Supplementary Table S4. Significantly expressed in regions that are cytogenetically associated with copy- number aberrations in aberrant tumors compared to normal kidney as based by GSEA and integration of , miRNA and methylation data.

Detected by miRNAs miRNA Mass- Cytoband Fold Change p-value concordantly Fold Change Spectrometry expressed in region (q-value %) (Fold Change) Overexpression 1q21 CTSS 9.76198 0.015806774 ANP32E 3.1243522 0.010197877 POLR3C 2.8023202 0.010197877 SCNM1 2.6866474 0.010197877 S100A13 2.6102252 0.015806774 SLC39A1 2.5888152 0.010197877 S100A11 2.4977353 0.023967674 1.1816 PLEKHO1 2.467553 0.015806774 GOLPH3L 2.3607595 0.023967674 HAX1 2.2079124 0.010197877 BOLA1 2.1552317 0.010197877 S100A10 2.1358588 0.035557915 1.5554 PSMD4 2.132948 0.010197877 SHC1 2.113438 0.010197877 FLAD1 2.094633 0.010197877 NOTCH2NL 2.0205522 0.035557915 CHD1L 1.9804109 0.010197877 SEC22B 1.973773 0.010197877 UBE2Q1 1.8184233 0.010197877 ARNT 1.7866888 0.015806774 INTS3 1.737892 0.010197877 LASS2 1.6981341 0.035557915 JTB 1.6820908 0.010197877 PSMB4 1.65356 0.010197877 MRPL9 1.639875 0.010197877 OAZ3 1.6028159 0.010197877 SETDB1 1.5752002 0.015806774 RNF115 1.5618018 0.015806774 UBAP2L 1.5583692 0.035557915 RAB13 1.5521057 0.010197877 DENND4B 1.406589 0.023967674 TARS2 1.3654745 0.023967674 ENSA 1.343265 0.023967674 0.5325 PMVK 1.3185868 0.010197877

1q22 RIT1 5.268354 0.010197877 C1orf61 3.1359932 0.023967674 SSR2 2.7798665 0.010197877 EFNA1 2.310088 0.010197877 DAP3 1.9625218 0.015806774 MTX1 1.8360254 0.035557915 KIAA0907 1.7114192 0.023967674 BGLAP 1.6771101 0.023967674 CCT3 1.6536148 0.015806774 0.8786 FDPS 1.6368296 0.035557915 RUSC1 1.5098684 0.010197877 GON4L 1.3837205 0.035557915

1q25 FAM129A 5.01957 0.015806774 NCF2 4.853107 0.023967674 CEP350 2.7693563 0.010197877 QSOX1 2.6968064 0.035557915 LAMC1 2.6204774 0.015806774 SOAT1 2.5788422 0.015806774 ARPC5 2.4033663 0.015806774 GLUL 2.3093946 0.015806774 CACYBP 2.083803 0.010197877 STX6 1.9979908 0.010197877 RABGAP1L 1.954621 0.015806774 TOR3A 1.9356376 0.010197877 TOR1AIP1 1.8326453 0.023967674 SMG7 1.7197734 0.023967674 KLHL20 1.594847 0.010197877 EDEM3 1.5597414 0.015806774

1q42 DEGS1 4.0734706 0.010197877 KCNK1 3.4703877 0.010197877 TTC13 3.2987132 0.010197877 ENAH 3.1603143 0.010197877 ACBD3 3.0855658 0.010197877 CNIH4 2.9197156 0.010197877 GUK1 2.898679 0.010197877 TBCE 2.8832018 0.010197877 EGLN1 2.6401546 0.010197877 TOMM20 2.4697633 0.010197877 RBM34 2.264009 0.010197877 LYST 2.2344882 0.015806774 NVL 2.1536267 0.010197877 GNPAT 2.0335913 0.010197877 LBR 2.002605 0.015806774 FBXO28 1.8666879 0.010197877 ARID4B 1.8549696 0.010197877 NID1 1.8161637 0.035557915 DISC1 1.6985904 0.010197877 TSNAX 1.679381 0.010197877 PARP1 1.6495545 0.015806774 ERO1LB 1.6259017 0.023967674 NUP133 1.6194867 0.010197877 GGPS1 1.6184005 0.015806774 URB2 1.505534 0.010197877 WDR26 1.4864568 0.015806774 PCNXL2 1.460323 0.023967674 TAF5L 1.3597175 0.015806774 CDC42BPA 1.3509861 0.035557915

1q44 CEP170 4.4912906 0.010197877 SMYD3 2.75279 0.010197877 PPPDE1 2.3757343 0.010197877 ZNF692 2.3266437 0.015806774 AHCTF1 1.6940893 0.015806774

2q14 INHBB 15.265408 0.000488805 INSIG2 3.7068357 0.000488805 DDX18 2.3646696 0.000488805 TMEM185B 2.1102257 0.001303913 TSN 2.0817976 0.003246108 0.9215 GYPC 2.0542576 0.005739856 POLR2D 2.0339456 0.000683158 RALB 1.9610797 0.003246108 ACTR3 1.9410403 0.000488805 MAP3K2 1.6434724 0.000683158 ERCC3 1.3958118 0.01639431

2q21 CXCR4 10.740518 0.000947449 DARS 3.3141515 0.000488805 MCM6 2.2828302 0.000488805 UBXN4 1.8602141 0.000683158 TUBA3D 1.821514 0.026494633 CCNT2 1.7565924 0.000683158 PTPN18 1.7350677 0.000488805 IMP4 1.6867584 0.000488805 RAB3GAP1 1.4213128 0.012753347

2q31 ITGA4 4.590233 0.000488805 PDK1 3.4428895 0.000488805 WIPF1 2.9118094 0.000683158 AGPS 2.5479503 0.001303913 SP3 2.283206 0.000488805 GORASP2 2.0737998 0.000683158 ATF2 1.9675384 0.001303913 HAT1 1.9185188 0.000488805 HNRNPA3 1.7925476 0.000683158 CYBRD1 1.7785245 0.01639431 PRKRA 1.7105325 0.000488805 METTL5 1.7062479 0.000488805 UBE2E3 1.6606967 0.001303913 OLA1 1.6466206 0.005739856 TLK1 1.5554247 0.009847163 PPIG 1.3935852 0.0333108 TTC30A 1.3776512 0.041574918 SSB 1.3639404 0.009847163 0.2709 NFE2L2 1.3138406 0.012753347

2q33 CASP8 3.32299 0.000683158 FZD5 2.8289282 0.005739856 NRP2 2.2107196 0.000488805 CFLAR 2.1252425 0.003246108 MOBKL3 2.1207993 0.000488805 FASTKD2 1.9873654 0.000683158 SATB2 1.9683638 0.005739856 KLF7 1.8891034 0.001303913 CREB1 1.8552486 0.001303913 EEF1B2 1.757625 0.000488805 1.1198 BZW1 1.5571042 0.000488805 GTF3C3 1.5494763 0.000488805 BMPR2 1.5032349 0.004332901 SUMO1 1.4774989 0.007546423 CD28 1.3225219 0.041574918

