3.708E-158 AK5 1 1:153206051 1:153233575 rs16835086 4.9789E-146 1 1:154316434 1:154343958 rs2274988 3.0212E-129 ATP8B2 1 1:175738168 1:175769032 rs6425357 3.993E-138 2 2:62814166 2:62587031 rs6545961 8.1011E-133 2 2:62822891 2:62595756 rs6545963 5.0936E-148 2 2:134333012 2:133575441 rs17816830 7.577E-106 NCKAP5 2 2:134350570 2:133592999 rs6715224 7.4205E-116 NCKAP5 2 2:134912243 2:134154672 rs2139309 1.0862E-141 MGAT5 2 2:134917005 2:134159434 rs11692586 1.2038E-109 MGAT5 2 2:134972732 2:134215161 rs11679218 1.9411E-294 MGAT5 2 2:135260071 2:134502500 rs503562 1.2038E-134 TMEM163 2 2:135280039 2:134522468 rs579670 1.6506E-104 TMEM163 2 2:135285279 2:134527708 rs512375 0 TMEM163 2 2:135290221 2:134532650 rs655472 0 TMEM163 2 2:135290453 2:134532882 rs666614 0 TMEM163 2 2:135340840 2:134583270 rs842361 0 TMEM163 2 2:135393110 2:134635540 rs11684785 0 TMEM163 2 2:135430709 2:134673139 rs6745983 0 TMEM163 2 2:135469769 2:134712199 rs6747870 3.621E-148 TMEM163 2 2:135483381 2:134725811 rs3739034 1.3986E-179 2 2:135483534 2:134725964 rs3739036 1.3795E-186 2 2:135539967 2:134782397 rs6430538 0 2 2:135602601 2:134845031 rs6430545 0 ACMSD 2 2:135606879 2:134849309 rs1530557 0 ACMSD 2 2:135612422 2:134854852 rs6430547 0 ACMSD 2 2:135618982 2:134861412 rs6706537 0 ACMSD 2 2:135623517 2:134865947 rs7593370 0 ACMSD 2 2:135629927 2:134872357 rs12469941 0 ACMSD, CCNT2-AS1 2 2:135637338 2:134879768 rs2166480 0 ACMSD, CCNT2-AS1 2 2:135657471 2:134899901 rs10176573 0 ACMSD, CCNT2-AS1 2 2:135693537 2:134935967 rs6743206 0 CCNT2 2 2:135694379 2:134936809 rs1374289 0 CCNT2 2 2:135694848 2:134937278 rs4953938 0 CCNT2 2 2:135737908 2:134980338 rs4954209 0 MAP3K19

7

2 2:135762344 2:135004774 rs16831243 3.4073E-281 MAP3K19 2 2:135762656 2:135005086 rs10197646 2.8256E-243 MAP3K19 2 2:135775130 2:135017560 rs7581382 0 MAP3K19 2 2:135803425 2:135045855 rs4954218 0 MAP3K19 2 2:135907088 2:135149518 rs6730157 0 RAB3GAP1 2 2:136388473 2:135630903 rs10187054 0 R3HDM1 2 2:136419961 2:135662391 rs1446584 0 R3HDM1 2 2:136420690 2:135663120 rs4954280 0 R3HDM1 2 2:136462661 2:135705091 rs2117511 1.1141E-115 R3HDM1 UBXN4, 2 2:136499166 2:135741596 rs1438307 0 LOC107985946 2 2:136506927 2:135749357 rs6430585 0 UBXN4 2 2:136545844 2:135788274 rs1042712 0 LCT 2 2:136555525 2:135797955 rs2015532 0 LCT 2 2:136556182 2:135798612 rs3769013 3.9719E-298 LCT 2 2:136556480 2:135798910 rs3769012 0 LCT 2 2:136556805 2:135799235 rs872151 2.3461E-208 LCT 2 2:136557319 2:135799749 rs2322660 0 LCT 2 2:136561557 2:135803987 rs2304371 0 LCT 2 2:136571982 2:135814412 rs4954445 9.9116E-155 LCT 2 2:136614255 2:135856685 rs309180 0 MCM6 2 2:136628121 2:135870551 rs4988163 3.82E-290 MCM6 2 2:136637350 2:135879780 rs16832138 2.4721E-141 2 2:136641593 2:135884023 rs7581814 0 2 2:136694905 2:135937335 rs7573555 0 DARS1 2 2:136702601 2:135945031 rs6743537 0 DARS1 2 2:136719173 2:135961603 rs6430594 0 DARS1 2 2:136765951 2:136008381 rs309137 0 2 2:136770509 2:136012939 rs12471781 0 2 2:136786651 2:136029081 rs12475139 0 2 2:136806774 2:136049204 rs7371606 0 2 2:136808949 2:136051379 rs11693502 0 2 2:136910273 2:136152703 rs6715785 0 2 2:136921703 2:136164133 rs10180515 4.7368E-297 2 2:136956733 2:136199163 rs7578292 2.0556E-108 2 2:136963794 2:136206224 rs12691876 7.058E-244 2 2:136973781 2:136216211 rs1519528 6.3105E-244 LOC107985947 2 2:137037386 2:136279816 rs4954599 4.4646E-178 2 2:137057148 2:136299578 rs13008975 2.673E-159 2 2:137058248 2:136300678 rs4296479 1.3039E-146 2 2:137058433 2:136300863 rs4599171 9.0685E-242 2 2:137197151 2:136439581 rs7561441 2.2853E-217 2 2:137300091 2:136542521 rs10205768 0

