Table 2.
Associations of susceptibility loci with overall and estrogen receptor-positive and -negative breast cancer a
| BRCA1 carriers | BRCA2 carriers | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Overall | ER-negative | ER-positive | Overall | ER-negative | ER-positive | |||||||||||||||||
| Locus | SNP | Position b | Nearby gene | Ref c | Eff d | K e | MAF | HR (95% CI) | P -value | HR (95% CI) | P -value | HR (95% CI) | P -value | P het-value f | MAF | HR (95% CI) | P -value | HR (95% CI) | P -value | HR (95% CI) | P -value | P het-value f |
| 1p36.22 | rs616488 | 10566215 | PEX14 | A | G | No | 0.32 | 0.96 (0.92 to 1.01) | 0.10 | 0.95 (0.90 to 1.00) | 0.07 | 1.00 (0.90 to 1.10) | 0.92 | 0.47 | 0.33 | 0.98 (0.92 to 1.04) | 0.52 | 1.01 (0.88 to 1.16) | 0.94 | 0.97 (0.9 to 1.05) | 0.46 | 0.69 |
| 1p13.2 | rs12022378 | 114448389 | SYT6 | G | A | No | 0.16 | 1.03 (0.98 to 1.09) | 0.25 | 1.03 (0.97 to 1.10) | 0.31 | 1.03 (0.90 to 1.17) | 0.68 | 0.94 | 0.17 | 1.03 (0.95 to 1.12) | 0.42 | 1.16 (0.97 to 1.37) | 0.10 | 1.00 (0.91 to 1.1) | 1.00 | 0.15 |
| 1p11.2 | rs11249433 | 121280613 | FCGR1B | A | G | Yes | 0.41 | 0.99 (0.95 to 1.04) | 0.78 | 0.99 (0.94 to 1.03) | 0.55 | 1.02 (0.93 to 1.13) | 0.63 | 0.50 | 0.41 | 1.05 (0.99 to 1.12) | 0.09 | 1.04 (0.91 to 1.19) | 0.57 | 1.06 (0.99 to 1.13) | 0.12 | 0.84 |
| 1q32.1a | rs6678914 | 202187176 | LGR6 | G | A | No | 0.4 | 0.98 (0.94 to 1.02) | 0.39 | 0.96 (0.91 to 1.01) | 0.08 | 1.06 (0.97 to 1.17) | 0.21 | 0.07 | 0.41 | 1.04 (0.98 to 1.10) | 0.19 | 0.94 (0.82 to 1.08) | 0.39 | 1.07 (1.00 to 1.15) | 0.05 | 0.11 |
| 1q32.1b | rs4245739 | 204518842 | MDM4 | A | C | Yes | 0.28 | 1.10 (1.05 to 1.15) | 4.6 × 10 −5 | 1.12 (1.07 to 1.19) | 1.4 × 10 −5 | 1.02 (0.91 to 1.13) | 0.76 | 0.11 | 0.28 | 0.97 (0.91 to 1.04) | 0.38 | 1.09 (0.95 to 1.26) | 0.21 | 0.94 (0.87 to 1.01) | 0.10 | 0.07 |
| 2p24.1 | rs12710696 | 19320803 | OSR1 | G | A | No | 0.39 | 1.01 (0.97 to 1.06) | 0.51 | 1.01 (0.97 to 1.07) | 0.57 | 1.01 (0.92 to 1.12) | 0.77 | 1.00 | 0.38 | 1.00 (0.94 to 1.06) | 0.99 | 1.14 (1.00 to 1.30) | 0.05 | 0.96 (0.9 to 1.03) | 0.28 | 0.02 |
| 2q14.2 | rs4849887 | 121245122 | G | A | No | 0.11 | 1.02 (0.96 to 1.09) | 0.53 | 1.01 (0.94 to 1.09) | 0.78 | 1.05(0.90 to 1.23) | 0.49 | 0.64 | 0.11 | 0.98 (0.89 to 1.08) | 0.72 | 1.08 (0.87 to 1.33) | 0.49 | 0.96 (0.85 to 1.07) | 0.43 | 0.34 | |
| 2q31.1 | rs2016394 | 172972971 | DLX2 | G | A | No | 0.47 | 1.01 (0.97 to 1.06) | 0.54 | 1.03 (0.98 to 1.08) | 0.23 | 0.96 (0.87 to 1.06) | 0.39 | 0.21 | 0.46 | 0.99 (0.93 to 1.05) | 0.74 | 1.07 (0.94 to 1.22) | 0.32 | 0.97 (0.9 to 1.04) | 0.36 | 0.21 |
