Appendix 1—table 8. eQTLs in tumor and normal tissue.
Here, B is the effect allele. All local permutation p<0.05 are shown. Full table of eQTLs is given in Supplementary file 4.
| Tissue | Gene | ID | N | Best SNP | Distance | Nominal P |
Permutation P |
FDR |
|---|---|---|---|---|---|---|---|---|
| T |
RP11-
816J6.3 |
ENSG00000269889.1 | 82 | rs67795055 | 42457 | 9.10E-05 | 4.03E-04 | 0.224 |
| T | RUFY3 | ENSG00000018189.8 | 8 | rs7660770 | −972945 | 7.84E-04 | 6.68E-04 | 0.370 |
| T | TRIP13 | ENSG00000071539.9 | 22 | rs2736099 | 394581 | 1.63E-04 | 2.27E-03 | 1 |
| N | RN7SL832P | ENSG00000243819.3 | 28 | rs7570979 | 886958 | 4.06E-04 | 2.75E-03 | 1 |
| N | LNX1 | ENSG00000072201.9 | 25 | rs62323674 | 212300 | 7.12E-04 | 3.22E-03 | 1 |
| N |
RP11-
849F2.8 |
ENSG00000269928.1 | 5 | rs143094271 | −665038 | 2.43E-03 | 4.00E-03 | 1 |
| T | MIR5006 | ENSG00000264190.1 | 158 | rs9549254 | −907660 | 6.10E-04 | 4.42E-03 | 1 |
| N |
RP11-
423H2.3 |
ENSG00000249684.1 | 50 | rs183686 | −883235 | 3.36E-03 | 5.55E-03 | 1 |
| N | SLC7A3 | ENSG00000165349.7 | 148 | rs4360450 | 965 | 6.75E-04 | 7.38E-03 | 1 |
| T | ALPL | ENSG00000162551.9 | 52 | . | 521370 | 8.48E-04 | 7.59E-03 | 1 |
| N | PRRG4 | ENSG00000135378.3 | 167 | rs11031737 | −478718 | 3.99E-04 | 8.59E-03 | 1 |
| N |
RP11-
791G15.2 |
ENSG00000272275.1 | 28 | rs6432220 | 802714 | 1.24E-03 | 8.81E-03 | 1 |
| T | ZDHHC11B | ENSG00000206077.6 | 22 | rs2736099 | 576864 | 9.74E-04 | 1.02E-02 | 1 |
| T | ACAP1 | ENSG00000072818.7 | 5 | rs78378222 | 331903 | 4.83E-03 | 1.04E-02 | 1 |
| N | HNRNPA1P48 | ENSG00000224578.3 | 20 | rs55881068 | −212266 | 4.97E-03 | 1.12E-02 | 1 |
| T | WNT4 | ENSG00000162552.10 | 52 | rs12042083 | 28933 | 1.30E-03 | 1.16E-02 | 1 |
| T | LRRIQ4 | ENSG00000188306.6 | 82 | rs13074500 | 25860 | 2.96E-03 | 1.20E-02 | 1 |
| T | TEX11 | ENSG00000120498.9 | 148 | rs11795627 | 208650 | 1.30E-03 | 1.23E-02 | 1 |
| T | AC011994.1 | ENSG00000265583.1 | 28 | rs11685032 | −73236 | 1.84E-03 | 1.32E-02 | 1 |
| T | FRMD7 | ENSG00000165694.5 | 215 | rs5933158 | 367012 | 8.40E-04 | 1.33E-02 | 1 |
| N | TRAPPC1 | ENSG00000170043.7 | 5 | rs138420351 | −133601 | 7.23E-03 | 1.44E-02 | 1 |
| T |
RP11-
423H2.1 |
ENSG00000170089.11 | 72 | rs353496 | −806511 | 9.37E-03 | 1.51E-02 | 1 |
| N | SDHAP3 | ENSG00000185986.10 | 22 | rs11742908 | −297655 | 1.42E-03 | 1.58E-02 | 1 |
| T | CDC42-IT1 | ENSG00000230068.2 | 52 | rs10917167 | 118400 | 2.10E-03 | 1.80E-02 | 1 |
| N |
RP11-
362K14.6 |
ENSG00000270096.1 | 82 | rs12638862 | −35245 | 4.49E-03 | 1.96E-02 | 1 |
| T | TNRC6B | ENSG00000100354.16 | 32 | rs12484951 | 262253 | 8.29E-03 | 1.97E-02 | 1 |
| N | DNAH2 | ENSG00000183914.10 | 5 | rs143094271 | −157571 | 9.73E-03 | 1.98E-02 | 1 |