8

2 2:137341944 2:136584374 rs12691894 3.2503E-168 2 2:137433213 2:136675643 rs11681380 1.189E-166 2 2:137475070 2:136717500 rs7582192 3.998E-183 2 2:137514418 2:136756848 rs1427591 4.568E-133 2 2:137610518 2:136852948 rs778207 2.4135E-210 THSD7B 2 2:137612229 2:136854659 rs778202 2.788E-111 THSD7B 2 2:137614786 2:136857216 rs1429978 2.0282E-201 THSD7B 2 2:160867553 2:160011042 rs2667012 2.0504E-110 PLA2R1 2 2:160891688 2:160035177 rs17830904 4.1242E-103 PLA2R1 2 2:160906931 2:160050420 rs10929965 1.738E-120 PLA2R1 PLA2R1, 2 2:160912652 2:160056141 rs925410 4.4774E-127 LOC105373717 PLA2R1, 2 2:160914156 2:160057645 rs17831251 4.8957E-122 LOC105373717 PLA2R1, 2 2:160914540 2:160058029 rs6707458 2.1251E-120 LOC105373717 PLA2R1, 2 2:160915106 2:160058595 rs16844715 5.5049E-131 LOC105373717 2 2:166924472 2:166067962 rs1461197 2.0952E-102 SCN1A 2 2:177977545 2:177112817 rs2588865 1.9699E-149 LOC105373760 2 2:177991618 2:177126890 rs2706137 5.0089E-139 LOC105373760 3 3:14582939 3:14541432 rs9863287 6.8447E-149 GRIP2 3 3:45846769 3:45805277 rs17763742 7.9471E-149 LOC107986082 3 3:72193422 3:72144271 rs4676861 6.8938E-114 3 3:72194452 3:72145301 rs9881029 1.3915E-111 3 3:72195240 3:72146089 rs11128252 1.0507E-104 3 3:81427818 3:81378667 rs275360 9.7298E-107 3 3:123719219 3:124000372 rs9289229 1.412E-113 3 3:127416142 3:127697299 rs782440 7.9597E-153 MGLL 3 3:127417202 3:127698359 rs782437 3.9149E-148 MGLL 3 3:127426929 3:127708086 rs1071912 6.2622E-133 MGLL 3 3:127427910 3:127709067 rs7630666 4.1413E-116 MGLL 3 3:127431401 3:127712558 rs3773135 1.7845E-110 MGLL 3 3:159861147 3:160143360 rs9880646 4.6586E-142 IL12A-AS1 3 3:178995657 3:179277869 rs9813206 5.9692E-116 4 4:38768533 4:38766912 rs10470854 3.5358E-115 4 4:38787216 4:38785595 rs12233670 1.2828E-163 4 4:38894380 4:38892759 rs6835514 3.9318E-204 FAM114A1 4 4:46494121 4:46492104 rs12510295 1.8854E-118 4 4:84909466 4:83988313 rs4693665 2.3081E-158 LOC101928978 4 4:100260274 4:99339117 rs1693476 2.4068E-157 ADH1C 4 4:100262041 4:99340884 rs1789903 1.4449E-164 ADH1C 4 4:100263778 4:99342621 rs1789911 8.5916E-158 ADH1C 4 4:100285148 4:99363991 rs1154435 6.8643E-138