| 2q31.1 | rs1550623 | 174212894 | CDCA7 | A | G | No | 0.15 | 1.01 (0.95 to 1.07) | 0.72 | 1.02 (0.95 to 1.09) | 0.54 | 0.97 (0.85 to 1.12) | 0.72 | 0.57 | 0.15 | 0.97 (0.89 to 1.06) | 0.49 | 1.03 (0.87 to 1.23) | 0.70 | 0.95 (0.87 to 1.05) | 0.31 | 0.41 |
| 2q35 | rs13387042 | 217905832 | TNP1 | A | G | Yes | 0.47 | 0.98 (0.94 to 1.02) | 0.41 | 1.02 (0.97 to 1.07) | 0.37 | 0.86 (0.78 to 0.95) | 1.9 × 10 −3 | 2.3 × 10 −3 | 0.48 | 0.99 (0.93 to 1.05) | 0.68 | 0.98 (0.87 to 1.12) | 0.82 | 0.99 (0.93 to 1.06) | 0.74 | 0.96 |
| 2q35 | rs16857609 | 218296508 | DIRC3 | G | A | No | 0.26 | 1.04 (1.00 to 1.09) | 0.06 | 1.03 (0.98 to 1.09) | 0.23 | 1.08 (0.97 to 1.21) | 0.14 | 0.47 | 0.27 | 0.96 (0.90 to 1.03) | 0.26 | 0.87 (0.74 to 1.01) | 0.08 | 0.99 (0.92 to 1.07) | 0.82 | 0.14 |
| 3p26.1 | rs6762644 | 4742276 | ITPR1 | A | G | No | 0.36 | 1.04 (0.99 to 1.08) | 0.09 | 1.00 (0.95 to 1.05) | 0.92 | 1.16 (1.05 to 1.28) | 2.9 × 10 −3 | 0.01 | 0.37 | 0.98 (0.93 to 1.05) | 0.61 | 1.08 (0.94 to 1.24) | 0.27 | 0.96 (0.89 to 1.03) | 0.24 | 0.13 |
| 3p24.1 | rs4973768 | 27416013 | SLC4A7 | G | A | Yes | 0.49 | 1.01 (0.97 to 1.06) | 0.47 | 0.99 (0.95 to 1.04) | 0.81 | 1.09 (0.99 to 1.19) | 0.07 | 0.10 | 0.5 | 1.08 (1.02 to 1.15) | 7.8 × 10 −3 | 1.05 (0.92 to 1.20) | 0.46 | 1.10 (1.02 to 1.18) | 0.01 | 0.58 |
| 3p24.1 | rs12493607 | 30682939 | TGFBR2 | C | G | No | 0.35 | 0.99 (0.95 to 1.04) | 0.73 | 0.99 (0.94 to 1.04) | 0.63 | 1.01 (0.92 to 1.11) | 0.85 | 0.70 | 0.34 | 0.98 (0.92 to 1.04) | 0.54 | 1.07 (0.93 to 1.22) | 0.35 | 0.96 (0.89 to 1.03) | 0.23 | 0.17 |
| 4q24 | rs9790517 | 106084778 | TET2 | G | A | No | 0.23 | 0.98 (0.94 to 1.03) | 0.51 | 0.97 (0.92 to 1.03) | 0.30 | 1.03 (0.92 to 1.15) | 0.61 | 0.37 | 0.22 | 0.97 (0.91 to 1.05) | 0.48 | 0.91 (0.77 to 1.07) | 0.25 | 0.99 (0.91 to 1.08) | 0.88 | 0.35 |
| 4q34.1 | rs6828523 | 175846426 | EBF1 | C | A | No | 0.11 | 1.03 (0.96 to 1.1) | 0.41 | 1.03 (0.95 to 1.11) | 0.47 | 1.02 (0.88 to 1.19) | 0.78 | 0.94 | 0.1 | 0.98 (0.89 to 1.08) | 0.72 | 1.05 (0.85 to 1.30) | 0.64 | 0.96 (0.86 to 1.08) | 0.51 | 0.49 |
| 5p15.33 | rs10069690 | 1279790 | TERT | G | A | Yes | 0.28 | 1.21 (1.15 to 1.26) | 1.1 × 10 −15 | 1.24 (1.18 to 1.31) | 2.7 × 10 −15 | 1.09 (0.98 to 1.22) | 0.09 | 0.04 | 0.27 | 1.11 (1.04 to 1.19) | 1.6 × 10 −3 | 1.25 (1.08 to 1.44) | 3.2 × 10 −3 | 1.08 (1.00 to 1.17) | 0.06 | 0.09 |