2q35 FN1 8.120778 0.000488805 hsa-mir-26b 1.31 (1.79) ABCB6 2.397112 0.005739856 ARPC2 2.1204307 0.000683158 0.7844 GLB1L 1.9961697 0.0333108 GMPPA 1.9406874 0.001303913 FAM134A 1.9120542 0.000683158 BARD1 1.8814435 0.000488805 TUBA4A 1.8720274 0.002413473 SLC11A1 1.829439 0.003246108 RPL37A 1.763065 0.007546423 TNS1 1.7354904 0.007546423 DNPEP 1.6505007 0.001303913 CHPF 1.639396 0.007546423 ABCA12 1.6195434 0.004332901 XRCC5 1.5910383 0.000947449 0.87305 TMBIM1 1.5723928 0.000947449 CTDSP1 1.5558088 0.001780769 AAMP 1.4740679 0.001780769 ATIC 1.4343871 0.009847163 1.4799 TTLL4 1.3766862 0.003246108 ZNF142 1.3214235 0.000488805 SMARCAL1 1.3041657 0.041574918

2q37 CXCR7 10.251854 0.000488805 ARL4C 9.658784 0.000947449 COL6A3 4.8711605 0.000947449 1.2049 SP140L 4.822962 0.000488805 PER2 4.1587543 0.000683158 INPP5D 3.3945892 0.000488805 SP110 3.2637749 0.000488805 DGKD 3.1446507 0.000488805 SP100 2.160613 0.000488805 COPS8 1.8716531 0.000488805 DTYMK 1.8269827 0.000947449 LRRFIP1 1.7215176 0.001303913 AGAP1 1.6282012 0.020918602 GPC1 1.5549986 0.004332901 PASK 1.543047 0.007546423 ATG16L1 1.5267144 0.026494633 NCL 1.5078771 0.000683158 1.0335 GIGYF2 1.489731 0.003246108 HDAC4 1.4740222 0.020918602 EIF4E2 1.4704136 0.003246108 PPP1R7 1.4094073 0.01639431 STK25 1.3836355 0.001780769 PDE6D 1.3616095 0.002413473 PTMA 1.3396994 0.003246108 0.242 PSMD1 1.3308164 0.026494633 0.8167 MTERFD2 1.3152962 0.020918602 SP140 1.3001416 0.005739856

3q22 TMEM22 4.500529 0.000169439 NCK1 3.620709 0.000307674 TOPBP1 2.6931446 0.000169439 CDV3 2.0546012 0.013543603 PIK3CB 1.9918627 0.002091405 PPP2R3A 1.7996869 0.008764828 STAG1 1.6545988 0.004385488 CEP63 1.6402913 0.001242747 CCRL1 1.5385426 0.03668277 SRPRB 1.5006251 0.030368468 DNAJC13 1.4213734 0.006995319 DBR1 1.3919446 0.000228949 ARMC8 1.3527949 0.008764828

3q27 RTP4 7.795233 0.000307674 RFC4 3.8885708 0.000169439 BCL6 3.7772555 0.000169439 YEATS2 2.6565862 0.000169439 LAMP3 2.5523694 0.001242747 RPL39L 2.0561025 0.000169439 ALG3 1.6738241 0.00161652 AP2M1 1.6302135 0.000722671 PSMD2 1.4683233 0.008764828 0.6382 LPP 1.4637492 0.000307674 SENP2 1.3727192 0.006995319 DGKG 1.3685753 0.001242747 DVL3 1.3599557 0.020492934 TRA2B 1.3590808 0.030368468 PARL 1.355134 0.008764828

5q23 LOX 12.834539 1.22902E-06 TNFAIP8 3.8264449 9.79505E-07 SEMA6A 2.7450953 0.000633349 LMNB1 2.2102 1.37569E-06 PRRC1 1.663295 0.000950152 HINT1 1.5353914 3.56647E-05 CSNK1G3 1.5164657 0.000227996 PRR16 1.4605479 0.000111073

5q32 CSF1R 2.8840358 4.13589E-06 ABLIM3 2.5277743 2.40504E-05 CSNK1A1 2.2102826 1.18476E-05 TCERG1 2.2099056 8.73802E-07 SLC26A2 2.1698449 3.56647E-05 DPYSL3 1.9686625 0.001914197 1.4613 FBXO38 1.3943073 8.68384E-06 HMGXB3 1.3495334 1.31276E-05

5q33 FABP6 10.780219 9.79505E-07 HAVCR1 7.7247443 6.33735E-06 PTTG1 5.683904 5.50723E-07 GM2A 4.5404496 5.50723E-07 TNIP1 2.657786 4.35941E-07 ABLIM3 2.5277743 2.40504E-05 SPARC 2.4942126 1.60941E-05 C5orf54 2.413408 3.23423E-05 THG1L 2.1583326 1.37569E-06 CNOT8 2.0564885 2.17593E-05 ITK 1.9198433 0.000145976 MFAP3 1.9190756 9.79505E-07 SYNPO 1.8133662 0.006055969 DCTN4 1.7041705 2.93154E-05 SLC36A1 1.6894366 0.000687516 RBM22 1.6332747 2.14913E-06 G3BP1 1.5301784 3.71287E-06 MRPL22 1.490277 3.56647E-05 FAM114A2 1.4814578 5.70018E-06 LARP1 1.4760405 0.006482345 RPS14 1.4669524 2.14913E-06 ADAM19 1.4467303 0.001774201 SAP30L 1.3902687 2.65591E-05 MED7 1.3325255 0.000493733

5q34 HMMR 1.5221938 0.002064275 RARS 1.4988883 5.12458E-06

5q35 STC2 8.697442 1.22902E-06 hsa-miR-340 2.52 (2.28) LCP2 5.5473084 4.35941E-07 DOCK2 5.1859183 2.67838E-06 NPM1 2.281376 9.79505E-07 0.644 LMAN2 2.2646983 7.79129E-07 NOP16 2.1928248 4.60488E-06 DDX41 2.169652 4.35941E-07 CCDC99 2.1630523 5.70018E-06 STK10 2.1619737 6.94375E-07 TMED9 2.1564095 4.90101E-07 MGAT1 2.062733 1.22902E-06 HNRNPH1 1.9325768 0.000208743 CANX 1.8921642 0.000111073 2.8414 FAF2 1.8170985 4.60488E-06 GNB2L1 1.7806926 5.50723E-07 HNRNPAB 1.7117598 0.000158681 CLK4 1.7107768 0.000351895 KCNMB1 1.6697279 0.001303257 TRIM52 1.6401281 0.000493733 RGS14 1.607999 3.56647E-05 MAPK9 1.5965695 1.45388E-05 RNF130 1.5944601 6.33735E-06 F12 1.5839262 0.003215071 ZNF354A 1.5276195 7.04237E-06 RUFY1 1.5183303 9.79505E-07 FBXW11 1.4421728 0.006482345 SQSTM1 1.4277887 0.000271607 NHP2 1.4173329 2.98787E-06 UIMC1 1.4169445 0.000111073 RNF44 1.3964739 0.00053672 CNOT6 1.3855804 0.000351895 LTC4S 1.3419076 0.003987213 DUSP1 1.994716 0.002581616 KCNMB1 1.6697279 0.001303257