9

4 4:112051824 4:111130668 rs294942 1.7679E-121 5 5:12652188 5:12652076 rs4701945 1.0737E-113 LINC01194 5 5:36368967 5:36368865 rs4602650 1.2844E-156 5 5:110472967 5:111137269 rs464275 8.8941E-116 5 5:127667613 5:128331921 rs467610 1.9221E-118 FBN2 6 6:28100640 6:28132862 rs1225710 3.6169E-110 ZSCAN16-AS1 6 6:28391465 6:28423688 rs2859365 1.5022E-105 LOC105374997 6 6:28415572 6:28447795 rs13215804 3.2454E-247 6 6:28417222 6:28449445 rs6903535 5.3975E-227 6 6:28542520 6:28574743 rs370520 2.8254E-143 ZBED9 6 6:28665362 6:28697585 rs7382146 2.9284E-246 6 6:31025713 6:31057936 rs2517524 5.7429E-227 HCG22 6 6:31030122 6:31062345 rs2517510 2.1639E-213 6 6:31030283 6:31062506 rs2523841 3.1373E-102 6 6:31030425 6:31062648 rs2523840 1.0374E-105 6 6:31042070 6:31074293 rs2523883 2.1844E-189 6 6:31042306 6:31074529 rs2517489 1.333E-193 6 6:31042608 6:31074831 rs2523881 3.6122E-186 6 6:31042769 6:31074992 rs2523880 3.1327E-183 6 6:31051388 6:31083611 rs2535318 5.7922E-199 6 6:31052098 6:31084321 rs2517471 1.4559E-209 6 6:31053867 6:31086090 rs2535306 1.6897E-208 6 6:31172655 6:31204878 rs2894180 1.4227E-104 6 6:31255500 6:31287723 rs2524051 1.0604E-101 6 6:31333939 6:31366162 rs7761068 7.9729E-155 6 6:31336649 6:31368872 rs2523533 5.3241E-132 6 6:31338844 6:31371067 rs2853986 6.4987E-109 6 6:31379931 6:31412154 rs1063635 1.0914E-182 MICA 6 6:31440552 6:31472775 rs3828886 5.3507E-128 HCG26 6 6:31622606 6:31654829 rs805297 1.0722E-239 BAG6, APOM 6 6:31721033 6:31753256 rs3131379 6.4564E-124 MSH5, MSH5-SAPCD1 6 6:31777946 6:31810169 rs2075800 6.498E-274 HSPA1L 6 6:31856070 6:31888293 rs486416 0 EHMT2 6 6:31883957 6:31916180 rs644045 1.7805E-290 C2 6 6:31919578 6:31951801 rs2072633 0 CFB, NELFE 6 6:32059867 6:32092090 rs1150753 3.0851E-115 TNXB 6 6:32066177 6:32098400 rs17421624 6.1378E-107 TNXB 6 6:32179896 6:32212119 rs2071286 5.8589E-182 NOTCH4 6 6:32200147 6:32232370 rs3134926 1.0354E-135 6 6:32216850 6:32249073 rs3115576 0 6 6:32217367 6:32249590 rs3130311 0 6 6:32288190 6:32320413 rs574710 0 TSBP1, TSBP1-AS1

10

6 6:32305690 6:32337913 rs926591 0 TSBP1, TSBP1-AS1 6 6:32313097 6:32345320 rs4959093 0 TSBP1, TSBP1-AS1 6 6:32345689 6:32377912 rs2894254 1.3814E-102 TSBP1-AS1 6 6:32389512 6:32421735 rs9268560 0 6 6:32408527 6:32440750 rs9268645 0 HLA-DRA 6 6:32429758 6:32461981 rs9268858 2.6355E-105 6 6:32431147 6:32463370 rs9268877 0 6 6:32626272 6:32658495 rs9273363 4.6192E-114 HLA-DQB1-AS1 6 6:32635296 6:32667519 rs6908943 8.5237E-209 HLA-DQB1 6 6:32689529 6:32721752 rs9461799 2.7363E-262 6 6:32690001 6:32722224 rs9469240 1.1987E-215 6 6:32711782 6:32744005 rs2227127 4.7688E-231 HLA-DQA2 6 6:32712104 6:32744327 rs9276429 1.3712E-125 HLA-DQA2 6 6:32712247 6:32744470 rs9276431 9.5047E-123 HLA-DQA2 6 6:32712384 6:32744607 rs9276432 2.0812E-163 HLA-DQA2 6 6:32730012 6:32762235 rs7453920 9.0877E-117 HLA-DQB2 6 6:32730086 6:32762309 rs2051549 1.0915E-122 HLA-DQB2 6 6:32736144 6:32768367 rs9296044 1.4247E-189 6 6:32762616 6:32794839 rs2857154 1.604E-137 6 6:32965942 6:32998165 rs176248 9.4573E-113 HLA-DPA1, HLA- 6 6:33045558 6:33077781 rs3135021 5.3374E-106 DPB1 6 6:52108062 6:52243264 rs1266828 6.1791E-102 IL17F 6 6:79190083 6:78480366 rs10943541 8.6659E-130 6 6:79212957 6:78503240 rs4632856 4.5023E-114 6 6:79232161 6:78522444 rs4706060 1.5481E-101 6 6:152942821 6:152621686 rs1744380 2.9702E-142 SYNE1 6 6:152950053 6:152628918 rs2057399 9.4303E-144 SYNE1 6 6:152951141 6:152630006 rs2623943 3.8621E-141 SYNE1 6 6:152966084 6:152644949 rs2758813 5.8971E-161 6 6:153007917 6:152686782 rs2800629 1.9736E-163 LOC105378061 6 6:153008261 6:152687126 rs2800630 1.5265E-111 LOC105378061 6 6:153047588 6:152726453 rs17782898 1.0266E-148 MYCT1 7 7:46637249 7:46597651 rs12673771 9.2381E-108 7 7:70706501 7:71241515 rs7811880 5.9623E-149 GALNT17 7 7:83213264 7:83583948 rs215302 9.2933E-111 SEMA3E 7 7:113954435 7:114314380 rs2690830 2.2058E-117 FOXP2 8 8:1359156 8:1410990 rs17680989 6.3512E-143 DLGAP2 9 9:16004012 9:16004014 rs1887665 8.225E-116 CCDC171 9 9:16563123 9:16563125 rs10756762 4.7495E-109 BNC2 10 10:60614717 10:58854957 rs7350384 1.7523E-135 11 11:18357270 11:18335723 rs4150581 2.6092E-119 GTF2H1 11 11:106327768 11:106457041 rs12798744 7.4776E-192