| 5p15.33 | rs7725218 | 1282414 | TERT | G | A | Yes | 0.36 | 1.08 (1.04 to 1.13) | 3.2 × 10 −4 | 1.09 (1.04 to 1.15) | 6.4 × 10 −4 | 1.05 (0.95 to 1.15) | 0.37 | 0.47 | 0.36 | 1.06 (0.99 to 1.12) | 0.08 | 1.07 (0.93 to 1.23) | 0.35 | 1.05 (0.98 to 1.13) | 0.17 | 0.85 |
| 5p15.33 | rs2736108 | 1297488 | TERT | G | A | Yes | 0.29 | 0.89 (0.85 to 0.93) | 4.2 × 10 −7 | 0.86 (0.82 to 0.91) | 1.1 × 10 −7 | 0.98 (0.88 to 1.08) | 0.68 | 0.04 | 0.3 | 0.93(0.88 to 1.00) | 0.04 | 0.91 (0.78 to 1.05) | 0.20 | 0.94 (0.87 to 1.02) | 0.13 | 0.67 |
| 5p12 | rs10941679 | 44706498 | MRPS30 | A | G | Yes | 0.25 | 0.99 (0.94 to 1.04) | 0.61 | 0.99 (0.94 to 1.05) | 0.84 | 0.97 (0.86 to 1.08) | 0.54 | 0.66 | 0.24 | 1.07 (1.00 to 1.15) | 0.03 | 1.09 (0.94 to 1.27) | 0.24 | 1.07 (0.99 to 1.15) | 0.09 | 0.78 |
| 5q11.2 | rs889312 | 56031884 | MAP3K1 | A | C | Yes | 0.29 | 1.01 (0.97 to 1.06) | 0.52 | 0.99 (0.94 to 1.05) | 0.82 | 1.09 (0.98 to 1.21) | 0.12 | 0.15 | 0.3 | 1.04 (0.98 to 1.11) | 0.21 | 0.99 (0.86 to 1.14) | 0.90 | 1.06 (0.98 to 1.14) | 0.14 | 0.44 |
| 5q11.3 | rs10472076 | 58184061 | RAB3C | A | G | No | 0.37 | 1.00 (0.96 to 1.05) | 0.83 | 0.98 (0.94 to 1.03) | 0.52 | 1.08 (0.98 to 1.18) | 0.13 | 0.11 | 0.38 | 0.99 (0.93 to 1.05) | 0.78 | 1.02 (0.89 to 1.17) | 0.78 | 0.98 (0.92 to 1.05) | 0.64 | 0.66 |
| 5q11.3 | rs1353747 | 58337481 | PDE4D | A | C | No | 0.09 | 0.98 (0.91 to 1.05) | 0.53 | 0.95 (0.88 to 1.04) | 0.28 | 1.06 (0.90 to 1.24) | 0.50 | 0.29 | 0.09 | 0.95 (0.86 to 1.05) | 0.35 | 1.02 (0.81 to 1.27) | 0.88 | 0.94 (0.83 to 1.05) | 0.26 | 0.52 |
| 5q33.3 | rs1432679 | 158244083 | A | G | No | 0.44 | 1.05 (1.00 to 1.09) | 0.03 | 1.03 (0.98 to 1.08) | 0.25 | 1.10 (1.01 to 1.21) | 0.04 | 0.21 | 0.45 | 1.01 (0.95 to 1.07) | 0.79 | 0.92 (0.81 to 1.04) | 0.16 | 1.04 (0.97 to 1.11) | 0.30 | 0.09 | |
| 6p25.3 | rs11242675 | 1318878 | FOXQ1 | A | G | No | 0.35 | 0.96 (0.92 to 1) | 0.06 | 0.94 (0.90 to 0.99) | 0.03 | 1.01 (0.91 to 1.11) | 0.90 | 0.28 | 0.36 | 1.01 (0.95 to 1.07) | 0.79 | 1.02 (0.89 to 1.18) | 0.75 | 1.00 (0.93 to 1.08) | 0.90 | 0.83 |
| 6p24.3 | rs9348512 | 10456706 | TFAP2A | C | A | Yes | 0.34 | 1.00 (0.95 to 1.04) | 0.87 | 1.00 (0.95 to 1.05) | 0.88 | 1.00 (0.90 to 1.10) | 0.95 | 1.00 | 0.34 | 0.85 (0.8 to 0.9) | 9.2 × 10 −8 | 0.79 (0.69 to 0.91) | 1.1 × 10 −3 | 0.86 (0.8 to 0.92) | 3.4 × 10 −5 | 0.32 |
| 6p23 | rs204247 | 13722523 | RANBP9 | A | G | No | 0.44 | 1.00 (0.96 to 1.04) | 0.98 | 1.00 (0.95 to 1.04) | 0.84 | 1.01 (0.92 to 1.12) | 0.75 | 0.72 | 0.44 | 1.09 (1.03 to 1.15) | 3.4 × 10 −3 | 1.08 (0.94 to 1.24) | 0.25 | 1.09 (1.02 to 1.17) | 9.7 × 10 −3 | 0.93 |
