Spreadsheet: 51ee5b9a-4280-4b96-b539-381bcc2e186f
Sheet: Sheet1

Supplementary Table 1.  Top-scoring SNPs using ADT analysis (p ≤ 0.005) from 178 TCGA samples.  Pairs of SNPs that are in LD are indicated by colored rows.  For groups of SNPs in LD, a reference to a Supplementary Figure is given. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10
rsID | chromosome | position (hg18) | A amplified over B | B amplified over A | ADT P-value | nearest gene (within 100kb) | in transcribed region | SNP Hit in LD | r2 of SNP in LD | [NAME]
rs3134884 | 4 | 55261023 | 1 | 12 | 0.00341796875 | KIT | Yes
rs10487575 | 7 | 4252828 | 24 | 6 | 0.00143090635538102 | [NAME] | Yes | rs10951486 | 0.95 | Ver_2_Rel_22
rs10951486 | 7 | 4260502 | 24 | 5 | 0.000546112656593324 | [NAME] | Yes | rs10487575 | 0.95 | Ver_2_Rel_22
rs9690101 | 7 | 4754138 | 27 | 5 | 0.000113074202090502 | FOXK1 | Yes
rs3735461 | 7 | 7646169 | 32 | 12 | 0.00365776682792785 | [NAME] | Yes
rs10255873 | 7 | 8526816 | 23 | 6 | 0.00231570005416871 | NXPH1 | Yes | See Supp Figure AA |  | Ver_2_Rel_22
[NAME] | 7 | 8529408 | 25 | 4 | 0.000103715807199478 | NXPH1 | Yes | See Supp Figure AA |  | Ver_2_Rel_22
rs1557841 | 7 | 8533529 | 27 | 6 | 0.000324063468724489 | NXPH1 | Yes | See Supp Figure AA |  | Ver_2_Rel_22
rs965483 | 7 | 8904473 | 28 | 8 | 0.00119324296247214 |  |  | rs1017266 | 0.77 | Ver_2_Rel_22
rs1017266 | 7 | 8912697 | 28 | 8 | 0.00119324296247214 |  |  | rs965483 | 0.77 | Ver_2_Rel_22
rs2016550 | 7 | 8926821 | 3 | 17 | 0.00257682800292969
[NAME] | 7 | 11536259 | 10 | 29 | 0.00337784791190643 | THSD7A | Yes | See Supp Figure BB |  | Ver_3_Rel_2
rs40 | 7 | 11554809 | 10 | 30 | 0.00222143377322937 | THSD7A | Yes | See Supp Figure BB |  | Ver_3_Rel_2
rs2107479 | 7 | 11566565 | 25 | 8 | 0.00455138413235546 | THSD7A | Yes | See Supp Figure BB |  | Ver_3_Rel_2
rs1467344 | 7 | 11750482 | 18 | 4 | 0.00434350967407227 | THSD7A | Yes | See Supp Figure BB |  | Ver_3_Rel_2
rs10950366 | 7 | 11758146 | 18 | 4 | 0.00434350967407227 | THSD7A | Yes | See Supp Figure BB |  | Ver_3_Rel_2
rs765001 | 7 | 14084874 | 11 | 30 | 0.0043240049344604 | DGKB | No
rs6980441 | 7 | 19973318 | 29 | 10 | 0.00337784791190643
rs4722357 | 7 | 24409436 | 32 | 11 | 0.0019139610012644 |  |  | rs9785009 | 0.56 | Ver_2_Rel_22
rs9785009 | 7 | 24420723 | 33 | 12 | 0.00245890032209673 |  |  | rs4722357 | 0.56 | Ver_2_Rel_22
rs864249 | 7 | 28235781 | 25 | 8 | 0.00455138413235546 | JAZF1 | No
rs12540480 | 7 | 28713438 | 24 | 7 | 0.00332689285278321 | [NAME] | Yes