11

12 12:79777844 12:79384064 rs7308297 8.9404E-129 SYT1 12 12:92502080 12:92108304 rs17251453 8.0703E-151 LINC01619 14 14:89901962 14:89435618 rs12885505 5.3732E-108 FOXN3 15 15:28080166 15:27835020 rs4778193 1.2432E-104 OCA2 15 15:28114289 15:27869143 rs4778201 6.9511E-108 OCA2 15 15:28282741 15:28037595 rs1448485 3.4642E-137 OCA2 15 15:28283507 15:28038361 rs16950821 2.5378E-148 OCA2 15 15:28283689 15:28038543 rs8024968 2.301E-151 OCA2 15 15:28443658 15:28198512 rs8041209 1.0209E-101 HERC2 15 15:28488888 15:28243742 rs8028689 3.0396E-109 HERC2 15 15:28496195 15:28251049 rs6497292 7.5041E-111 HERC2 15 15:28510895 15:28265749 rs2240202 2.3415E-104 HERC2 15 15:28513364 15:28268218 rs916977 0 HERC2 15 15:28530359 15:28285213 rs12592730 9.7612E-105 HERC2 15 15:84444878 15:83776126 rs11638104 4.9925E-187 ADAMTSL3 16 16:83896399 16:83862794 rs409861 1.1792E-119 18 18:63415573 18:65748337 rs10460125 6.4247E-148 CDH7 18 18:63435260 18:65768024 rs7237421 1.6093E-140 CDH7 18 18:63439141 18:65771905 rs8092259 9.2425E-140 CDH7 18 18:63443029 18:65775793 rs7228669 8.2144E-142 CDH7 18 18:63444000 18:65776764 rs1942831 5.489E-136 CDH7 18 18:63444300 18:65777064 rs8093720 6.0772E-140 CDH7 19 19:35887129 19:35396227 rs16970288 6.5672E-125 21 21:20974589 21:19602275 rs1079827 2.6652E-140 22 22:29836926 22:29440937 rs5763240 1.2746E-106 RFPL1, RFPL1S

Notes: p-values smaller than 2.225074e-308 are treated as 0 based on the algorithm of Cody's (1988) subroutine MACHAR in current implementations of R use 32-bit integers and use IEC 60559 floating-point (double precision) arithmetic.