| 6q14 | rs17530068 | 82193109 | FAM46A | A | G | Yes | 0.25 | 1.03 (0.98 to 1.08) | 0.23 | 1.03 (0.97 to 1.09) | 0.29 | 1.03 (0.92 to 1.14) | 0.63 | 0.95 | 0.25 | 1.10 (1.03 to 1.18) | 7.2 × 10 −3 | 1.07 (0.92 to 1.25) | 0.40 | 1.11 (1.02 to 1.2) | 0.01 | 0.70 |
| 6q25.1 | rs3757318 | 151914113 | ESR1 | G | A | Yes | 0.08 | 1.20 (1.11 to 1.29) | 1.1 × 10 −6 | 1.24 (1.14 to 1.35) | 5.6 × 10 −7 | 1.06 (0.89 to 1.26) | 0.51 | 0.12 | 0.09 | 1.15 (1.03 to 1.28) | 0.01 | 1.33 (1.07 to 1.65) | 9.1 × 10 −3 | 1.09 (0.96 to 1.24) | 0.17 | 0.12 |
| 6q25.1 | rs2046210 | 151948366 | ESR1 | G | A | Yes | 0.37 | 1.16 (1.12 to 1.21) | 2.4 × 10 −12 | 1.20 (1.15 to 1.26) | 2.8 × 10 −13 | 1.04 (0.94 to 1.15) | 0.42 | 0.01 | 0.37 | 1.06 (0.99 to 1.12) | 0.07 | 1.15 (1.00 to 1.33) | 0.04 | 1.03 (0.96 to 1.1) | 0.43 | 0.17 |
| 7q35 | rs720475 | 144074929 | ARHGEF5 | G | A | Yes | 0.26 | 0.98 (0.93 to 1.03) | 0.36 | 0.98 (0.93 to 1.04) | 0.54 | 0.96 (0.86 to 1.08) | 0.53 | 0.79 | 0.26 | 0.99 (0.92 to 1.06) | 0.71 | 0.94 (0.80 to 1.09) | 0.41 | 1.00 (0.93 to 1.08) | 0.96 | 0.45 |
| 8p12 | rs9693444 | 29509616 | DUSP4 | C | A | Yes | 0.33 | 1.01 (0.96 to 1.05) | 0.80 | 1.01 (0.96 to 1.06) | 0.69 | 0.99 (0.90 to 1.09) | 0.83 | 0.72 | 0.33 | 0.98 (0.93 to 1.05) | 0.61 | 0.92 (0.80 to 1.07) | 0.28 | 1.00 (0.94 to 1.07) | 0.94 | 0.32 |
| 8q21.11 | rs6472903 | 76230301 | A | C | Yes | 0.17 | 1.01 (0.96 to 1.07) | 0.74 | 1.01 (0.95 to 1.08) | 0.77 | 1.01 (0.89 to 1.14) | 0.89 | 0.99 | 0.16 | 0.97 (0.90 to 1.05) | 0.48 | 0.95 (0.79 to 1.14) | 0.56 | 0.98 (0.89 to 1.07) | 0.66 | 0.75 | |
| 8q21.11 | rs2943559 | 76417937 | HNF4G | A | G | Yes | 0.08 | 1.06 (0.98 to 1.14) | 0.12 | 1.07 (0.98 to 1.17) | 0.12 | 1.02 (0.86 to 1.22) | 0.78 | 0.68 | 0.09 | 1.10 (1.00 to 1.22) | 0.05 | 1.14 (0.91 to 1.43) | 0.27 | 1.09 (0.97 to 1.23) | 0.13 | 0.77 |
| 8q24.21 | rs11780156 | 129194641 | MYC | G | A | No | 0.19 | 0.95 (0.9 to 1) | 0.05 | 0.96 (0.90 to 1.02) | 0.15 | 0.93 (0.82 to 1.05) | 0.23 | 0.70 | 0.19 | 0.97 (0.90 to 1.04) | 0.44 | 0.95 (0.81 to 1.12) | 0.56 | 0.98 (0.9 to 1.06) | 0.60 | 0.79 |
| 8q24.21 | rs13281615 | 128355618 | A | G | Yes | 0.43 | 1.02 (0.98 to 1.06) | 0.44 | 1.01 (0.96 to 1.06) | 0.73 | 1.04 (0.95 to 1.15) | 0.38 | 0.55 | 0.43 | 1.03 (0.97 to 1.09) | 0.33 | 1.05 (0.92 to 1.20) | 0.44 | 1.02 (0.96 to 1.1) | 0.51 | 0.71 | |
| 9p21.3 | rs1011970 | 22062134 | CDKN2B | C | A | Yes | 0.17 | 1.02 (0.97 to 1.08) | 0.47 | 1.07 (1.00 to 1.14) | 0.05 | 0.87 (0.76 to 0.99) | 0.04 | 9.3 × 10 −3 | 0.17 | 1.03 (0.95 to 1.11) | 0.50 | 1.11 (0.94 to 1.32) | 0.21 | 1.00 (0.92 to 1.1) | 0.95 | 0.29 |
