Table III.
Effect sizes for previously published melanoma risk loci in our melanoma GWAS
| Ref | Gene | CHR | SNP | MA | Other studies | Our study | ||
|---|---|---|---|---|---|---|---|---|
| P | OR | P | OR | |||||
| Barrett et al. (15) | — | 1 | rs7412746 | C | 9.0×10−11 | 0.89 (0.85–0.95) | 1.9×10−4 | 0.86 (0.79–0.93) |
| Barrett et al. (15) | PARP1 | 1 | rs3219090 | T | 9.3×10−8 | 0.82 (NA) | 0.005 | 0.89 (0.82–0.97) |
| Falchi. et al. (14) | CASP8 | 2 | rs13016963 | A | 8.6×10−10 | 1.14 (1.09–1.19) | 0.15 | 1.06 (0.98–1.15) |
| Amos et al. (17) | CLPTM1L/TERT | 5 | rs401681 | C | 0.004 | 0.73 (0.59–0.91) | 0.05 | 0.93 (0.85–1.00) |
| Brown et al. (12) | MTAP/CDKN2A | 9 | rs7023329 | G | 4.0×10−7 | 0.85 (0.80–0.91) | 2.3×10−5 | 0.85 (0.78–0.91) |
| Bishop. et al. (13) | MTAP | 9 | rs10757257 | G | 3.4×10−8 | 1.23 (1.15–1.30) | 3.9×10−5 | 1.18 (1.09–1.28) |
| Nan et al. (10) | TYR | 11 | rs1126809* | A | 2.8×10−7 | 1.21 (1.13–1.30) | 5.6×10−8 | 1.25 (1.15–1.35) |
| Brown et al. (12) | TYR | 11 | rs1393350 | A | 2.4×10−14 | 1.29 (1.21–1.38) | 6.7×10−5 | 1.20 (1.10–1.32) |
| Falchi. et al. (14) | CCND1 | 11 | rs1485933 | A | 0.0012 | 1.11 (1.04–1.18) | / | / |
| Falchi. et al. (14) | ATM | 11 | rs1801516 | A | 3.4×10−9 | 0.84 (0.78–0.90) | 0.03 | 0.88 (0.78–0.99) |
| Brown et al. (12) | MC1R | 16 | rs258322 | A | 2.5×10−27 | 1.67 (1.52–1.83) | 1.6×10−9 | 1.50 (1.31–1.71) |
| Gudbjartsson et al. (11) | PIGU | 20 | rs910873 | C | 9.9×10−16 | 1.75 (1.53–2.01) | 9.8×10−5 | 1.42 (1.19–1.69) |
| Gudbjartsson et al. (11) | MYH7B | 20 | rs1885120 | G | 9.8×10−16 | 1.78 (1.54–2.04) | 7.1×10−5 | 1.43 (1.20–1.69) |
| Falchi. et al. (14) | MX2 | 21 | rs45430 | G | 2.9×10−9 | 0.88 (0.85–0.92) | 0.035 | 0.90 (0.81–0.99) |
| Bishop. et al. (13) | PLA2G6 | 22 | rs132985 | C | 2.6×10−7 | 1.23 (1.15–1.30) | 2.8×10−5 | 1.18 (1.10–1.28) |
CHR, chromosome; MA, minor allele and also test allele; NA, not available; OR, odds ratio; our study, Harvard and MD Anderson melanoma GWAS; Ref, reference.
*SNP rs1126809 was not included in our GWAS, and we used SNP rs1847134 as substitution, the LD between the two SNPs is 0.96. SNP rs1485933 was not included in our GWAS, nor any SNPs in high linkage disequilibrium with it.