rs1420130 | 7 | 29485505 | 9 | 28 | 0.00256320799235255 | CHN2 | Yes | Negligible LD
rs1468784 | 7 | 29489574 | 18 | 4 | 0.00434350967407227 | CHN2 | Yes | Negligible LD
rs2530552 | 7 | 34664901 | 30 | 8 | 0.000471986742923037 | NPSR1 | Yes | See Supp Figure CC |  | Ver_2_Rel_22
rs425990 | 7 | 34668324 | 35 | 10 | 0.000247087784600809 | NPSR1 | Yes | See Supp Figure CC |  | Ver_2_Rel_22
rs2530571 | 7 | 34677105 | 10 | 29 | 0.00337784791190643 | NPSR1 | Yes | See Supp Figure CC |  | Ver_2_Rel_22
rs324389 | 7 | 34744239 | 32 | 11 | 0.0019139610012644 | NPSR1 | Yes | See Supp Figure CC |  | Ver_2_Rel_22
rs10267134 | 7 | 34769628 | 5 | 20 | 0.00407731533050537 | NPSR1 | Yes | See Supp Figure CC |  | Ver_2_Rel_22
rs10278663 | 7 | 34774996 | 21 | 4 | 0.000910520553588867 | NPSR1 | Yes | See Supp Figure CC |  | Ver_2_Rel_22
rs17199888 | 7 | 34830864 | 24 | 5 | 0.000546112656593324 | NPSR1 | Yes | See Supp Figure CC |  | Ver_2_Rel_22
rs7782269 | 7 | 38285115 | 31 | 11 | 0.00288724797428586 | TARP | No | rs1860517 | 0.64 | Ver_2_Rel_22
rs1860517 | 7 | 38297335 | 34 | 11 | 0.000824082359599745 | TARP | No | rs7782269 | 0.64 | Ver_2_Rel_22
[NAME] | 7 | 40885914 | 23 | 6 | 0.00231570005416871 | C7orf10 | No
rs1025541 | 7 | 43525797 | 2 | 18 | 0.000402450561523438 | [NAME] | Yes
rs6946623 | 7 | 48889215 | 1 | 12 | 0.00341796875 | CDC14C | No
rs6965611 | 7 | 52134879 | 22 | 5 | 0.00151371955871582 |  |  | See Supp Figure DD |  | Ver_2_Rel_22
rs2464946 | 7 | 52135582 | 23 | 5 | 0.000912234187126161 |  |  | See Supp Figure DD |  | Ver_2_Rel_22
rs11238181 | 7 | 52192893 | 27 | 7 | 0.000821395311504603 |  |  | See Supp Figure DD |  | Ver_2_Rel_22
rs2330099 | 7 | 52450076 | 25 | 8 | 0.00455138413235546 |  |  | rs12718639 | 0.87 | Ver_2_Rel_22
rs12718639 | 7 | 52472931 | 28 | 9 | 0.00256320799235255 |  |  | rs2330099 | 0.87 | Ver_2_Rel_22
rs13222385 | 7 | 55219087 | 35 | 10 | 0.000247087784600809 | EGFR | Yes | rs6970262 | 0.29 | Ver_2_Rel_22
rs6970262 | 7 | 55227257 | 42 | 19 | 0.00444401947106688 | EGFR | Yes | rs13222385 | 0.29 | Ver_2_Rel_22
rs6943261 | 7 | 66903120 | 19 | 3 | 0.000855445861816406
rs1879873 | 7 | 68376008 | 15 | 2 | 0.002349853515625
rs7802500 | 7 | 69544961 | 25 | 8 | 0.00455138413235546 | AUTS2 | Yes
rs7808818 | 7 | 70592167 | 31 | 11 | 0.00288724797428586 | WBSCR17 | Yes
rs1167835 | 7 | 75006498 | 18 | 4 | 0.00434350967407227 | [NAME] | Yes
rs804025 | 7 | 76038186 | 9 | 32 | 0.000430857042374556 | POMZP3 | No
rs3823787 | 7 | 77611068 | 8 | 27 | 0.00187822547741234 | MAGI2 | Yes | Negligible LD |  | Ver_3_Rel_2