| 9q31.2 | rs10759243 | 110306115 | KLF4 | C | A | No | 0.31 | 0.98 (0.94 to 1.02) | 0.39 | 0.98 (0.93 to 1.03) | 0.49 | 0.98 (0.88 to 1.08) | 0.64 | 0.93 | 0.29 | 1.00 (0.94 to 1.06) | 0.94 | 0.94 (0.81 to 1.09) | 0.40 | 1.01 (0.94 to 1.09) | 0.69 | 0.37 |
| 9q31.2 | rs865686 | 110888478 | KLF4 | A | C | Yes | 0.36 | 0.99 (0.95 to 1.04) | 0.77 | 1.02 (0.97 to 1.07) | 0.52 | 0.92 (0.83 to 1.02) | 0.11 | 0.10 | 0.36 | 0.99 (0.93 to 1.05) | 0.75 | 1.16 (1.01 to 1.34) | 0.04 | 0.94 (0.88 to 1.01) | 0.12 | 0.01 |
| 10p12.31 | rs7072776 | 22032942 | MLLT10 | G | A | No | 0.31 | 0.99 (0.94 to 1.03) | 0.52 | 0.96 (0.91 to 1.01) | 0.11 | 1.08 (0.98 to 1.20) | 0.12 | 0.04 | 0.3 | 0.99 (0.92 to 1.05) | 0.67 | 0.88 (0.77 to 1.02) | 0.08 | 1.02 (0.94 to 1.09) | 0.66 | 0.09 |
| 10p12.31 | rs11814448 | 22315843 | DNAJC1 | A | C | No | 0.02 | 1.10 (0.94 to 1.29) | 0.22 | 1.25 (0.93 to 1.69) | 0.15 | 0.50 | ||||||||||
| 10q21.2 | rs10995190 | 64278682 | ZNF365 | G | A | Yes | 0.15 | 0.99 (0.93 to 1.05) | 0.70 | 1.02 (0.96 to 1.09) | 0.49 | 0.88 (0.76 to 1.00) | 0.06 | 0.05 | 0.15 | 0.94 (0.86 to 1.02) | 0.16 | 0.92 (0.76 to 1.12) | 0.43 | 0.95 (0.86 to 1.04) | 0.26 | 0.84 |
| 10q22.3 | rs704010 | 80841148 | ZMIZ1 | G | A | Yes | 0.37 | 1.01 (0.97 to 1.06) | 0.48 | 0.99(0.94 to 1.04) | 0.61 | 1.12 (1.01 to 1.23) | 0.03 | 0.03 | 0.38 | 1.01 (0.95 to 1.07) | 0.86 | 1.02 (0.90 to 1.16) | 0.78 | 1.00 (0.93 to 1.07) | 0.96 | 0.83 |
| 10q25.2 | rs7904519 | 114773927 | TCF7L2 | A | G | Yes | 0.47 | 1.09 (1.05 to 1.14) | 1.6 × 10 −5 | 1.09 (1.04 to 1.14) | 6.4 × 10 −4 | 1.12 (1.02 to 1.23) | 0.02 | 0.59 | 0.47 | 1.02 (0.96 to 1.08) | 0.56 | 0.89 (0.78 to 1.01) | 0.07 | 1.06 (0.99 to 1.13) | 0.10 | 0.02 |
| 10q26.12 | rs2981579 | 123337335 | FGFR2 | G | A | Yes | 0.42 | 0.99 (0.95 to 1.04) | 0.81 | 0.92 (0.87 to 0.96) | 6.9 × 10 −4 | 1.29 (1.17 to 1.43) | 3.1 × 10 −7 | 7.5 × 10 −9 | 0.44 | 1.24 (1.16 to 1.31) | 5.4 × 10 −12 | 1.05 (0.92 to 1.20) | 0.44 | 1.29 (1.21 to 1.38) | 2.2 × 10 −13 | 7.3 × 10 −3 |
| 10q26.12 | rs11199914 | 123093901 | FGFR2 | G | A | No | 0.33 | 1.02 (0.98 to 1.07) | 0.27 | 1.04 (0.99 to 1.10) | 0.09 | 0.96 (0.86 to 1.06) | 0.43 | 0.17 | 0.33 | 0.95 (0.90 to 1.02) | 0.15 | 0.90 (0.78 to 1.03) | 0.13 | 0.97 (0.9 to 1.04) | 0.44 | 0.33 |
| 11p15.5 | rs3817198 | 1909006 | LSP1 | A | G | Yes | 0.33 | 1.08 (1.03 to 1.13) | 6.5 × 10 −4 | 1.08 (1.03 to 1.14) | 2.9 × 10 −3 | 1.07 (0.97 to 1.18) | 0.17 | 0.89 | 0.34 | 1.11 (1.04 to 1.18) | 9.3 × 10 −4 | 0.98 (0.85 to 1.13) | 0.80 | 1.15 (1.07 to 1.24) | 1.1 × 10 −4 | 0.06 |