12

Table S3. Genes detected by analysis based on KLFDAPC reduced features but not detected when using geographic coordinates. Gene functions and associated phenotypes were annotated against NCBI gene databases (https://www.ncbi.nlm.nih.gov/gene/ and https://www.ncbi.nlm.nih.gov/gap/phegeni). Outlier SNPs that were not located within a known gene are excluded. BP BP Gene References CHR rsID p-values Genes Gene Name Genotype associations (GRCh37) (GRCh38) into functions 6.873162433 Tumor promoter in Solute carrier Alzheimer's disease; 1:76083408, 1:75617723, rs2057519, 97588E-166; HCC 1 SLC44A5 family 44- capecitabine sensitivity; 1:76083667 1:75617982 rs4949869 3.703345916 (Hepatocellular member 5 Fatigue; Obesity 35216E-131 carcinoma) Inhibits apoptosis and promotes Circadian Rhythm; Sleep autophagy as well Adenylate Initiation and Maintenance 1 1:77944732 1:77479047 rs11162351 3.708E-158 AK5 as proliferation in kinase 5 Disorders; Education; human gastric Sodium; Body Mass Index cancer; refractory epilepsy Transport ATPase phosphatidylserine phospholipid 1 1:154316434 1:154343958 rs2274988 3.0212E-129 ATP8B2 and Cell Adhesion Molecules transporting phosphatidylethanol 8B2 amine cognitive performance in Glutamate the CANTAB; Platelet Signaling receptor receptor Function; 3 3:14582939 3:14541432 rs9863287 6.8447E-149 GRIP2 complex adaptor interacting Neuropsychological Tests; activity protein 2 Platelet Function Tests; Alkaline Phosphatase This gene encodes a serine hydrolase of 4.141327151 Venous 3:127427910 3:127709067 the AB hydrolase rs7630666, 14975E-116; monoglyceride Thromboembolism;Platelet 3 ,3:12743140 , MGLL superfamily that rs3773135 1.784481631 lipase Function 1 3:127712558 catalyzes the 11762E-110 Tests;Erythropoietin conversion of monoacylglycerides

13

BP BP Gene References CHR rsID p-values Genes Gene Name Genotype associations (GRCh37) (GRCh38) into functions to free fatty acids and glycerol. The encoded protein plays a critical role in several physiological processes including pain and nociperception through hydrolysis of the endocannabinoid 2- arachidonoylglycero l. Celiac Disease; Liver IL12A-AS1 is bona Cirrhosis, Biliary; major IL12A antisense fide susceptibility 3 3:159861147 3:160143360 rs9880646 4.66E-142 IL12A-AS1 depressive disorder; RNA 1 genes for Behcet's multiple sclerosis; primary disease. biliary cirrhosis Long intergenic non-protein 5 5:12652188 5:12652076 rs4701945 1.07E-113 LINC01194 coding RNA 1194 Elastic fiber Migraine Disorders; Sleep; assembly; Body Height; Breast 5 5:127667613 5:128331921 rs467610 1.92E-118 FBN2 Fibrillin 2 congenital Feeding; Electromagnetic contractural Radiation arachnodactyly Diabetes Mellitus, Type 1; HLA complex 6 6:31440552 6:31472775 rs3828886 5.35E-128 HCG26 Hodgkin Disease; Colitis, group 26 Ulcerative BAG BAG6 regulates APOM: Diabetes Mellitus, 6 6:31622606 6:31654829 rs805297 1.07E-239 BAG6, APOM cochaperone 6; ciliogenesis APOM: Type 1

14

BP BP Gene References CHR rsID p-values Genes Gene Name Genotype associations (GRCh37) (GRCh38) into functions apolipoprotein Interaction Between M; Apolipoprotein M Gene Single- Nucleotide Polymorphisms and Obesity and its Effect on Type 2 Diabetes Mellitus Susceptibility; Associated with systemic lupus erythematosus DNA mismatch Diabetes Mellitus, Type 1; repair and meiotic Lupus Erythematosus, recombination; Systemic; Platelet Function MSH5, MSH5- MutS homolog epigenetic 6 6:31721033 6:31753256 rs3131379 6.46E-124 Tests; Lupus SAPCD1 5 mechanism for Erythematosus, Systemic; premature ovarian Pulmonary Disease; insufficiency Hypertension pathogenesis. Diabetes Mellitus, Type 1; Connective tissue Lupus Erythematosus, 3.085110701 disorder Ehlers- Systemic; Diabetes 6:32059867 6:32092090 rs1150753 6156E-115; Danlos syndrome; 6 TNXB Tenascin XB Mellitus, Type 1; Lupus 6:32066177 6:32098400 rs17421624 6.137774896 cervical Erythematosus, Systemic; 93273E-107 cancer;gastric Diabetes Mellitus; dysfunction. Psoriasis Vitiligo;Lymphoma, B- TSBP1 and Cell, Marginal Zone;Crohn BTNL2 6 6:32345689 6:32377912 rs2894254 1.3814E-102 TSBP1-AS1 Disease;Breast antisense RNA Neoplasms;Osteoarthritis, 1 Knee