| N | SALL1 | ENSG00000103449.7 | 20 | rs12933686 | 308913 | 9.53E-03 | 2.13E-02 | 1 |
| T |
XXyac-
YRM2039.2 |
ENSG00000181404.13 | 71 | rs138821078 | 659705 | 1.69E-03 | 2.22E-02 | 1 |
| N | ITPRIP | ENSG00000148841.11 | 8 | rs9419958 | −395949 | 1.43E-02 | 2.39E-02 | 1 |
| T |
RNASEK-
C17orf49 |
ENSG00000161939.14 | 5 | . | 501685 | 1.19E-02 | 2.43E-02 | 1 |
| T | UQCRFS1P1 | ENSG00000226085.2 | 32 | rs1807579 | 256926 | 1.06E-02 | 2.44E-02 | 1 |
| T | FOXO1 | ENSG00000150907.6 | 166 | rs9549260 | 124299 | 2.94E-03 | 2.61E-02 | 1 |
| T | NDUFS6 | ENSG00000145494.7 | 22 | rs7734992 | −521387 | 2.81E-03 | 2.82E-02 | 1 |
| T |
RP11-
259O2.3 |
ENSG00000249731.1 | 22 | rs7710703 | −680704 | 2.89E-03 | 2.84E-02 | 1 |
| T | CDC42 | ENSG00000070831.11 | 52 | rs41307810 | −25076 | 3.35E-03 | 2.91E-02 | 1 |
| T |
RP3-
363L9.1 |
ENSG00000227064.1 | 215 | rs3764771 | −830073 | 2.03E-03 | 2.97E-02 | 1 |
| T |
RP11-
362K14.7 |
ENSG00000270135.1 | 82 | rs67795055 | 18611 | 7.45E-03 | 3.07E-02 | 1 |
| N | AMIGO2 | ENSG00000139211.5 | 155 | rs9706162 | −606808 | 6.28E-03 | 3.08E-02 | 1 |
| T | LPIN1 | ENSG00000134324.7 | 28 | rs11685032 | −143427 | 5.06E-03 | 3.33E-02 | 1 |
| T | MBNL3 | ENSG00000076770.10 | 215 | rs1263155 | 190718 | 2.55E-03 | 3.37E-02 | 1 |
| N | TOX3 | ENSG00000103460.12 | 5 | rs12325192 | −983789 | 3.24E-02 | 3.38E-02 | 1 |
| N | DANCR | ENSG00000226950.2 | 23 | rs62325482 | 885823 | 8.24E-03 | 3.54E-02 | 1 |
| T | DMRT1 | ENSG00000137090.7 | 71 | rs12004436 | −158261 | 3.09E-03 | 3.64E-02 | 1 |
| N | NT5C2 | ENSG00000076685.14 | 8 | rs1265164 | 828913 | 2.05E-02 | 3.75E-02 | 1 |
| T |
TMEM256-
PLSCR3 |
ENSG00000187838.12 | 5 | rs138420351 | 407016 | 1.77E-02 | 3.81E-02 | 1 |
| T |
RP11-
401P9.4 |
ENSG00000261685.2 | 20 | rs12933686 | 799079 | 1.64E-02 | 3.84E-02 | 1 |
| N | CTC1 | ENSG00000178971.9 | 5 | rs143094271 | −667090 | 1.89E-02 | 4.03E-02 | 1 |
| N | SULT1B1 | ENSG00000173597.4 | 19 | rs13133166 | 13318 | 1.49E-02 | 4.04E-02 | 1 |
| N | TNK1 | ENSG00000174292.8 | 5 | rs143094271 | 179248 | 2.24E-02 | 4.21E-02 | 1 |
| T | SOX15 | ENSG00000129194.3 | 5 | rs138420351 | 208566 | 2.02E-02 | 4.30E-02 | 1 |
| T | UGT2A1 | ENSG00000173610.7 | 19 | rs1587766 | 112959 | 2.06E-02 | 4.31E-02 | 1 |
| T |
RP4-
607I7.1 |
ENSG00000255521.1 | 34 | rs2553783 | −82085 | 2.66E-02 | 4.41E-02 | 1 |
| N | SENP3 | ENSG00000161956.8 | 5 | rs78378222 | 106559 | 2.19E-02 | 4.45E-02 | 1 |
| N | KDM6B | ENSG00000132510.6 | 5 | rs143094271 | −280121 | 2.16E-02 | 4.54E-02 | 1 |
| T | SKIL | ENSG00000136603.9 | 82 | rs34194057 | −525916 | 1.13E-02 | 4.63E-02 | 1 |
| T | EPHB2 | ENSG00000133216.12 | 52 | . | −680104 | 6.04E-03 | 4.97E-02 | 1 |