| 11q13.1 | rs3903072 | 65583066 | SNX32 | C | A | No | 0.47 | 0.99 (0.95 to 1.03) | 0.69 | 1.00 (0.95 to 1.05) | 0.94 | 0.96 (0.87 to 1.05) | 0.39 | 0.44 | 0.47 | 0.97 (0.91 to 1.03) | 0.34 | 0.89 (0.78 to 1.01) | 0.07 | 1.00 (0.93 to 1.07) | 0.91 | 0.12 |
| 11q13.3 | rs554219 | 69331642 | CCND1 | C | G | Yes | 0.12 | 1.03 (0.97 to 1.09) | 0.37 | 1.00 (0.93 to 1.08) | 0.96 | 1.12 (0.97 to 1.29) | 0.12 | 0.20 | 0.13 | 1.09 (1.00 to 1.19) | 0.05 | 0.90 (0.73 to 1.10) | 0.31 | 1.15 (1.04 to 1.26) | 5.0 × 10 −3 | 0.04 |
| 11q13.3 | c11_pos69088342 | 69379161 | C | A | Yes | 0.06 | 1.03 (0.95 to 1.13) | 0.45 | 1.00 (0.90 to 1.12) | 0.95 | 1.14 (0.93 to 1.39) | 0.20 | 0.30 | 0.06 | 1.07 (0.95 to 1.21) | 0.28 | 0.85 (0.64 to 1.14) | 0.29 | 1.14 (0.99 to 1.3) | 0.08 | 0.09 | |
| 11q13.3 | rs494406 | 69344241 | G | A | Yes | 0.25 | 1.02 (0.97 to 1.07) | 0.46 | 1.02 (0.97 to 1.08) | 0.42 | 1.00 (0.90 to 1.12) | 0.97 | 0.74 | 0.26 | 1.05 (0.98 to 1.12) | 0.16 | 1.03 (0.89 to 1.19) | 0.66 | 1.05 (0.98 to 1.14) | 0.18 | 0.80 | |
| 11q24.3 | rs11820646 | 129461171 | BARX2 | G | A | No | 0.39 | 0.93 (0.89 to 0.97) | 5.9 × 10 −4 | 0.94 (0.90 to 0.99) | 0.03 | 0.88 (0.79 to 0.97) | 8.9 × 10 −3 | 0.20 | 0.39 | 0.92 (0.86 to 0.97) | 4.2 × 10 −3 | 0.95 (0.83 to 1.09) | 0.45 | 0.91 (0.84 to 0.97) | 5.9 × 10 −3 | 0.56 |
| 12p13.1 | rs12422552 | 14413931 | ATF7IP | G | C | No | 0.27 | 1.01 (0.97 to 1.06) | 0.63 | 1.01 (0.96 to 1.07) | 0.68 | 1.01 (0.91 to 1.13) | 0.85 | 0.99 | 0.28 | 1.00 (0.93 to 1.06) | 0.92 | 1.02 (0.88 to 1.19) | 0.79 | 0.99 (0.92 to 1.07) | 0.79 | 0.73 |
| 12p11.22 | rs10771399 | 28155080 | PTHLH | A | G | Yes | 0.10 | 0.85 (0.80 to 0.91) | 1.9 × 10 −6 | 0.83 (0.77 to 0.9) | 1.2 × 10 −5 | 0.91 (0.78 to 1.06) | 0.24 | 0.36 | 0.1 | 0.89 (0.81 to 0.98) | 0.02 | 0.72 (0.56 to 0.91) | 6.6 × 10 −3 | 0.94 (0.84 to 1.05) | 0.25 | 0.05 |
| 12q22 | rs17356907 | 96027759 | NTN4 | A | G | No | 0.29 | 0.95 (0.91 to 1.00) | 0.03 | 0.94 (0.90 to 1.00) | 0.03 | 0.98 (0.88 to 1.09) | 0.71 | 0.56 | 0.3 | 0.99 (0.93 to 1.06) | 0.78 | 0.95 (0.83 to 1.10) | 0.51 | 1.00 (0.93 to 1.08) | 0.96 | 0.55 |
| 12q24.21 | rs1292011 | 115836522 | TBX3 | A | G | Yes | 0.41 | 1.00 (0.96 to 1.05) | 0.82 | 1.04 (0.99 to 1.10) | 0.08 | 0.88 (0.80 to 0.97) | 0.01 | 4.39 × 10 −3 | 0.41 | 0.92 (0.87 to 0.98) | 0.01 | 1.07 (0.94 to 1.23) | 0.29 | 0.88 (0.82 to 0.95) | 5.7 × 10 −4 | 0.01 |
| 13q13.1 | rs11571833 | 32972626 | BRCA2 | T | A | No | 0.01 | 1.02 (0.83 to 1.26) | 0.83 | 1.05 (0.83 to 1.34) | 0.66 | 0.92 (0.53 to 1.59) | 0.75 | 0.66 | 0.03 | 0.95 (0.78 to 1.16) | 0.62 | 0.91 (0.58 to 1.41) | 0.66 | 0.97 (0.78 to 1.2) | 0.76 | 0.80 |