rs5000370 | 7 | 78342291 | 33 | 9 | 0.000271539234290686 | MAGI2 | Yes | Negligible LD |  | Ver_3_Rel_2
rs514463 | 7 | 78342667 | 1 | 12 | 0.00341796875 | MAGI2 | Yes | Negligible LD |  | Ver_3_Rel_2
rs1799025 | 7 | 78345117 | 7 | 25 | 0.00210240157321096 | MAGI2 | Yes | Negligible LD |  | Ver_3_Rel_2
rs10230672 | 7 | 82786530 | 33 | 13 | 0.00453386158218906 | [NAME] | No
rs11971791 | 7 | 85452694 | 27 | 9 | 0.00393317302223295
rs801900 | 7 | 88854531 | 24 | 7 | 0.00332689285278321 | ZNF804B | No
rs1963647 | 7 | 103231266 | 5 | 20 | 0.00407731533050537 | RELN | Yes | See Supp Figure EE |  | Ver_3_Rel_2
rs262375 | 7 | 103240293 | 4 | 18 | 0.00434350967407227 | RELN | Yes | See Supp Figure EE |  | Ver_3_Rel_2
rs264375 | 7 | 103251554 | 2 | 19 | 0.00022125244140625 | RELN | Yes | See Supp Figure EE |  | Ver_3_Rel_2
rs10273020 | 7 | 104126785 | 28 | 9 | 0.00256320799235255 | [NAME] | Yes | See Supp Figure FF |  | Ver_3_Rel_2
rs4730037 | 7 | 104129973 | 27 | 9 | 0.00393317302223295 | [NAME] | Yes | See Supp Figure FF |  | Ver_3_Rel_2
rs4367471 | 7 | 104170109 | 20 | 4 | 0.00154387950897217 | [NAME] | Yes | See Supp Figure FF |  | Ver_3_Rel_2
rs4132013 | 7 | 104189945 | 5 | 27 | 0.000113074202090502 | [NAME] | Yes | See Supp Figure FF |  | Ver_3_Rel_2
rs557657 | 7 | 105186362 | 6 | 24 | 0.00143090635538102 | ATXN7L1 | Yes
rs6959338 | 7 | 111505248 | 33 | 8 | 0.000112221426206816 | DOCK4 | Yes | rs10256513 | 0.93 | Ver_2_Rel_22
rs10256513 | 7 | 111506569 | 29 | 8 | 0.000752897060010583 | DOCK4 | Yes | rs6959338 | 0.93 | Ver_2_Rel_22
rs6976018 | 7 | 118605006 | 22 | 6 | 0.00371916592121124
rs9641684 | 7 | 121791202 | 32 | 9 | 0.000430857042374556 | CADPS2 | Yes | See Supp Figure GG |  | Ver_3_Rel_2
rs2189601 | 7 | 121805219 | 9 | 28 | 0.00256320799235255 | CADPS2 | Yes | See Supp Figure GG |  | Ver_3_Rel_2
rs9969220 | 7 | 122158943 | 25 | 8 | 0.00455138413235546 | CADPS2 | Yes | See Supp Figure GG |  | Ver_3_Rel_2
rs11769359 | 7 | 122781159 | 25 | 8 | 0.00455138413235546 | IQUB | No
rs2106200 | 7 | 125944592 | 33 | 13 | 0.00453386158218906 | GRM8 | Yes
rs6977152 | 7 | 126991066 | 10 | 0 | 0.001953125 | GCC1 | No | rs10267162 | 0.95 | Ver_3_Rel_2
rs10267162 | 7 | 126999408 | 10 | 0 | 0.001953125 | GCC1 | No | rs6977152 | 0.95 | Ver_3_Rel_2
rs109829 | 7 | 128181186 | 8 | 25 | 0.00455138413235546 | [NAME] | Yes
rs6943859 | 7 | 129489462 | 14 | 2 | 0.004180908203125 | KLHDC10 | No
rs13226219 | 7 | 129806727 | 12 | 1 | 0.00341796875 | CPA1 | No