7p11 EGFR 4.7125716 0.000911119 SEC61G 3.532728 0.000911119 ECOP 1.7628075 0.001835603 CCT6A 1.6685832 0.000911119 1.2462 CHCHD2 1.4644227 0.001299361

7p12-p13 IGFBP3 23.004494 0.000911119 BLVRA 2.849211 0.000911119 C7orf44 2.8272998 0.000911119 POLD2 1.6862991 0.000911119 PPIA 1.6685386 0.002568832 1.4314 ZMIZ2 1.57176 0.011984701 TBRG4 1.4438506 0.001835603 NUDCD3 1.3836794 0.002568832

7p22 PDGFA 3.4718678 0.001299361 EIF3B 2.4791636 0.000911119 NUDT1 2.342937 0.001835603 KDELR2 2.2065747 0.000911119 HEATR2 2.0652852 0.000911119 ZNF12 1.952269 0.002568832 RALA 1.8869026 0.000911119 FTSJ2 1.824297 0.000911119 ZDHHC4 1.6204516 0.001835603 FSCN1 1.5831097 0.011984701 1.244 MICALL2 1.5497963 0.011984701 IQCE 1.544052 0.001835603 CHST12 1.5070275 0.00489131 KIAA0415 1.3124044 0.001835603 EIF2AK1 1.310334 0.006655606

7q11 RFC2 4.679652 0.000169439 PTPN12 3.068053 0.000411218 PION 2.8314557 0.000307674 ZNF107 2.2563603 0.001242747 TBL2 2.0641713 0.000950249 LAT2 2.0561678 0.00161652 C7orf42 1.9993391 0.000546622 GUSB 1.8622737 0.000307674 1.2371 PHTF2 1.8448749 0.004385488 BAZ1B 1.7478722 0.000307674 HSPB1 1.6614248 0.000411218 CLIP2 1.643121 0.000546622 RABGEF1 1.5372063 0.002091405 EIF4H 1.4902446 0.00161652 1.3206 NSUN5 1.4598182 0.004385488 BCL7B 1.4360013 0.003444695 PMS2L5 1.433569 0.000950249 PMS2L2 1.4038088 0.00161652 CRCP 1.4011819 0.001242747 PMS2L1 1.3890635 0.002091405 WBSCR22 1.3689988 0.008764828

7q22 NPTX2 23.932865 0.000169439 hsa-miR-25 1.86 (0) ARPC1B 5.364929 0.000169439 1.4482 hsa-miR-93 2.30 (3.13) PUS7 3.3499336 0.000169439 hsa-miR-106b 3.59 (0) MCM7 3.3017707 0.000228949 NAMPT 2.915563 0.000546622 PLOD3 2.78144 0.000169439 DPY19L2P2 2.679699 0.002691283 PILRA 2.2107816 0.002691283 PVRIG 2.0615327 0.000411218 ARPC1A 2.0254211 0.003444695 BUD31 2.0110419 0.000228949 ORC5L 1.9549506 0.000307674 POP7 1.8684255 0.001242747 RINT1 1.8402599 0.000169439 DNAJC2 1.8144609 0.000722671 BCAP29 1.7161973 0.003444695 SMURF1 1.6773839 0.000169439 COG5 1.649367 0.006995319 ORAI2 1.6283089 0.000169439 TRRAP 1.5917906 0.010924034 PRKRIP1 1.5598888 0.002091405 ZNF3 1.4961591 0.005553516 POLR2J 1.4510939 0.002691283 ZNF394 1.4492106 0.002091405 GNB2 1.4477414 0.000546622 GAL3ST4 1.4392163 0.002691283 ZKSCAN5 1.4130806 0.002691283 COPS6 1.3679748 0.008764828 PIK3CG 1.362949 0.010924034 CPSF4 1.3585126 0.00161652 CBLL1 1.3490103 0.005553516 PSMC2 1.3333286 0.003444695 0.9433

7q32 HIG2 23.173512 0.000169439 CALU 4.1346583 0.006995319 KLHDC10 1.8849814 0.008764828 SND1 1.723107 0.000169439 ARF5 1.6790918 0.000228949 C7orf54 1.5878574 0.000411218 RBM28 1.514489 0.004385488

7q36 EZH2 4.78446 0.000169439 NCAPG2 2.9865181 0.000546622 RARRES2 2.6343596 0.003444695 PDIA4 2.5021574 0.000546622 GIMAP4 2.3523042 0.000228949 WDR60 2.1053722 0.010924034 PAXIP1 1.9576992 0.001242747 GIMAP5 1.8588288 0.000411218 DNAJB6 1.8580647 0.013543603 GIMAP6 1.7489245 0.000950249 CDK5 1.5321912 0.008764828 UBE3C 1.4887027 0.004385488 CUL1 1.4485264 0.006995319 RHEB 1.3841236 0.008764828 REPIN1 1.3359224 0.013543603 ZNF282 1.3000402 0.006995319

11q12 MS4A4A 7.98693 0.006655606 MS4A6A 6.5540257 0.002568832 SLC43A3 4.6356077 0.000911119 RARRES3 3.261867 0.001835603 UBE2L6 3.1704175 0.000911119 PLA2G16 3.067557 0.000911119 SLC15A3 3.0101824 0.000911119 SERPING1 2.8843646 0.001835603 3.66505 FEN1 2.2828023 0.000911119 LPXN 2.2299414 0.001835603 C11orf9 1.997048 0.008972547 SSRP1 1.8825314 0.000911119 WDR74 1.8623163 0.002568832 C11orf10 1.8483038 0.002568832 CCDC86 1.8247854 0.000911119 AHNAK 1.6699907 0.001835603 CLP1 1.6320897 0.002568832 TIMM10 1.3949488 0.00489131 FTH1 1.3895897 0.008972547 EEF1G 1.3437171 0.001835603

11q13 CCND1 5.70199 0.000911119 ANO1 3.212007 0.001299361 SERPINH1 2.9052012 0.001299361 UCP2 2.7305384 0.00489131 SLCO2B1 2.4377742 0.00489131 EFEMP2 2.3664014 0.000911119 CCDC85B 2.3622606 0.000911119 FOLR2 2.275694 0.006655606 FAM89B 2.2476158 0.001299361 TCIRG1 2.093487 0.000911119 RPS3 1.940776 0.000911119 OTUB1 1.8689623 0.000911119 MRPL11 1.8372352 0.000911119 PPP1R14B 1.832652 0.000911119 FAU 1.8286489 0.000911119 FIBP 1.821591 0.00489131 EHBP1L1 1.7848366 0.000911119 C11orf24 1.7661351 0.008972547 GSTP1 1.6857998 0.002568832 VEGFB 1.6245266 0.002568832 SAC3D1 1.6233141 0.015861332 AIP 1.6172112 0.008972547 NADSYN1 1.6085417 0.00489131 FADD 1.5698645 0.003561337 POLD4 1.5522602 0.011984701 BAD 1.5276574 0.00489131 HSPC152 1.4952998 0.000911119 PPME1 1.4746312 0.00489131 DRAP1 1.4509481 0.002568832 KDM2A 1.441457 0.001835603 TMEM134 1.4391592 0.008972547 PPFIA1 1.4219077 0.011984701 FCHSD2 1.4066187 0.011984701 RELA 1.3846062 0.006655606 RAB6A 1.3242707 0.015861332

