Affected by subtype, n (MAF) | Positive | Negative | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Subtype | Sample | SNP | Locus | Position b | Nearby gene | Ref c | Eff d | Reported e | Positive | Negative | Unknown | Number unaffected (MAF) | HR (95% CI) | P -value | HR (95% CI) | P -value | P het-value f |
ER status | BRCA1 carriers | rs10069690 | 5p15.33 | 1332790 | TERT | G | A | Yes | 819 (0.27) | 2,635 (0.3) | 4,331 (0.3) | 7,449 (0.26) | 1.09 (0.98 to 1.22) | 0.09 | 1.24 (1.18 to 1.31) | 2.7 × 10−15 | 0.04 |
rs2046210 | 6q25.1 | 151990059 | C6orf97 | G | A | Yes | 819 (0.36) | 2,639 (0.39) | 4,338 (0.38) | 7,453 (0.35) | 1.04 (0.94 to 1.15) | 0.42 | 1.2 (1.15 to 1.26) | 2.8 × 10−13 | 0.01 | ||
rs2811708 | 9p21 | 21963422 | CDKN2A/B | C | A | Yes | 816 (0.24) | 2,634 (0.31) | 4,336 (0.28) | 7,445 (0.28) | 0.82 (0.73 to 0.91) | 2.9 × 10−4 | 1.13 (1.07 to 1.19) | 7.3 × 10−6 | 3.9 × 10−7 | ||
rs45631579 | 10q26 | 123328965 | FGFR2 | A | G | Yes | 819 (0.48) | 2,639 (0.4) | 4,337 (0.42) | 7,455 (0.41) | 1.29 (1.17 to 1.43) | 2.6 × 10−7 | 0.92 (0.87 to 0.96) | 4.7 × 10−4 | 5.1 × 10−9 | ||
rs2590275 | 12p12 | 28057334 | PTHLH | G | C | Yes | 819 (0.26) | 2,639 (0.25) | 4,338 (0.26) | 7,454 (0.28) | 0.92 (0.83 to 1.03) | 0.14 | 0.87 (0.82 to 0.92) | 5.3 × 10−7 | 0.34 | ||
rs2363956 | 19p13.11 | 17255124 | ANKLE1 | C | A | Yes | 819 (0.47) | 2,635 (0.53) | 4,334 (0.52) | 7,447 (0.48) | 0.98 (0.89 to 1.08) | 0.71 | 1.25 (1.19 to 1.31) | 6.4 × 10−20 | 1.6 × 10−5 | ||
BRCA2 carriers | rs2162540 | 10q26 | 123342126 | FGFR2 | A | G | Yes | 1450 (0.47) | 426 (0.41) | 2,348 (0.44) | 3,783 (0.38) | 1.34 (1.25 to 1.43) | 3.6 × 10−16 | 1.08 (0.94 to 1.23) | 0.27 | 6.1 × 10−3 | |
rs17271951 | 16q12.1 | 51095541 | TOX3 | A | G | Yes | 1490 (0.32) | 434 (0.28) | 2,397 (0.3) | 3,879 (0.25) | 1.29 (1.2 to 1.39) | 8.4 × 10−12 | 1.14 (0.99 to 1.31) | 0.08 | 0.14 | ||
PR status | BRCA1 carriers | rs10069690 | 5p15.33 | 1332790 | TERT | G | A | Yes | 662 (0.27) | 2,481 (0.29) | 4,642 (0.3) | 7,449 (0.26) | 1.10 (0.98 to 1.24) | 0.09 | 1.24 (1.17 to 1.3) | 1.3 × 10−14 | 0.11 |
