Table 2.
SNPs associated with total nevus count and cutaneous melanoma (CM) in their respective meta-analyses
| SNP | Position (hg19) | Combined P | CM P | Nevus P | Gene/interval |
|---|---|---|---|---|---|
| rs869329 | 9:21804693 | 7.48E−67 | 1.14E−31 | 2.12E−37* | MTAP |
| rs11532907 | 9:21844772 | 1.72E−34 | 1.42E−19 | 2.30E−17 | |
| rs132985 | 22:38563471 | 2.07E−28 | 4.76E−12 | 3.06E−18* | PLA2G6 |
| rs2005974 | 22:38537112 | 3.30E−23 | 7.83E−11 | 3.31E−14 | |
| rs12203592 | 6:396321 | 5.84E−01 | 8.22E−01 | 4.21E−67* | IRF4 |
| rs7313352 | 12:88949124 | 2.27E−05 | 6.61E−01 | 8.40E−09 | KITLG** |
| rs600951 | 9:224742 | 9.89E−13 | 5.52E−06 | 1.95E−08* | DOCK8** |
| rs10816595 | 9:110709735 | 1.70E−14 | 1.49E−07 | 1.08E−08 | 9q31.2 |
| rs251464 | 5:149196234 | 1.92E−09 | 4.58E−04 | 4.71E−07 | PPARGC1B |
| rs4670813 | 2:38317710 | 1.14E−10 | 2.40E−05 | 5.70E−07 | CYP1B1 |
| rs1640875 | 12:13069524 | 3.30E−11 | 4.08E−07 | 5.72E−06* | GPRC5A** |
| rs1148732 | 12:13068291 | 1.08E−09 | 2.08E−04 | 6.21E−07 | |
| rs55875066 | 2:240076002 | 1.35E−09 | 2.16E−04 | 7.59E−07 | HDAC4** |
| rs12696304 | 3:169481271 | 8.30E−10 | 1.64E−05 | 5.73E−06 | TERC |
| rs117648907 | 15:33277710 | 1.13E−10 | 1.43E−06 | 6.52E−06 | FMN1** |
| rs45575338 | 10:5784151 | 2.16E−08 | 2.87E−04 | 1.02E−05 | FAM208B** |
| rs1484375 | 9:109067561 | 1.56E−10 | 2.30E−08 | 1.35E−04 | 9q31.1 |
| rs2357176 | 14:64409313 | 3.89E−08 | 1.74E−05 | 1.95E−04 | SYNE2** |
| rs34466956 | 19:3353622 | 2.92E−08 | 1.02E−05 | 2.22E−04 | NFIC** |
| rs1636744 | 7:16984280 | 1.29E−09 | 1.84E−09 | 0.002 | TCONS_l2_00025686 |
| rs380286 | 5:1320247 | 3.18E−14 | 1.66E−17 | 0.003* | TERT |
| rs2695237 | 1:226603635 | 1.49E−11 | 3.59E−13 | 0.004 | PARP1 |
| rs73008229 | 11:108187689 | 8.21E−11 | 1.38E−12 | 0.006 | ATM |
| rs72704658 | 1:150833010 | 1.90E−10 | 3.88E−12 | 0.007 | SETDB1 |
| rs12596638 | 16:54115829 | 2.30E−08 | 1.81E−09 | 0.014 | FTO |
| rs416981 | 21:42745414 | 3.90E−10 | 3.28E−15 | 0.063 | MX2 |
| rs75570604 | 16:89846677 | 1.64E−45 | 6.24E−92 | 0.067 | MC1R |
| rs7582362 | 2:202176294 | 4.32E−06 | 8.88E−09 | 0.134 | CASP8 |
| rs498136 | 11:69367118 | 1.42E−06 | 1.01E−10 | 0.209 | TPCN2/CCND1 |
| rs56238684 | 20:33236696 | 5.14E−13 | 8.36E−25 | 0.215 | ASIP |
| rs2125570 | 6:21166705 | 9.14E−05 | 3.27E−08 | 0.351 | CDKAL1 |
| rs184628474 | 14:91185865 | 4.32E−07 | 4.63E−14 | 0.415 | TTC7B |
| rs10830253 | 11:89028043 | 2.32E−11 | 1.01E−26 | 0.605 | TYR |
| rs250417 | 5:33952378 | 5.18E−05 | 2.30E−12 | 0.755 | SLC45A2 |
| rs4778138 | 15:28335820 | 5.52E−03 | 3.11E−09 | 0.935 | OCA2 |
The weighted Stouffer method was used to combine the nevus and melanoma P values (Combined P). The SNP with the smallest combined P value under each peak is shown, but the table rows are ordered by strength of association to nevus count. In three cases where significant between-study heterogeneity is detected (unadjusted Phom < 0.05, denoted by *), the nevus P value is from the random-effects model of Han and Eskin38, and a result for a nearby SNP where Phom > 0.05 is included on the line beneath (italicized) to confirm genome-wide significance (in the case of IRF4 and DOCK8, there is no such nearby SNP).
*Unadjusted Phom < 0.05
**Novel loci