11q14 RAB38 2.9208286 0.000911119 TMEM135 2.5380766 0.000911119 PRSS23 2.167044 0.000911119 KCTD14 2.067461 0.011984701 C11orf73 1.9139929 0.001299361 CREBZF 1.6693631 0.008972547 CCDC90B 1.6091952 0.001299361 CLNS1A 1.5804836 0.002568832 EED 1.5322858 0.006655606 GAB2 1.5211884 0.002568832 FZD4 1.4932492 0.015861332 ALG8 1.4282173 0.008972547

11q23 NNMT 77.38523 0.000911119 3.2572 MCAM 5.5773377 0.000911119 MPZL2 5.1878023 0.001299361 IL10RA 4.9640193 0.001299361 HSPB2 3.6526902 0.000911119 CD3D 3.571158 0.003561337 DIXDC1 2.4092748 0.001299361 RBM7 2.099891 0.000911119 ZNF259 1.9335544 0.000911119 ALG9 1.9283185 0.002568832 2.48945 CRYAB 1.7838053 0.011984701 C11orf57 1.7630674 0.006655606 ARHGEF12 1.4334453 0.002568832 RPS25 1.3445363 0.002568832

12p13 ENO2 15.649661 4.865E-05 1.8115 VWF 13.281776 0.000105586 CD163 6.0124803 0.000282108 C1R 5.0476713 0.000282108 C1S 4.949597 0.000221847 CLEC2B 4.66488 6.32159E-05 CLEC7A 4.3986263 4.865E-05 SLC2A3 3.853733 0.000567769 C1RL 3.809806 0.000135723 C3AR1 3.7572336 0.000357454 CSDA 3.004484 4.865E-05 TEAD4 2.726262 4.865E-05 C12orf4 2.6736548 4.865E-05 RAD51AP1 2.6320994 0.000221847 POU5F1P3 2.5892355 0.000711741 CD4 2.509035 0.000173833 TAPBPL 2.4500844 0.000105586 C12orf5 2.337002 0.001106586 CLEC4A 2.3243923 0.000221847 TPI1 2.3075743 0.000135723 1.3969 GAPDH 2.2569053 0.000135723 2.3475 IFFO1 2.2345917 4.865E-05 TNFRSF1A 2.2189476 0.000282108 CCND2 2.1814523 0.006768741 LTBR 2.1641285 0.000135723 CLEC2D 2.0429237 8.18466E-05 OLR1 1.9987966 0.001696221 PTPN6 1.8433444 0.000135723 M6PR 1.8308514 0.000282108 ETV6 1.8303165 0.000451307 KDM5A 1.7347827 0.000282108 FOXM1 1.7323442 0.000135723 TULP3 1.723852 0.001106586 NOP2 1.6987089 0.000173833 LPCAT3 1.6986471 0.002088939 NCAPD2 1.6859876 0.000889049 RPL13P5 1.6840355 0.001372472 ATF7IP 1.646293 0.001372472 EMG1 1.6445929 0.002088939 MAGOHB 1.6423533 0.000173833 CDKN1B 1.5164346 0.005613233 DYRK4 1.5147424 0.000282108 KLRB1 1.5106701 0.016382353 FOXJ2 1.4741824 0.001106586 PHB2 1.447331 0.000357454 LRRC23 1.3994046 0.003820066 NINJ2 1.3867277 0.000889049 DDX47 1.3634212 0.000711741 ADIPOR2 1.344004 0.002563516 TSPAN9 1.3297207 0.006768741

12q12 TWF1 2.3134782 0.007777804 IRAK4 1.8993536 0.003506386 YAF2 1.6042188 0.006772368

12q13 NDUFA4L2 64.08346 0.000357454 hsa-miR-196a 1.73 (3.13) SHMT2 4.4800878 4.865E-05 SLC38A1 3.9205265 4.865E-05 FKBP11 3.798632 0.000282108 ITGA5 3.4976664 0.000105586 NCKAP1L 2.9358382 8.18466E-05 DNAJC22 2.9298146 0.001372472 PRIM1 2.8621795 8.18466E-05 RACGAP1 2.6592042 6.32159E-05 TUBA1B 2.6587665 4.865E-05 KRT18 2.2520263 0.001696221 CDK2 2.2493043 0.000567769 TUBA1C 2.2153275 4.865E-05 SMAGP 2.1427095 0.002088939 TUBA1A 2.0786529 0.000889049 1.387 TMEM194A 2.03424 0.000105586 KRT8 1.9840353 0.004638759 SPATS2 1.9493597 0.000221847 PA2G4 1.8015115 0.000567769 MFSD5 1.7943906 0.000889049 STAT2 1.7641463 0.000282108 BIN2 1.7299684 0.000282108 C12orf10 1.707712 0.000711741 CSRNP2 1.7033466 0.000451307 MYL6B 1.6851046 0.000889049 HNRNPA1 1.6757094 0.000357454 CD63 1.6544183 4.865E-05 CBX5 1.6259754 0.001372472 RPAP3 1.6134547 0.002563516 CNPY2 1.6100379 0.009740121 C12orf44 1.5944185 0.002088939 ATP5G2 1.5661222 0.003820066 MARS 1.5541817 0.000451307 PFDN5 1.522911 8.18466E-05 TIMELESS 1.5185109 0.003134851 DDX23 1.5178 0.000357454 OBFC2B 1.5103565 0.01382302 COPZ1 1.4815803 0.002563516 1.2217 ARF3 1.4614278 0.009740121 EIF4B 1.3895594 0.01382302 RPS26 1.3875382 0.011623421 DCTN2 1.3021663 0.000567769 1.65 FAM62A 1.6185428 0.001106586

12q14 XPOT 2.379726 0.000451307 hsa-miR-26a OS9 1.7699733 0.000451307 has-let-7i 1.71 (0) TBK1 1.6140596 0.000451307 MON2 1.6087942 0.008133745 CDK4 1.6037104 0.001696221 CAND1 1.6030141 0.001372472 TSPAN31 1.5116675 8.18466E-05 USP15 1.4665006 0.008133745 TMEM5 1.4562546 0.002563516

12q23 CHST11 2.878205 0.000357454 GNPTAB 2.551823 4.865E-05 APAF1 2.5020764 6.32159E-05 NT5DC3 2.4555144 6.32159E-05 NR1H4 2.2371473 0.002563516 CKAP4 2.2330723 8.18466E-05 ARL1 1.9143332 0.000711741 ELK3 1.8625778 0.008133745 TXNRD1 1.8283358 0.000567769 TDG 1.8160003 0.002088939 HSP90B1 1.7987081 0.001696221 1.2976 TMPO 1.7918996 0.001106586 IGF1 1.6739446 0.003134851 KIAA1033 1.6371336 0.004638759 SART3 1.6190393 0.000567769 PWP1 1.6110387 0.000567769 PMCH 1.5172081 0.000451307 NUP37 1.4926137 0.002563516 SNRPF 1.4918324 0.000711741 UTP20 1.4762542 0.001696221 C12orf48 1.4254476 0.000357454 NFYB 1.3863605 0.011623421 ACTR6 1.3784055 0.003820066 CCDC53 1.3423446 0.001106586