rs2046210 | 6q25.1 | 151990059 | C6orf97 | G | A | Yes | 662 (0.37) | 2,485 (0.39) | 4,649 (0.38) | 7,453 (0.35) | 1.09 (0.98 to 1.21) | 0.12 | 1.18 (1.13 to 1.24) | 2.0 × 10−11 | 0.19 | ||
rs45631626 | 10q26 | 123327325 | FGFR2 | G | A | Yes | 662 (0.49) | 2,485 (0.4) | 4,647 (0.42) | 7,455 (0.42) | 1.33 (1.2 to 1.48) | 1.3 × 10−7 | 0.92 (0.88 to 0.97) | 9.6 × 10−4 | 5.3 × 10−9 | ||
rs2590275 | 12p12 | 28057334 | PTHLH | G | C | Yes | 662 (0.26) | 2,485 (0.25) | 4,649 (0.26) | 7,454 (0.28) | 0.92 (0.82 to 1.03) | 0.16 | 0.87 (0.82 to 0.92) | 8.2 × 10−7 | 0.45 | ||
rs8100241 | 19p13.11 | 17253894 | ANKLE1 | G | A | Yes | 657 (0.51) | 2,473 (0.47) | 4,628 (0.48) | 7,420 (0.52) | 0.98 (0.88 to 1.09) | 0.71 | 0.81 (0.78 to 0.85) | 1.8 × 10−17 | 2.4 × 10−3 | ||
BRCA2 carriers | rs10017576 | 4q28.3 | 139799629 | G | A | No | 1099 (0.38) | 591 (0.43) | 2,639 (0.41) | 3,880 (0.43) | 0.83 (0.77 to 0.89) | 8.9 × 10−7 | 1.02 (0.92 to 1.14) | 0.67 | 2.7 × 10−3 | ||
rs4376461 | 8p12 | 32822117 | NRG1 | C | A | No | 1099 (0.15) | 591 (0.10) | 2,640 (0.14) | 3,881 (0.15) | 1.00 (0.9 to 1.12) | 0.93 | 0.6 (0.5 to 0.73) | 2.4 × 10−7 | 1.4 × 10−5 | ||
rs45631588 | 10q26 | 123341292 | FGFR2 | A | G | Yes | 1099 (0.47) | 591 (0.43) | 2,640 (0.45) | 3,881 (0.39) | 1.33 (1.23 to 1.44) | 2.7 × 10−13 | 1.15 (1.03 to 1.28) | 0.01 | 0.04 | ||
rs17271951 | 16q12.1 | 51095541 | TOX3 | A | G | Yes | 1099 (0.32) | 591 (0.28) | 2,631 (0.3) | 3,879 (0.25) | 1.32 (1.21 to 1.43) | 4.3 × 10−11 | 1.14 (1.01 to 1.29) | 0.03 | 0.07 | ||
HER2 status | BRCA1 carriers | rs17008885 | 2p13.2 | 73303647 | SMYD5 | T | A | No | 182 (0.19) | 1,816 (0.3) | 5,799 (0.3) | 7,455 (0.31) | 0.54 (0.43 to 0.69) | 7.8 × 10−7 | 0.99 (0.95 to 1.04) | 0.78 | 3.8 × 10−6 |
rs10069690 | 5p15.33 | 1332790 | TERT | G | A | Yes | 181 (0.23) | 1,813 (0.29) | 5,791 (0.3) | 7,449 (0.26) | 0.9 (0.71 to 1.13) | 0.36 | 1.24 (1.18 to 1.3) | 3.4 × 10−17 | 0.01 | ||
rs2046210 | 6q25.1 | 151990059 | C6orf97 | G | A | Yes | 182 (0.39) | 1,816 (0.4) | 5,798 (0.38) | 7,453 (0.35) | 1.12 (0.91 to 1.38) | 0.29 | 1.17 (1.11 to 1.22) | 1.5 × 10−10 | 0.71 | ||
rs10843055 | 12p12 | 28063088 | PTHLH | A | C | Yes | 171 (0.06) | 1,743 (0.06) | 5,615 (0.06) | 7,234 (0.07) | 0.79 (0.52 to 1.2) | 0.26 | 0.79 (0.72 to 0.87) | 6.2 × 10−7 | 0.99 | ||