| 14q13.3 | rs2236007 | 37132769 | PAX9 | G | A | No | 0.21 | 0.97 (0.92 to 1.02) | 0.19 | 0.95 (0.90 to 1.01) | 0.13 | 1.01 (0.90 to 1.14) | 0.87 | 0.42 | 0.21 | 0.99 (0.92 to 1.07) | 0.83 | 1.20 (1.03 to 1.40) | 0.02 | 0.94 (0.86 to 1.02) | 0.13 | 8.5 × 10 −3 |
| 14q24.1 | rs2588809 | 68660428 | G | A | No | 0.19 | 0.96 (0.91 to 1.01) | 0.09 | 0.95 (0.89 to 1.01) | 0.13 | 0.97 (0.86 to 1.09) | 0.56 | 0.85 | 0.2 | 1.01 (0.94 to 1.09) | 0.82 | 0.95 (0.80 to 1.13) | 0.55 | 1.03 (0.94 to 1.12) | 0.55 | 0.44 | |
| 14q24.1 | rs999737 | 69034682 | RAD51L1 | G | A | Yes | 0.21 | 0.96 (0.91 to 1.01) | 0.09 | 0.98 (0.92 to 1.04) | 0.43 | 0.90 (0.80 to 1.01) | 0.07 | 0.22 | 0.22 | 0.97 (0.91 to 1.05) | 0.48 | 0.95 (0.81 to 1.11) | 0.53 | 0.98 (0.91 to 1.06) | 0.65 | 0.72 |
| 14q32.11 | rs941764 | 91841069 | CCDC88C | A | G | No | 0.34 | 1.03 (0.98 to 1.07) | 0.23 | 1.02 (0.97 to 1.07) | 0.47 | 1.05 (0.95 to 1.17) | 0.34 | 0.62 | 0.34 | 1.03 (0.97 to 1.09) | 0.39 | 1.00 (0.88 to 1.14) | 0.97 | 1.04 (0.97 to 1.11) | 0.32 | 0.61 |
| 16q12.1a | rs3803662 | 52586341 | TOX3 | G | A | Yes | 0.29 | 1.06 (1.01 to 1.11) | 0.02 | 1.01 (0.96 to 1.07) | 0.65 | 1.22 (1.10 to 1.35) | 1.5 × 10 −4 | 2.39 × 10 −3 | 0.29 | 1.24 (1.16 to 1.32) | 6.2 × 10 −11 | 1.12 (0.97 to 1.30) | 0.11 | 1.27 (1.18 to 1.36) | 1.5 × 10 −10 | 0.15 |
| 16q12.1b | rs11075995 | 53855291 | FTO | A | T | No | 0.24 | 1.01 (0.96 to 1.06) | 0.61 | 0.98 (0.93 to 1.04) | 0.60 | 1.11 (0.99 to 1.24) | 0.07 | 0.07 | 0.24 | 1.02(0.95 to 1.09) | 0.59 | 1.01 (0.86 to 1.18) | 0.94 | 1.02 (0.94 to 1.11) | 0.57 | 0.85 |
| 16q12.1b | rs17817449 | 53813367 | FTO | A | C | No | 0.41 | 0.95 (0.91 to 0.99) | 0.02 | 0.94 (0.89 to 0.98) | 9.8 × 10 −3 | 1.00 (0.91 to 1.10) | 0.99 | 0.26 | 0.41 | 0.94 (0.88 to 1.00) | 0.03 | 1.05 (0.91 to 1.21) | 0.49 | 0.91 (0.85 to 0.97) | 6.6 × 10 −3 | 0.08 |
| 16q23.2 | rs13329835 | 80650805 | CDYL2 | A | G | No | 0.23 | 1.04 (0.99 to 1.09) | 0.09 | 1.03 (0.97 to 1.09) | 0.29 | 1.08 (0.97 to 1.21) | 0.17 | 0.48 | 0.24 | 1.03 (0.96 to 1.11) | 0.35 | 0.94 (0.81 to 1.10) | 0.43 | 1.06 (0.98 to 1.15) | 0.13 | 0.17 |
| 17q22 | rs6504950 | 53056471 | COX11 | G | A | Yes | 0.27 | 0.98 (0.94 to 1.03) | 0.49 | 0.99 (0.94 to 1.04) | 0.70 | 0.96 (0.87 to 1.07) | 0.49 | 0.68 | 0.27 | 1.04 (0.97 to 1.11) | 0.24 | 1.08 (0.94 to 1.24) | 0.27 | 1.03 (0.95 to 1.11) | 0.46 | 0.54 |