[NAME] | 7 | 130322355 | 34 | 13 | 0.00308767646151865 | FLJ43663 | Yes
rs6948145 | 7 | 134785342 | 2 | 14 | 0.004180908203125 | CNOT4 | Yes
rs4475425 | 7 | 136225739 | 24 | 6 | 0.00143090635538102 | CHRM2 | Yes | Negligible LD |  | Ver_2_Rel_22
rs10488600 | 7 | 136255998 | 15 | 2 | 0.002349853515625 | CHRM2 | Yes | Negligible LD |  | Ver_2_Rel_22
rs11772948 | 7 | 136407310 | 0 | 10 | 0.001953125 | CHRM2 | No | Negligible LD |  | Ver_2_Rel_22
rs11770381 | 7 | 137951574 | 32 | 11 | 0.0019139610012644 | SVOPL | Yes
[NAME] | 7 | 140919185 | 29 | 9 | 0.00165805252618157 | AGK | Yes
rs10250704 | 7 | 150195351 | 25 | 7 | 0.00210240157321096 | [NAME] | No
rs2878957 | 7 | 153888040 | 25 | 7 | 0.00210240157321096 | DPP6 | Yes
rs1730175 | 7 | 154586596 | 23 | 6 | 0.00231570005416871 | HTR5A | No
rs4716752 | 7 | 157000871 | 22 | 6 | 0.00371916592121124 | PTPRN2 | No
rs708139 | 12 | 33624532 | 0 | 9 | 0.00390625
rs12975955 | 19 | 5170803 | 11 | 0 | 0.0009765625 | PTPRS | Yes
rs3852876 | 19 | 7190555 | 9 | 0 | 0.00390625 | INSR | Yes
rs952444 | 19 | 7992055 | 16 | 2 | 0.001312255859375 | ELAVL1 | No
rs1474472 | 19 | 15581533 | 15 | 2 | 0.002349853515625 | CYP4F8 | No
rs2562644 | 19 | 20522325 | 2 | 14 | 0.004180908203125 | ZNF737 | Yes
rs10404352 | 19 | 34479271 | 18 | 3 | 0.00148963928222656 | UQCRFS1 | No
rs1874492 | 19 | 36388218 | 12 | 1 | 0.00341796875 | DKFZp566F0947 | No
rs12461253 | 19 | 36461603 | 0 | 10 | 0.001953125 | TSHZ3 | Yes
rs11665874 | 19 | 38600200 | 9 | 0 | 0.00390625 | PEPD | Yes
rs12151280 | 19 | 42759730 | 15 | 1 | 0.000518798828125 | ZNF540 | Yes | rs2290999 | 0.97 | Ver_3_Rel_2
rs2290999 | 19 | 42830727 | 13 | 1 | 0.0018310546875 | ZFP30 | Yes | rs12151280 | 0.97 | Ver_3_Rel_2
rs1643461 | 19 | 43160181 | 10 | 0 | 0.001953125 | SIPA1L3 | Yes
rs3213255 | 19 | 48769347 | 16 | 3 | 0.004425048828125 | XRCC1 | Yes
rs370156 | 19 | 59864351 | 0 | 9 | 0.00390625 | LILRB4 | No
rs6509957 | 19 | 60949851 | 2 | 15 | 0.002349853515625 | NLRP9 | No
[NAME] | 20 | 5182887 | 17 | 2 | 0.000728607177734376 | PROKR2 | No
rs6055550 | 20 | 8044130 | 20 | 5 | 0.00407731533050537 | PLCB1 | No
rs4813919 | 20 | 10119007 | 20 | 5 | 0.00407731533050537 | SNAP25 | No | rs6039763 | 0.86 | Ver_2_Rel_22
rs6039763 | 20 | 10131517 | 3 | 18 | 0.00148963928222656 | SNAP25 | No | rs4813919 | 0.86 | Ver_2_Rel_22
rs6077978 | 20 | 10880018 | 3 | 16 | 0.004425048828125
rs6040836 | 20 | 11609444 | 20 | 5 | 0.00407731533050537
rs4814154 | 20 | 12652804 | 9 | 0 | 0.00390625 |  |  | [NAME] | 1 | Ver_3_Rel_2