12q24 SCARB1 6.2540517 0.001828783 HSPB8 5.454665 0.001828783 SDS 3.8735201 0.001828783 CORO1C 3.5471332 0.001828783 TMED2 3.2046106 0.005883939 OAS1 2.894441 0.002356957 ANKLE2 2.796788 0.001828783 KNTC1 2.5019665 0.001828783 SELPLG 2.4613168 0.002680086 RFC5 2.3606331 0.011927204 P2RX4 2.2482572 0.005081878 SH2B3 2.236677 0.002680086 GIT2 2.127639 0.007777804 C12orf24 2.1046882 0.003065616 MLEC 1.9740444 0.007777804 ATP2A2 1.9562038 0.001828783 ARPC3 1.9498146 0.001937521 GOLGA3 1.9422044 0.001828783 NCOR2 1.879715 0.004557903 RPLP0 1.8723598 0.001828783 WSB2 1.8542365 0.002680086 ANAPC5 1.8473028 0.011927204 ARL6IP4 1.8186601 0.002680086 OAS2 1.7944185 0.003065616 P2RX7 1.779584 0.001828783 CHFR 1.7795035 0.005081878 OAS3 1.7751935 0.008975465 CDK2AP1 1.7722914 0.001937521 UBC 1.7573205 0.001937521 2.1816 PUS1 1.7331235 0.003994343 SSH1 1.7169564 0.007777804 TAOK3 1.6808437 0.00212026 ZNF84 1.672692 0.005883939 RAN 1.6532179 0.005883939 DENR 1.6463028 0.003065616 TRIAP1 1.6388098 0.008975465 MED13L 1.6142005 0.027104776 ZNF26 1.5860808 0.015730055 MPHOSPH9 1.5701799 0.008975465 TCTN1 1.5478817 0.005883939 MLXIP 1.5260354 0.027104776 STX2 1.5058167 0.011927204 CAMKK2 1.4600103 0.015730055 PTPN11 1.4593782 0.010345777 OASL 1.450786 0.010345777 ZCCHC8 1.4433038 0.027104776 SBNO1 1.4425064 0.002356957 RNF34 1.4205961 0.001828783 ATP6V0A2 1.4171482 0.015730055 BRAP 1.4128227 0.011927204 EIF2B1 1.4118671 0.002356957 TRAFD1 1.4040751 0.004557903 PPP1CC 1.4035268 0.013709282 CLIP1 1.3836473 0.008975465 RAB35 1.3759016 0.015730055 IFT81 1.3543102 0.045482263 RPL6 1.3542941 0.005883939

13q12 SLC46A3 1.890755 0.030055966 RNF6 1.500461 0.006069277 ATP8A2 1.4114263 0.024098728 TUBA3C 1.3085907 0.04583026

13q34 CDC16 1.3543209 0.030055966

15q23 FEM1B 1.8843379 0.010197877 hsa-miR-629 3.70 (0) RPLP1 1.4705117 0.010197877

15q24 COMMD4 2.050787 0.035557915 TBC1D2B 2.0143714 0.023967674 TSPAN3 1.7649868 0.010197877 CSK 1.5989788 0.010197877 ADPGK 1.5226713 0.010197877 PML 1.308796 0.015806774

15q25 BCL2A1 6.7092385 0.010197877 TM6SF1 6.497982 0.015806774 NMB 4.961821 0.010197877 TMED3 3.014055 0.010197877 ALPK3 2.1777272 0.010197877 HDGFRP3 2.0456703 0.035557915 ST20 1.7952751 0.035557915 IDH3A 1.7629496 0.015806774 EFTUD1 1.6409279 0.010197877 WDR61 1.4169896 0.035557915 PSMA4 1.3265251 0.023967674

16p12 TMEM159 2.3812034 0.000488805 IL4R 2.2309372 0.020918602 UBFD1 2.1326842 0.001303913 IGSF6 1.9583573 0.002413473 COQ7 1.8946029 0.001303913 DCTN5 1.8659236 0.003246108 PRKCB 1.6646826 0.041574918 C16orf88 1.6542548 0.000488805 LOC81691 1.5785733 0.000488805 GDE1 1.5403005 0.0333108 ERI2 1.5078685 0.009847163 XYLT1 1.5065948 0.004332901 PALB2 1.3998682 0.003246108 ARL6IP1 1.3865948 0.020918602 RPS15A 1.3389788 0.000488805 SMG1 1.3386229 0.026494633 LCMT1 1.312358 0.003246108

Underexpression 1p21 F3 -2.6110916 0.001303913 ABCD3 -2.5815346 0.000488805 EXTL2 -2.4288983 0.000683158 DBT -2.2380302 0.000683158 AGL -2.0485628 0.001303913 1.4585 RTCD1 -1.5350739 0.09383939 PTBP2 -1.4121369 0.005739856 CCDC76 -1.4044906 0.020918602 CDC14A -1.3373878 0.005739856

1p22 TGFBR3 -8.491916 0.000488805 CYR61 -7.020074 0.000488805 DDAH1 -3.3725047 0.000488805 1.04045 CCBL2 -2.142662 0.000683158 MCOLN3 -2.5642684 0.000947449 BCAR3 -2.030022 0.001780769 FNBP1L -1.9499693 0.001780769 LRRC8D -1.6428621 0.003246108 PKN2 -1.4359144 0.009847163

1p31 PTGER3 -25.010237 0.000488805 CTH -4.354625 0.000488805 ACADM -4.1359634 0.000488805 0.3938 GIPC2 -4.124153 0.002413473 DNAJC6 -3.6849895 0.001780769 GADD45A -3.2416766 0.001780769 LPHN2 -2.2193797 0.01639431 CRYZ -2.0795681 0.001780769 1.3097 PTGFR -1.9044491 0.000488805 DIRAS3 -1.6587932 0.020918602 PIGK -1.5376087 0.0333108 PRKACB -1.4698626 0.001780769 TNNI3K -1.4282532 0.012753347 LEPROT -1.4131866 0.01639431 USP33 -1.4083297 0.0333108

1p32 ECHDC2 -2.714277 0.001303913 0.8142 CPT2 -2.4615023 0.002413473 ACOT11 -2.4042149 0.004332901 OSBPL9 -2.0185657 0.000488805 ZFYVE9 -1.9116511 0.002413473 SCP2 -1.8856713 0.000683158 RNF11 -1.8159295 0.000947449 PRKAA2 -1.6208817 0.007546423 USP24 -1.5183494 0.005739856