15

BP BP Gene References CHR rsID p-values Genes Gene Name Genotype associations (GRCh37) (GRCh38) into functions This gene belongs to the HLA class II alpha chain family. The encoded protein 1.371174305 forms a heterodimer 37082E- with a class II beta 125;9.50470 major chain. It is located 6:32712104; 6:32744327; rs9276429; 704815684E- histocompatibili in intracellular Diabetes Mellitus, Type 1; 6:32712247; 6:32744470; rs9276431; 6 123;9.08765 HLA-DQA2 ty complex, vesicles and plays a Crohn Disease;Giant Cell 6:32730012; 6:32762235; rs7453920; 393316865E- class II, DQ central role in the Arteritis;Alopecia Areata 6:32730086 6:32762309 rs2051549 117;1.09146 alpha 2 peptide loading of 91646404E- MHC class II 122 molecules by helping to release the CLIP molecule from the peptide binding site. HLA-DPA1 belongs to the HLA class II alpha chain paralogues. This class II molecule is major a heterodimer Anti-Neutrophil histocompatibili consisting of an Cytoplasmic Antibody- HLA-DPA1, 6 6:33045558 6:33077781 rs3135021 5.3374E-106 ty complex, alpha (DPA) and a Associated HLA-DPB1 class II, DP beta (DPB) chain, Vasculitis;Hepatitis B, alpha 1 both anchored in the Chronic membrane. It plays a central role in the immune system by presenting peptides derived from

16

BP BP Gene References CHR rsID p-values Genes Gene Name Genotype associations (GRCh37) (GRCh38) into functions extracellular proteins. The protein encoded by this gene is a cytokine that shares sequence similarity with IL17. This cytokine is expressed by activated T cells, and has been shown to stimulate the production of Glomerular Filtration several other Rate;gemcitabine;Pancreati 6 6:52108062 6:52243264 rs1266828 6.1791E-102 IL17F interleukin 17F cytokines, including c Carcinoma;Platelet IL6, IL8, and Function Tests CSF2/GM_CSF. This cytokine is also found to inhibit the angiogenesis of endothelial cells and induce endothelial cells to produce IL2, TGFB1/TGFB, and monocyte chemoattractant protein-1. This gene encodes a lipoprotein A-I; Attention spectrin repeat spectrin repeat Deficit Disorder with containing containing protein Hyperactivity;Bipolar 6 6:152951141 6:152630006 rs2623943 3.8621E-141 SYNE1 nuclear expressed in Disorder;Child envelope protein skeletal and smooth Development Disorders, 1 muscle, and Pervasive

17

BP BP Gene References CHR rsID p-values Genes Gene Name Genotype associations (GRCh37) (GRCh38) into functions peripheral blood lymphocytes, that localizes to the nuclear membrane. uncharacterized 6 6:153008261 6:152687126 rs2800630 1.5265E-111 LOC105378061 LOC105378061 Colitis and modulates colonic inflammation; regulator in intestinal inflammation that regulates intestinal Cerebrospinal Fluid; 7 7:83213264 7:83583948 rs215302 9.29E-111 SEMA3E Semaphorin 3E epithelium Cholesterol, HDL; Atrial apoptosis; Fibrillation; Asthma modulating immune cells and structural cells function in the airways; allergic asthma; cell proliferation. Coiled-coil Body Weight; Body Mass 9 9:16004012 9:16004014 rs1887665 8.22E-116 CCDC171 domain - Index; Carotid Artery containing 171 Diseases Associated with Autosomal- Dominant Congenital Lower Scoliosis; Melanosis; Body 9 9:16563123 9:16563125 rs10756762 4.75E-109 BNC2 Basonuclin 2 Urinary-Tract Height; Bronchodilator Obstruction; related Agents to risk of adolescent idiopathic scoliosis globally; oxidative

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BP BP Gene References CHR rsID p-values Genes Gene Name Genotype associations (GRCh37) (GRCh38) into functions stress response. Development and progression of the spinal deformity in adolescent idiopathic scoliosis Molecular Basis for Synaptotagmin-1- Associated Blood Pressure; Body Mass Synaptotagmin Neurodevelopmenta Index; Lipids; Respiratory 12 12:79777844 12:79384064 rs7308297 8.94E-129 SYT1 1 l Disorder; Function; Cholesterol, Association HDL between cognitive performance; Competing endogenous RNA Long intergenic and regulates miR- non-protein 27a/FOXO1- Platelet Function Tests; 12 12:92502080 12:92108304 rs17251453 8.07E-151 LINC01619 coding RNA mediated ER stress Education; Schizophrenia 1619 and podocyte injury in diabetic nephropathy RFPL1: ret Neocortex finger protein development; metal HIV-1; Vascular RFPL1, 22 22:29836926 22:29440937 rs5763240 1.27E-106 like 1; RFPL1: ion binding; Calcification; Platelet RFPL1S antisense RNA ubiquitin-protein Function 1 transferase activity