[NAME] | 20 | 12654277 | 9 | 0 | 0.00390625 |  |  | rs4814154 | 1 | Ver_3_Rel_2
rs4510290 | 20 | 13094314 | 12 | 1 | 0.00341796875 | SPTLC3 | Yes
rs1923342 | 20 | 13128632 | 20 | 3 | 0.00048828125 | ISM1 | No | See Supp Figure WW |  | Ver_2_Rel_22
rs6131447 | 20 | 13132251 | 18 | 3 | 0.00148963928222656 | ISM1 | No | See Supp Figure WW |  | Ver_2_Rel_22
rs6109753 | 20 | 13138909 | 4 | 19 | 0.00259947776794434 | ISM1 | No | See Supp Figure WW |  | Ver_2_Rel_22
rs6105047 | 20 | 13140648 | 20 | 3 | 0.00048828125 | ISM1 | No | See Supp Figure WW |  | Ver_2_Rel_22
rs13433297 | 20 | 13247735 | 16 | 2 | 0.001312255859375 | ISM1 | No | See Supp Figure WW |  | Ver_2_Rel_22
[NAME] | 20 | 13259983 | 16 | 2 | 0.001312255859375 | ISM1 | No | See Supp Figure WW |  | Ver_2_Rel_22
rs8120608 | 20 | 15202051 | 18 | 1 | 7.62939453125e-05 | MACROD2 | Yes | See [NAME] Figure XX |  | Ver_2_Rel_22
rs367114 | 20 | 15510826 | 21 | 5 | 0.00249391794204712 | MACROD2 | Yes | See [NAME] Figure XX |  | Ver_2_Rel_22
rs453573 | 20 | 15512114 | 18 | 4 | 0.00434350967407227 | MACROD2 | Yes | See [NAME] Figure XX |  | Ver_2_Rel_22
rs6043472 | 20 | 15635866 | 14 | 2 | 0.004180908203125 | MACROD2 | Yes | See [NAME] Figure XX |  | Ver_2_Rel_22
rs6044739 | 20 | 17263942 | 1 | 15 | 0.000518798828125 | PCSK2 | Yes | See Supp Figure YY |  | Ver_3_Rel_2
rs6075193 | 20 | 17268057 | 2 | 14 | 0.004180908203125 | PCSK2 | Yes | See Supp Figure YY |  | Ver_3_Rel_2
rs6080665 | 20 | 17302667 | 3 | 16 | 0.004425048828125 | PCSK2 | Yes | See Supp Figure YY |  | Ver_3_Rel_2
rs17401989 | 20 | 20206183 | 0 | 9 | 0.00390625 | C20orf26 | Yes
rs6138822 | 20 | 26109415 | 14 | 2 | 0.004180908203125 | C20orf191 | No
rs4812744 | 20 | 41918763 | 2 | 14 | 0.004180908203125 | TOX2 | No | See Supp Figure ZZ |  | Ver_3_Rel_2
rs6124601 | 20 | 41921670 | 13 | 1 | 0.0018310546875 | TOX2 | No | See Supp Figure ZZ |  | Ver_3_Rel_2
rs6130470 | 20 | 41922255 | 13 | 1 | 0.0018310546875 | TOX2 | No | See Supp Figure ZZ |  | Ver_3_Rel_2
rs465880 | 20 | 51422033 | 12 | 1 | 0.00341796875 | [NAME] | Yes
rs922376 | 20 | 52137010 | 17 | 2 | 0.000728607177734376 | BCAS1 | No
rs6092090 | 20 | 53265063 | 9 | 0 | 0.00390625
rs6027439 | 20 | 58252675 | 0 | 9 | 0.00390625
rs6143006 | 20 | 60260199 | 12 | 1 | 0.00341796875 | OSBPL2 | Yes
rs4603829 | 20 | 61439336 | 12 | 0 | 0.00048828125 | CHRNA4 | No | rs4809538 | 0.51 | Ver_2_Rel_22
rs4809538 | 20 | 61440620 | 0 | 9 | 0.00390625 | CHRNA4 | No | rs4603829 | 0.51 | Ver_2_Rel_22
rs6089770 | 20 | 61861458 | 0 | 9 | 0.00390625 | [NAME] | Yes