1p36 CLCNKB -21.513214 0.000488805 hsa-miR-200b 0.22 (0) ALDH4A1 -9.108054 0.000683158 1.02555 hsa-miR-200b* 0.74 (1.79) MAN1C1 -8.060461 0.001780769 hsa-miR-200a 0.42 (0) RAP1GAP -5.6716685 0.000488805 hsa-miR-429 0.23 (0) AKR7A3 -5.263788 0.001780769 RNF186 -3.8556798 0.007546423 FCN3 -3.5384014 0.007546423 NR0B2 -2.9829412 0.000947449 CAMK2N1 -2.8848548 0.007546423 PRKCZ -2.7371714 0.001303913 RERE -2.6634948 0.000488805 HMGCL -2.58011 0.000488805 0.7703 PINK1 -2.4990432 0.000488805 AKR7A2 -2.4437664 0.000488805 1.0148 DNAJC11 -2.443441 0.000488805 ARHGEF10L -2.4230113 0.000488805 ICMT -2.207231 0.000947449 VPS13D -2.1257784 0.000488805 PIGV -2.1037006 0.000488805 APITD1 -2.0947626 0.000683158 KIF1B -2.0660872 0.000488805 ACOT7 -2.0639777 0.0333108 ALPL -2.0573113 0.012753347 CTNNBIP1 -1.995235 0.000683158 SDHB -1.9932016 0.002413473 TCEB3 -1.8833405 0.000488805 MFN2 -1.8063792 0.004332901 PGD -1.7502158 0.002413473 0.8431 NOL9 -1.7339257 0.000488805 CASP9 -1.7054665 0.007546423 CDA -1.6930678 0.0333108 SPEN -1.678056 0.009847163 DNAJC16 -1.6638454 0.000488805 ZBTB40 -1.649072 0.005739856 LYPLA2 -1.6279714 0.003246108 CNKSR1 -1.5936087 0.003246108 CLCN6 -1.5918157 0.026494633 KLHL21 -1.5793577 0.020918602 AJAP1 -1.5565196 0.000488805 PAFAH2 -1.5558577 0.005739856 TMEM51 -1.5364941 0.000947449 DFFA -1.5310102 0.0333108 CLSTN1 -1.515215 0.003246108 FBXO2 -1.5082095 0.007546423 SRRM1 -1.4937419 0.005739856 OTUD3 -1.4836516 0.007546423 WDTC1 -1.4635353 0.002413473 LRRC47 -1.4515966 0.004332901 ARID1A -1.4489956 0.003246108 ECE1 -1.4470655 0.020918602 MUL1 -1.4452276 0.012753347 LUZP1 -1.4183333 0.004332901 DHDDS -1.4137248 0.01639431 FBXO42 -1.385308 0.003246108 LDLRAP1 -1.3833185 0.001303913 CDC42 -1.3832303 0.000947449 CASZ1 -1.3728344 0.005739856 MRPL20 -1.3531826 0.026494633 C1orf144 -1.3488806 0.007546423

2q33 AOX1 -11.11567 0.003561337 PLCL1 -6.6838384 0.000911119 FZD7 -2.594811 0.001299361 NDUFS1 -2.2811754 0.00489131 C2orf47 -1.9940252 0.001299361 NDUFB3 -1.7165382 0.000911119 HSPD1 -1.6646105 0.003561337 0.4896 ABI2 -1.504639 0.003561337 CYP20A1 -1.4481248 0.00489131 INO80D -1.3472424 0.006655606

2q35 IGFBP2 -5.1055794 0.016298022 hsa-miR-375 0.48 (0) OBSL1 -2.2792678 0.01864035 DNAJB2 -2.131178 0.015162837 IGFBP5 -1.9986757 0.015162837 NHEJ1 -1.7810917 0.021384338 BCS1L -1.5188166 0.021384338 RNF25 -1.5139511 0.015162837 FEV -1.326169 0.025440978

2q37 EFHD1 -16.979813 0.000911119 RAB17 -5.121099 0.000911119 SH3BP4 -3.23283 0.001299361 THAP4 -3.1195683 0.000911119 AGXT -3.1164303 0.001299361 ITM2C -2.5689545 0.000911119 ATG4B -2.0342157 0.000911119 HDLBP -1.973038 0.001299361 KCNJ13 -1.935905 0.001835603 SNED1 -1.9017657 0.003561337 GIGYF2 -1.7549703 0.000911119 RAMP1 -1.6949233 0.008972547 FARP2 -1.6489636 0.002568832 SCLY -1.6005402 0.003561337 CAB39 -1.5523397 0.002568832 C2orf54 -1.5452365 0.011984701 ILKAP -1.5108578 0.002568832 ASB1 -1.4888543 0.002568832 PRLH -1.4604852 0.001835603 CAPN10 -1.4453862 0.000911119 ALPPL2 -1.4008411 0.003561337 STK25 -1.3880905 0.00489131 ARMC9 -1.3585374 0.001835603 ANKMY1 -1.3489957 0.000911119 MTERFD2 -1.3241819 0.011984701 PDCD1 -1.3241421 0.001835603 BOK -1.3238205 0.002568832 C2orf72 -1.3140182 0.000911119 TRPM8 -1.3034767 0.006655606

4q26 UGT8 -2.6914299 0.004385488

4q35 SLC25A4 -4.1493382 0.000950249 KLKB1 -3.5579967 0.000307674 ACSL1 -3.3810718 0.000307674 0.7584 F11 -3.348324 0.000169439 CDKN2AIP -2.4210892 0.000169439 SORBS2 -2.296915 0.013543603 UFSP2 -1.7147213 0.000169439 WWC2 -1.6041998 0.002691283 FRG1 -1.4350548 0.006995319 MTNR1A -1.3311014 0.00161652

6q12 LMBRD1 -2.1121042 0.000282108 PTP4A1 -1.9734273 0.006768741

6q14 BCKDHB -3.1072314 4.865E-05 MYO6 -2.5208662 4.865E-05 1.007 CGA -1.8757132 0.001106586 COX7A2 -1.387985 0.01382302 DOPEY1 -1.341411 0.003820066

6q21 SOBP -3.9283726 0.000105586 SLC16A10 -3.6603706 0.001106586 PDSS2 -2.4590247 6.32159E-05 CD164 -1.6202844 0.000173833 DDO -1.6067522 0.011623421 ATG5 -1.5788677 0.001106586 CDC40 -1.5027118 0.001106586 QRSL1 -1.4573321 0.000135723 WISP3 -1.3921852 0.000357454 FIG4 -1.3624959 0.004638759 HDAC2 -1.3022851 0.011623421

6q23 TCF21 -9.724438 4.865E-05 ALDH8A1 -8.903574 0.000105586 VNN1 -4.6026616 0.000567769 MOXD1 -3.2272348 0.008133745 CTGF -2.9915884 0.008133745 PEX7 -2.8490489 4.865E-05 MAP7 -2.7319303 0.000357454 ENPP1 -2.0071585 0.004638759 SGK1 -1.7649832 0.005613233 EYA4 -1.5102203 0.000889049 STX7 -1.4438487 0.001696221 TBPL1 -1.3490674 0.011623421