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Table S4. Genes identified by analysis based on geographic coordinates but not detected when using KLFDAPC reduced features. Gene functions and associated phenotypes were annotated against NCBI gene databases (https://www.ncbi.nlm.nih.gov/gene/ and https://www.ncbi.nlm.nih.gov/gap/phegeni). Outlier SNPs that were not located within a known gene are excluded. CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions 2 2:20310668 2:20110907 rs11679737 1.2002E-111 LAPTM4A- transmembrane modulates the Dental Caries; Platelet DT protein 178B rate-limiting Function; Leptin step of STIM1 puncta formation and therefore controls SOCE in inflammatory conditions 2 2:40289267 2:40062127 rs759361 5.5658E-104 SLC8A1- SLC8A1 AS1 antisense RNA 1 2 2:174486590 2:173621862 rs6722856 2.9251E-127 LOC107985 uncharacterized 961 3 3:178429939 3:178712151 rs9290663 4.5367E-112 KCNMB2, potassium an auxiliary beta Platelet Function; KCNMB2- calcium- subunit which Hippocampus; Angiotensin- AS1 activated decreases the Converting Enzyme channel activation time Inhibitors; Cough; subfamily M of MaxiK alpha Amyotrophic lateral regulatory beta subunit currents; sclerosis 1; subunit 2; modulations of KCNMB2 BK channel antisense RNA function by a 1 Slo1 mutation associated with epilepsy and dyskinesia

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions 4 4:38776303,4: 4:38774682, rs11466652 5.0508E-141 TLR10 toll like receptor Plays a Helicobacter 38776491,4:38 4:38774870, , 1 fundamental Infections;Alcohol 783964 4:38782343 rs11096957 role in pathogen Drinking;Blood , rs4321646 recognition and Pressure;Transferrin activation of innate immunity 6 6:28113373 6:28145595 rs1225715 1.3359E-139 ZKSCAN8 zinc finger with KRAB and SCAN domains 8 6 6:29256420 6:29288643 rs1884123 2.2056E-105 LOC101929 006, LOC105375 005 6 6:30103360 6:30135583 rs1541269 1.1572E-107 TRIM40 tripartite motif encodes a Psoriasis; Cardiomegaly; containing 40 member of the Behcet Syndrome; Multiple tripartite motif Sclerosis; Child (TRIM) protein Development Disorders, family. The Pervasive encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. 6 6:30152467 6:30184690 rs11158 4.2464E-119 TRIM26 tripartite motif The protein Schizophrenia; Attention containing 26 encoded by this Deficit Disorder with gene is a Hyperactivity; Bipolar

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions member of the Disorder; Child tripartite motif Development Disorders, (TRIM) family; Pervasive; Depressive TRIM26 Disorder overexpression inhibited cell proliferation, migration, and invasion in Papillary thyroid carcinoma cells. TRIM26 overexpression also suppressed the epithelial-to- mesenchymal transition process. 6 6:30739972 6:30772195 rs3132605 2.572E-102 HCG20 HLA complex group 20 6 6:31265554,6: 6:31297777, rs2524115, 3.9166E-141 LINC02571, long intergenic 31277686 6:31309909 rs1634788 LOC112267 non-protein 902 coding RNA 2571; uncharacterized LOC112267902 7 7:140975246 7:141275446 rs10247172 1.8457E-123 TMEM178B transmembrane Tmem178 Dental Caries; Platelet protein 178B modulates the Function; Schizophrenia; rate-limiting Platelet Function; Leptin step of STIM1 puncta formation and

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions therefore controls SOCE in inflammatory conditions. 7 7:16581890 7:16542265 rs6945188 4.6453E-101 LRRC72 leucine rich Child Development repeat Disorders, Pervasive; containing 72 Lipoprotein(a); Blood Urea Nitrogen 7 7:17978129 7:17938506 rs6973480 1.5727E-113 SNX13 sorting nexin 13 This gene Fibrinogen; Cholesterol, encodes a HDL; Influenza A Virus, PHOX domain- H1N1 Subtype; and RGS Caffeine;gamma-Linolenic domain- Acid containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositid e binding domain, and the SNX family members are involved in intracellular trafficking. The

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)- mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor 8 8:40575914 8:40718395 rs10091954 1.6933E-105 ZMAT4 zinc finger Myopia; Refraction, Ocular; matrin-type 4 Education; Refractive Errors; Glucose

