Table 2.
Estimates of P-values in different subtypes of breast cancer for genes containing SNPs replicated in multiple independent studies obtained from GWAS.
| Gene symbol | SNP ID (rs-ID) | Number of studies | LMA | LMB | ERBB | NLK | BASAL | BLK |
|---|---|---|---|---|---|---|---|---|
| CASP8 | rs1045485 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3020314 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3020390 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3020394 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs1884051 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs2228480 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3020396 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3020400 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3020401 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3798577 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.18 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| FGFR2 | rs2981582 | 9 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5.15 × 10−4 | 0.982236 | 5 × 10−6 |
| FGFR2 | rs2981579 | 7 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5.15 × 10−4 | 0.982236 | 5 × 10−6 |
| FGFR2 | rs2420946 | 5 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5.15 × 10−4 | 0.982236 | 5 × 10−6 |
| FGFR2 | rs1219648 | 5 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5.15 × 10−4 | 0.982236 | 5 × 10−6 |
| LSP1 | rs3817198 | 6 | 0.100053 | 6.8 × 10−3 | 0.676883 | 0.06848 | 0.597843 | 0.134961 |
| STXBP4 | rs6504950 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 1.65 × 10−4 | 5 × 10−6 |
| TGFB1 | rs1800470 | 3 | 5 × 10−6 | 3.5 × 10−5 | 2.5 × 10−5 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| TOX3 | rs12443621 | 3 | 5 × 10−6 | 2.6 × 10−4 | 8.6 × 10−4 | 0.419581 | 0.090054 | 5 × 10−6 |
| ADH1B | rs1042026 | 3 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| SORBS1 | rs10450393 | 2 | 5 × 10−6 | 5.7 × 10−3 | 2.5 × 10−4 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| ICAM5 | rs1056538 | 2 | 5 × 10−6 | 0.387298 | 0.189892 | 0.045497 | 5 × 10−6 | 1.72 × 10−3 |
| RB1 | rs198580 | 2 | 0.084304 | 2.7 × 10−4 | 0.168073 | 3.5 × 10−3 | 0.681552 | 1 × 10−5 |
| RNF146 | rs2180341 | 2 | 0.212725 | 0.029158 | 0.529813 | 0.766361 | 0.00659 | 0.976052 |
| RB1 | rs2854344 | 2 | 0.084304 | 2.75 × 10−4 | 0.168073 | 3.5 × 10−3 | 0.681552 | 1 × 10−5 |
| IGFBP3 | rs2854744 | 4 | 0.103283 | 0.058821 | 0.919706 | 0.067505 | 0.864765 | 2.24 × 10−3 |
| CDKN1A | rs3176336 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| CDKN1B | rs34330 | 2 | 0.107648 | 0.795089 | 3.25 × 10−4 | 2.2 × 10−3 | 5.15 × 10−4 | 3 × 10−5 |
| CDKN2A | rs3731239 | 2 | 0.28172 | 0.154304 | 0.196626 | 0.602623 | 0.039622 | 5 × 10−6 |
| LOC643714 | rs3803662 | 12 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| EHMT1 | rs4634736 | 2 | 5 × 10−6 | 0.007025 | 0.13664 | 1 × 10−5 | 0.035818 | 5 × 10−6 |
| SOD2 | rs4880 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 0.032173 | 5 × 10−6 |
| CCND1 | rs678653 | 2 | 5.45 × 10−4 | 5 × 10−6 | 2.5 × 10−5 | 0.096103 | 0.626906 | 5 × 10−6 |
| HCN1 | rs981782 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| CCNE1 | rs997669 | 2 | 0.463623 | 5 × 10−6 | 2.5 × 10−5 | 0.440789 | 0.00761 | 5 × 10−6 |
| RAD51L1 | rs999737 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 0.025663 | 5 × 10−6 |
| CDKN2B | rs1011970 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| CASP8 | rs10931936 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| ZNF365 | rs10995190 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| FGFR2 | rs11200014 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5.15 × 10−4 | 0.982236 | 5 × 10−6 |
| COX11 | rs1156287 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 3.7 × 10−4 | 5 × 10−6 |
| WRN | rs1346044 | 2 | 0.0167838 | 0.64972 | 0.894917 | 0.433395 | 0.00761 | 5 × 10−6 |
| GSTP1 | rs1695 | 3 | 5 × 10−6 | 5 × 10−6 | 2.75 × 10−3 | 0.082619 | 5 × 10−6 | 5 × 10−6 |
| RELN | rs17157903 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| CHEK2 | rs17879961 | 2 | 2 × 10−5 | 0.024433 | 0.018789 | 5 × 10−6 | 0.197886 | 5 × 10−6 |
| CDKN1A | rs1801270 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| H19 | rs2107425 | 2 | 0.042847 | 0.00114 | 2.58 × 10−3 | 0.027343 | 8 × 10−5 | 5 × 10−6 |
| IFNG | rs2430561 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| ESR1 | rs3020377 | 2 | 5 × 10−6 | 3 × 10−5 | 5 × 10−6 | 3.1 × 10−3 | 5 × 10−6 | 5 × 10−6 |
| COMT | rs4818 | 2 | 8.4 × 10−3 | 0.860185 | 5.27 × 10−3 | 7.13 × 10−3 | 0.304889 | 0.240923 |
| SLC4A7 | rs4973768 | 4 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 |
| RNF146 | rs6569479 | 2 | 0.2127251 | 0.029158 | 0.529813 | 0.766361 | 6.59 × 10−3 | 0.976052 |
| ZMIZ1 | rs704010 | 2 | 5 × 10−6 | 1 × 10−5 | 0.022029 | 0.048337 | 5 × 10−6 | 0.227309 |
| VDR | rs731236 | 2 | 2.2 × 10−3 | 0.022014 | 0.159809 | 0.476042 | 0.624336 | 9.16 × 10−3 |
| RAD51L1 | rs8009944 | 2 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 5 × 10−6 | 0.025663 | 5 × 10−6 |
| TOX3 | rs8051542 | 4 | 5 × 10−6 | 2.6 × 10−4 | 8.6 × 10−4 | 0.419581 | 0.090054 | 5 × 10−6 |
| MAP3K1 | rs889312 | 4 | 2.7 × 10−3 | 5 × 10−6 | 3.5 × 10−5 | 4.9 × 10−4 | 9.3 × 10−3 | 5 × 10−6 |
Notes: rs-ID is the SNP id, SNP(Pv) is the SNP P-value derived from GWAS. Due to the large number of studies in column 3, the SNP P-values are provided in Table A as supplementary data.
Abbreviations: LMA, luminal A; LMB, luminal B; ERBB, ; NLK, normal-like; BLK, basal-like.