6q24 EPM2A -2.5038443 4.865E-05 PEX3 -2.1585586 0.000711741 CCDC28A -2.0537417 4.865E-05 SF3B5 -1.697794 0.001106586 GRM1 -1.5246212 0.001372472 REPS1 -1.3000209 0.006768741

6q25 SLC22A2 -2.8339405 0.008133745 SYNE1 -2.5685928 8.18466E-05 1.0144 ESR1 -2.2121353 0.000567769 UST -1.7448719 0.003134851 GTF2H5 -1.6689472 6.32159E-05 TCP1 -1.663162 0.002563516 1.2802 IPCEF1 -1.538179 0.000173833 ZDHHC14 -1.5292158 0.002563516 PCMT1 -1.5209732 0.002088939 0.9004 KATNA1 -1.4092135 0.003134851 ACAT2 -1.377403 0.008133745 TULP4 -1.3617823 0.003134851 MRPL18 -1.3462474 0.006768741

8p11 SFRP1 -78.82839 1.40883E-05 PLAT -4.645309 1.40883E-05 C8orf4 -4.26624 3.39672E-05 PROSC -2.1934686 1.40883E-05 1.2089 ERLIN2 -1.9050825 3.39672E-05 VDAC3 -1.4920257 0.00572031 SLC20A2 -1.4715853 1.40883E-05 LSM1 -1.4683243 0.00221725 ASH2L -1.4355121 4.19671E-05 RAB11FIP1 -1.4140378 0.006646598 DDHD2 -1.406126 0.004912083

8p12 KIF13B -3.799703 1.40883E-05 HMBOX1 -1.6924793 0.006646598 PPP2CB -1.689077 0.000315432 NRG1 -1.6490415 0.002611368 GSR -1.3775569 0.026378946 C8orf41 -1.3450551 0.011847134 DUSP26 -1.33932 0.000176606 INTS9 -1.3315829 0.008913401 RBPMS -1.3096105 0.020379877

8p21 EPHX2 -7.783408 1.40883E-05 EGR3 -2.8047898 0.000315432 CCDC25 -2.1524184 1.76168E-05 XPO7 -1.8477161 7.89022E-05 ATP6V1B2 -1.7969836 0.003597712 PDLIM2 -1.7937388 0.003068585 EPB49 -1.761476 2.19778E-05 SH2D4A -1.5088856 0.000260579 R3HCC1 -1.4491982 0.000315432 PHYHIP -1.4304783 0.00021477 FZD3 -1.4036999 0.003068585 RHOBTB2 -1.4026002 0.000315432 CHMP7 -1.3992498 0.002611368 PTK2B -1.3857087 0.00221725 SFTPC -1.3846309 0.003068585 HR -1.3427289 0.001126516

8p23 DEFB1 -27.705252 1.76168E-05 hsa-miR-124 0.69 (4.62) MSRA -5.829739 1.40883E-05 MFHAS1 -2.6324136 0.000144888 FDFT1 -2.539955 1.40883E-05 MYOM2 -2.3435063 1.40883E-05 CLN8 -2.2847173 0.000260579 DLGAP2 -1.8575065 1.40883E-05 FAM86B1 -1.5231903 0.003597712 MTMR9 -1.4552071 0.000551833 CTSB -1.4100988 0.017854292 1.03255

9p13 AQP3 -5.2168283 0.001303913 GRHPR -3.3625052 0.000947449 AQP7 -3.318774 0.003246108 GALT -2.5403771 0.000488805 BAG1 -2.3657508 0.000488805 UNC13B -2.357195 0.000488805 RUSC2 -1.698641 0.000683158 ZBTB5 -1.6938094 0.005739856 PRSS3 -1.5658572 0.000683158 1.5712 PIGO -1.5651555 0.004332901 RNF38 -1.536028 0.003246108 RGP1 -1.5155336 0.000947449 UBAP2 -1.3738499 0.009847163 PAX5 -1.3695283 0.000683158 CLTA -1.3560579 0.012753347 2.1186

9p21 LRRC19 -7.1094227 0.000683158 hsa-miR-31 0.23 (1.79) ACO1 -3.1971056 0.003246108 0.93075 C9orf82 -1.6855391 0.000488805 IFT74 -1.5115336 0.012753347 KLHL9 -1.4922161 0.003246108 APTX -1.4727117 0.009847163 CDKN2A -1.325645 0.005739856

9p22 TYRP1 -7.0241637 0.000488805 SH3GL2 -5.3229685 0.001780769 MPDZ -1.7761254 0.004332901 BNC2 -1.6706934 0.009847163 CER1 -1.3000299 0.002413473

9p24 PTPRD -7.0227103 0.000488805 hsa-miR-101 GLDC -6.8691463 0.001780769 ERMP1 -4.025354 0.000488805 SLC1A1 -3.1770155 0.000488805 KANK1 -2.8876412 0.000683158 CDC37L1 -1.8859879 0.000683158 SMARCA2 -1.8130083 0.001303913 RANBP6 -1.3596748 0.004332901

9q34 ASS1 -13.039778 0.000488805 0.8699 CEL -2.9578874 0.000488805 TBC1D13 -2.8563676 0.000488805 LAMC3 -2.067886 0.003246108 COQ4 -1.9734997 0.003246108 FAM102A -1.9214023 0.009847163 SARDH -1.8996989 0.000683158 NELF -1.7963291 0.007546423 SPTAN1 -1.7693053 0.003246108 1.1218 CCBL1 -1.7624958 0.000947449 TSC1 -1.7472559 0.003246108 AGPAT2 -1.6962974 0.000947449 ADAMTSL2 -1.6783478 0.000488805 C9orf7 -1.6502984 0.003246108 ZER1 -1.6381918 0.001303913 PTGES2 -1.5966904 0.007546423 VAV2 -1.5815904 0.000947449 BRD3 -1.5440102 0.003246108 SURF2 -1.53936 0.012753347 ABO -1.5353174 0.000683158 POMT1 -1.5280976 0.001303913 FUT7 -1.4976943 0.004332901 GOLGA2 -1.461394 0.003246108 OLFM1 -1.4124936 0.012753347 DOLPP1 -1.3912395 0.012753347 SLC2A8 -1.3851354 0.012753347 C9orf9 -1.380589 0.001780769 ASB6 -1.3753369 0.005739856 SH3GLB2 -1.3391562 0.012753347 USP20 -1.3367515 0.000683158 GRIN1 -1.335601 0.000947449 C9orf78 -1.3294461 0.012753347 CELP -1.3189878 0.001303913 EDF1 -1.3111839 0.001780769

14q11 SLC7A8 -16.511494 4.59283E-06 PCK2 -12.200599 4.59283E-06 1.27755 SLC7A7 -3.80501 0.000207502 NDRG2 -2.8666945 4.59283E-06 BCL2L2 -2.1264424 4.59283E-06 PABPN1 -2.0504832 0.000109548 CCNB1IP1 -1.9894434 4.01762E-05 CPNE6 -1.8881421 4.76656E-05 THTPA -1.7235199 4.59283E-06 RBM23 -1.6466103 1.99752E-05 PARP2 -1.5953352 4.59283E-06 ABHD4 -1.5440408 0.000191568 SLC22A17 -1.466552 0.001222438 ACIN1 -1.4595654 0.00044588 PRMT5 -1.3828062 0.049534615 0.99075 SALL2 -1.365497 0.000517274 LRP10 -1.3128474 0.002403663 TOX4 -1.305048 0.011754679