| 18q11.2 | rs527616 | 24337424 | AQP4 | C | G | No | 0.37 | 0.99 (0.95 to 1.03) | 0.61 | 0.97 (0.93 to 1.02) | 0.30 | 1.04 (0.94 to 1.15) | 0.42 | 0.26 | 0.37 | 0.96 (0.9 to 1.02) | 0.19 | 0.95 (0.83 to 1.08) | 0.41 | 0.96 (0.9 to 1.03) | 0.30 | 0.82 |
| 18q11.2 | rs1436904 | 22824665 | A | C | No | 0.39 | 0.99 (0.95 to 1.03) | 0.68 | 1.00 (0.95 to 1.05) | 0.86 | 0.98 (0.89 to 1.08) | 0.63 | 0.74 | 0.39 | 0.96 (0.9 to 1.02) | 0.14 | 1.02 (0.89 to 1.17) | 0.79 | 0.94 (0.87 to 1.01) | 0.07 | 0.30 | |
| 19p13.11 | rs8170 | 17389704 | BABAM1 | G | A | Yes | 0.19 | 1.19 (1.12 to 1.25) | 2.9 × 10 −10 | 1.22 (1.15 to 1.30) | 1.7 × 10 −10 | 1.06 (0.95 to 1.20) | 0.30 | 0.05 | 0.19 | 0.98 (0.91 to 1.06) | 0.62 | 1.06 (0.90 to 1.25) | 0.51 | 0.96 (0.88 to 1.05) | 0.37 | 0.33 |
| 19p13.11 | rs4808801 | 18571141 | ELL | A | G | No | 0.32 | 0.98 (0.94 to 1.02) | 0.40 | 0.99 (0.94 to 1.05) | 0.81 | 0.94 (0.85 to 1.04) | 0.23 | 0.35 | 0.33 | 0.97 (0.91 to 1.03) | 0.33 | 1.07 (0.93 to 1.23) | 0.33 | 0.94 (0.87 to 1.01) | 0.10 | 0.11 |
| 19q13.31 | rs3760982 | 44286513 | KCNN4 | G | A | No | 0.46 | 1.03 (0.99 to 1.08) | 0.10 | 1.03 (0.98 to 1.08) | 0.19 | 1.04 (0.95 to 1.14) | 0.41 | 0.90 | 0.46 | 1.05 (0.99 to 1.12) | 0.09 | 0.97 (0.86 to 1.11) | 0.69 | 1.08 (1.01 to 1.15) | 0.03 | 0.19 |
| 21q21.1 | rs2823093 | 16520832 | NRIP1 | G | A | Yes | 0.27 | 0.95 (0.91 to 1) | 0.04 | 0.96 (0.91 to 1.02) | 0.17 | 0.92 (0.82 to 1.02) | 0.11 | 0.44 | 0.27 | 0.94 (0.88 to 1.01) | 0.09 | 1.07 (0.92 to 1.25) | 0.36 | 0.91 (0.84 to 0.98) | 0.02 | 0.06 |
| 22q12.2 | rs132390 | 29621477 | EMID1 | A | G | No | 0.03 | 0.98 (0.87 to 1.1) | 0.75 | 0.93 (0.81 to 1.07) | 0.30 | 1.16 (0.91 to 1.46) | 0.23 | 0.13 | 0.04 | 1.17 (1.00 to 1.37) | 0.05 | 0.92 (0.61 to 1.39) | 0.70 | 1.24 (1.04 to 1.49) | 0.02 | 0.22 |
| 22q13.1 | rs6001930 | 40876234 | SGSM3 | A | G | No | 0.11 | 1.07 (1.00 to 1.14) | 0.03 | 1.06 (0.98 to 1.15) | 0.14 | 1.11 (0.96 to 1.30) | 0.17 | 0.60 | 0.10 | 1.02 (0.92 to 1.12) | 0.71 | 0.94 (0.76 to 1.18) | 0.61 | 1.04 (0.93 to 1.16) | 0.48 | 0.44 |
aCI, Confidence interval; ER, Estrogen receptor; HR, Hazard ratio; MAF, Mean allele frequency; SNP, Single-nucleotide polymorphism. Results represent BRCA1 and BRCA2 mutation carriers for 74 previously reported breast cancer (BC) susceptibility variants from population-based studies. P-values <0.05 are shown in bold. bPosition in build 37. cReference allele. cEffect allele. eAssociation in BRCA1 and BRCA2 carriers has been reported before. fP-value for the difference between the association with ER-positive BC and the association with ER-negative BC.