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions 9 9:90135027 9:87520112 rs17399090 2.0581E-144 DAPK1 death associated Death- Platelet Function; Arterial protein kinase 1 associated Pressure; Blood Pressure; protein kinase 1 Cytokines; Vaccine Potency is a positive mediator of gamma- interferon induced programmed cell death. DAPK1 encodes a structurally unique 160-kD calmodulin dependent serine-threonine kinase that carries 8 ankyrin repeats and 2 putative P-loop consensus sites. It is a tumor suppressor candidate. 10 10:55958039 10:54198279 rs4278430 2.6581E-106 PCDH15 protocadherin This gene is a Vaccine Potency; Platelet related 15 member of the Function; Hand Strength; cadherin Bone Density; Bronchial superfamily. Provocation Family members encode integral membrane proteins that

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions mediate calcium- dependent cell- cell adhesion. It plays an essential role in maintenance of normal retinal and cochlear function. Mutations in this gene result in hearing loss and Usher Syndrome Type IF (USH1F). 11 11:8589648 11:8568101 rs9736791 1.2434E-118 STK33 serine/threonine take part in the Body Mass Index; Platelet kinase 33 regulation of Function; Blood Pressure; ERKs signaling Alanine Transaminase; pathway; Ankle Brachial Index STK33 has pro- tumor function and is a critical downstream mediator of KLF4 in gastric cancer. STK33 may serve as a potential prognostic marker and therapeutic

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions target for gastric cancer; inhibition of STK33 in small cell lung carcinoma cells suppressed the cell proliferation and invasion while induced cell apoptosis; 12 12:129922249, 12:12943770 rs11060347 5.2467E-117 TMEM132D transmembrane TMEM132D Cholesterol; Platelet 2:129905838 4,12:129421 , protein 132D may serve as Function; Cognition 293 rs10773658 predictors of Disorders; Cognitive CD8+ T- Dysfunction; lymphocyte Immunoglobulins infiltration and as favorable prognostic markers in early stage ovarian cancer with important consequences for diagnosis;may increase vulnerability to panic disorder (PD) by modulating oligodendrocyte

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions s and GABA and dopaminergic functions in related brain regions, altering neuronal processing of anxiety-related emotionl signals 12 12:1478570 12:1369404 rs11061714 1.8317E-102 ERC1 ELKS/RAB6- A family of Child Development interacting/CAS RIM-binding Disorders, T family proteins; RIMs Pervasive;Obesity;Body member 1 are active zone Weight;Platelet Function proteins that Tests;Anthropometry regulate neurotransmitter release. 16 16:7081093 16:7031092 rs11645481 3.6133E-142 RBFOX1 RNA binding The Fox-1 Myopia; Autosomal fox-1 homolog 1 family of RNA- dominant compelling helio binding proteins ophthalmic outburst is evolutionarily syndrome; Platelet conserved, and Function; Age of Onset; regulates tissue- Alzheimer Disease; specific Calcium-Binding Proteins alternative splicing in metazoa. Fox-1 recognizes a (U)GCAUG stretch in regulated exons

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions or in flanking introns. The protein binds to the C-terminus of ataxin-2 and may contribute to the restricted pathology of spinocerebellar ataxia type 2 (SCA2). Ataxin- 2 is the product of the SCA2 gene which causes familial neurodegenerati ve diseases. Fox-1 and ataxin-2 are both localized in the trans-Golgi network. 16 16:11369205,1 16:11275348 rs1559394,r 6.448753166 PRM2,PRM protamine 2; Protamines substitute for 6:11390728 ,16:1129687 s11640295 60758E-112, 3,LOC10537 protamine 3 histones in the chromatin of 1 2.327125500 1082 sperm during the haploid 1104E-101 phase of spermatogenesis, and are the major DNA- binding proteins in the nucleus of sperm in many vertebrates. They package the sperm DNA into a highly condensed complex

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions in a volume less than 5% of a somatic cell nucleus. 17 17:60680468 17:62603107 rs6504112 5.4294E-110 TLK2 tousled like This gene Longevity kinase 2 encodes a nuclear serine/threonine kinase that was first identified in Arabidopsis. The encoded protein is thought to function in the regulation of chromatin assembly in the S phase of the cell cycle by regulating the levels of a histone H3/H4 chaperone. This protein is associated with double-strand break repair of DNA damage caused by radiation. 17 17:70097607 17:72101466 rs9894720 9.3284E-136 SOX9-AS1 SOX9 antisense SOX9-AS1 gamma-Glutamyltransferase RNA 1 aggravates Hepatocellular

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CHR BP(Grch37) BP(Grch38) rsID p. values Genes Gene name Gene Genotype associations references into functions carcinoma (HCC) progression and metastasis in vitro and in vivo. Study demonstrates that SOX9-AS1 sponges miR- 5590-3p to elevate SOX9 expression, and that SOX9 in turn transcriptionally activates SOX9- AS1.

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