14q12 DHRS1 -2.5579534 5.54857E-06 PRKD1 -2.504975 1.99752E-05 SDR39U1 -2.108381 5.54857E-06 COCH -1.9154326 6.67912E-05 GMPR2 -1.8718363 5.64661E-05 ARHGAP5 -1.6306528 0.00038377 REC8 -1.5262891 4.76656E-05 TM9SF1 -1.4027736 0.001609165 NUBPL -1.3187398 0.00354341

14q13 C14orf147 -1.7056395 6.67912E-05 KIAA0391 -1.476482 0.001063115 MBIP -1.4033751 2.38419E-05

14q21 CDKL1 -1.9639364 1.16415E-05 ATP5S -1.8134117 2.38419E-05 CTAGE5 -1.7787784 1.99752E-05 KLHDC2 -1.7522479 5.64661E-05 L2HGDH -1.5875351 2.38419E-05 SOS2 -1.5465149 6.67912E-05 FAM179B -1.3862213 0.00354341 FKBP3 -1.356943 0.001609165

14q22 GCH1 -2.9353695 0.00038377 C14orf105 -2.8416824 7.88858E-05 PELI2 -2.5428283 5.64661E-05 FBXO34 -2.263056 8.06136E-06 MUDENG -2.2437584 8.06136E-06 FERMT2 -2.1431055 7.88858E-05 MAPK1IP1L -1.7633004 4.59283E-06 SAV1 -1.7192346 2.38419E-05 CGRRF1 -1.685358 4.01762E-05 BMP4 -1.6802483 0.013147499 KTN1 -1.5954976 3.38127E-05 0.74245

14q23 TMEM30B -9.353352 4.59283E-06 HSPA2 -5.514845 4.59283E-06 GPHN -5.0177884 3.38127E-05 MPP5 -2.7680082 4.59283E-06 DAAM1 -2.6222804 2.84144E-05 SGPP1 -2.2895417 0.000242524 ATP6V1D -2.1513863 3.38127E-05 SYNE2 -2.1126335 4.76656E-05 PLEKHG3 -1.9945592 1.67104E-05 DHRS7 -1.8589369 2.38419E-05 PPM1A -1.77297 2.38419E-05 MTHFD1 -1.753241 4.01762E-05 1.2867 RAB15 -1.7417512 7.88858E-05 ACTR10 -1.536937 9.69475E-06 MNAT1 -1.3669592 0.000151221 GPX2 -1.3257567 0.00354341 0.8865

14q24 ALDH6A1 -16.066687 4.59283E-06 0.8104 ARG2 -15.023884 4.01762E-05 ENTPD5 -6.4405074 9.69475E-06 FOS -5.0605774 1.39581E-05 RDH11 -2.8451805 9.69475E-06 COX16 -2.2401416 6.69303E-06 SYNJ2BP -2.2354302 4.59283E-06 PIGH -2.1426082 5.54857E-06 COQ6 -2.0405922 6.69303E-06 GSTZ1 -2.0282314 3.38127E-05 EXD2 -2.0250368 5.54857E-06 KIAA0317 -1.920954 6.69303E-06 C14orf1 -1.7412302 1.16415E-05 VTI1B -1.7377657 6.69303E-06 PNMA1 -1.6676008 6.67912E-05 YLPM1 -1.4924794 0.000207502 ABCD4 -1.4838419 6.67912E-05 AHSA1 -1.4810544 0.000800504 ALKBH1 -1.4393547 0.000093031 FAM164C -1.4310614 2.84144E-05 C14orf169 -1.34051 0.00455635 RBM25 -1.3368942 0.000283035 NEK9 -1.3298033 2.84144E-05 ZNF410 -1.3103356 0.000599209 C14orf45 -1.3036801 0.041021463

14q31 KCNK10 -2.7949378 4.59283E-06 FLRT2 -1.957936 0.00311798 ZC3H14 -1.6804653 5.64661E-05 SPATA7 -1.3700268 0.011754679 PTPN21 -1.3629067 0.000207502

17p13 MYH10 -4.144812 0.0040752 0.87225 PER1 -4.1016297 0.006111785 CLDN7 -3.7093875 0.0040752 C17orf91 -2.6488252 0.018770974 SLC25A11 -2.6309252 0.0040752 TRPV1 -2.5565774 0.006111785 ACADVL -2.4702368 0.0040752 KIAA0664 -2.4281237 0.0040752 KIF1C -2.4130118 0.0040752 VAMP2 -2.2336674 0.0040752 SHPK -2.050427 0.006111785 SGSM2 -2.0154922 0.0040752 MYH8 -2.0121317 0.006111785 RNMTL1 -1.9737664 0.0040752 RANGRF -1.9415458 0.006111785 CRK -1.9298035 0.0040752 GLOD4 -1.9035732 0.006111785 0.9164 KDM6B -1.8745964 0.00902344 SPAG7 -1.8630852 0.0040752 PRPF8 -1.8334504 0.0040752 ATP1B2 -1.8124943 0.006111785 PAFAH1B1 -1.8071938 0.0040752 TSR1 -1.7873822 0.013115905 SRR -1.777462 0.0040752 CHD3 -1.7499595 0.0040752 ZNF232 -1.7292933 0.013115905 FXR2 -1.7276075 0.0040752 MYO1C -1.6935558 0.0040752 NUP88 -1.6648505 0.0040752 CTNS -1.6402328 0.00902344 TIMM22 -1.623723 0.036713865 STX8 -1.6128395 0.0040752 PITPNA -1.6061198 0.00902344 ALOX12P2 -1.5933323 0.018770974 ZZEF1 -1.588815 0.00902344 RPH3AL -1.5789173 0.026453404 C17orf59 -1.5656781 0.00902344 RNF167 -1.5436816 0.0040752 ACAP1 -1.5380886 0.0040752 YWHAE -1.516611 0.0040752 0.8359 C1QBP -1.5138955 0.026453404 INPP5K -1.4432847 0.0040752 TNK1 -1.4047775 0.00902344 POLR2A -1.3848497 0.0040752 DOC2B -1.3723925 0.0040752 ARHGEF15 -1.3717 0.006111785 SOX15 -1.3572888 0.036713865 CAMTA2 -1.3499546 0.00902344 OR1D2 -1.337166 0.006111785 EIF5A -1.3305459 0.026453404 0.6179 SENP3 -1.3302438 0.0040752 SMG6 -1.3202077 0.00902344 ALOXE3 -1.3171515 0.00902344 ATP2A3 -1.3143101 0.018770974 TMEM93 -1.3134004 0.018770974 GABARAP -1.3104292 0.00902344 DLG4 -1.308932 0.036713865 MINK1 -1.3005959 0.018770974 Bolded genes coincide with significant focal gains and losses as detected by JISTIC. The remaining regions coincide with broad regions of gains and losses.