rs4808616 | 19p13.11 | 17264033 | ANKLE1 | C | A | Yes | 176 (0.35) | 1,782 (0.32) | 5,706 (0.32) | 7,339 (0.28) | 1.37 (1.11 to 1.69) | 3.8 × 10−3 | 1.2 (1.14 to 1.26) | 6.8 × 10−13 | 0.25 | ||
BRCA2 carriers | rs4305889 | 8q12.1 | 60352785 | TOX | A | G | No | 121 (0.18) | 845 (0.09) | 3,353 (0.11) | 3,874 (0.1) | 2.04 (1.53 to 2.71) | 8.7 × 10−7 | 0.96 (0.85 to 1.08) | 0.47 | 1.0 × 10−5 | |
rs45631588 | 10q26 | 123341292 | FGFR2 | A | G | Yes | 121 (0.45) | 847 (0.46) | 3,362 (0.45) | 3,881 (0.39) | 1.27 (0.98 to 1.63) | 0.07 | 1.28 (1.19 to 1.37) | 2.1 × 10−12 | 0.95 | ||
rs3817197 | 11p15.5 | 1862750 | LSP1 | G | A | Yes | 121 (0.55) | 847 (0.44) | 3,353 (0.45) | 3,877 (0.47) | 1.30 (1.02 to 1.64) | 0.03 | 0.84 (0.79 to 0.9) | 9.1 × 10−7 | 1.3 × 10−3 | ||
rs17271951 | 16q12.1 | 51095541 | TOX3 | A | G | Yes | 121 (0.29) | 847 (0.31) | 3,353 (0.3) | 3,879 (0.25) | 1.10 (0.85 to 1.41) | 0.47 | 1.27 (1.18 to 1.37) | 6.9 × 10−11 | 0.3 | ||
Triple-negativeg | BRCA1 carriers | rs10069690 | 5p15.33 | 1332790 | TERT | G | A | Yes | 579 (0.27) | 1,307 (0.3) | 5,899 (0.3) | 7,449 (0.26) | 1.06 (0.94 to 1.19) | 0.34 | 1.27 (1.2 to 1.36) | 5.2 × 10−14 | 0.02 |
rs2046210 | 6q25.1 | 151990059 | C6orf97 | G | A | Yes | 580 (0.37) | 1,310 (0.41) | 5,906 (0.38) | 7,453 (0.35) | 1.01 (0.91 to 1.13) | 0.79 | 1.23 (1.16 to 1.31) | 5.5 × 10−12 | 6.8 × 10−3 | ||
rs9512729 | 13q12.2 | 26974865 | LNX2 | G | A | No | 580 (0.34) | 1,309 (0.43) | 5,902 (0.41) | 7,454 (0.41) | 0.76 (0.69 to 0.85) | 9.1 × 10−7 | 1.08 (1.02 to 1.15) | 0.01 | 1.2 × 10−6 | ||
rs8100241 | 19p13.11 | 17253894 | ANKLE1 | G | A | Yes | 577 (0.5) | 1,304 (0.46) | 5,877 (0.48) | 7,420 (0.52) | 0.94 (0.85 to 1.04) | 0.22 | 0.81 (0.76 to 0.86) | 2.4 × 10−13 | 0.03 | ||
BRCA2 carriers | rs2162540 | 10q26 | 123342126 | FGFR2 | A | G | Yes | 735 (0.46) | 133 (0.36) | 3,356 (0.44) | 3,783 (0.38) | 1.39 (1.29 to 1.49) | 9.8 × 10−20 | 0.83 (0.67 to 1.03) | 0.10 | 4.0 × 10−5 | |
rs1362548 | 16q12.1 | 51121452 | TOX3 | C | G | Yes | 760 (0.32) | 136 (0.29) | 3,434 (0.31) | 3,881 (0.26) | 1.26 (1.17 to 1.36) | 1.0 × 10−9 | 1.18 (0.94 to 1.49) | 0.16 | 0.63 |