Risk associated with overall breast cancer for 172 SNPs
| Overall breast cancer risk (24) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Locus | Locus discovery referencea | Genes | rs ID | Alleles | MAFb | Refined SNP referencec | Subtyped | ORe (95% CI)f | Pg | Combined Ph |
| 2q33.1 | (99) | CASP8/ALS2CR12 | rs1830298 | T/C | 0.28 | (100) | Overall | 1.06 (1.04–1.08) | 1.7 × 10−08 | 1.9 × 10−16 |
| 5q11.2 | (12) | MAP3K1 | rs62355902 | A/T | 0.16 | (12) | Overall | 1.18 (1.15–1.21) | 8.5 × 10−42 | 6.8 × 10−98 |
| 8q24.21 | (12) | — | rs13281615 | A/G | 0.41 | (12) | Overall | 1.11 (1.09–1.13) | 5 × 10−28 | 1.9 × 10−57 |
| 11p15.5 | (12) | LSP1 | rs3817198 | T/C | 0.32 | (12) | Overall | 1.05 (1.03–1.07) | 6.2 × 10−07 | 9.9 × 10−19 |
| 16q12.1 | (12) | TOX3 | rs4784227 | C/T | 0.24 | (101) | Overall | 1.23 (1.2–1.25) | 7 × 10−88 | 6.8 × 10−201 |
| 10q26.13 | (12) | FGFR2 | rs2981578 | T/C | 0.47 | (102) | Overall | 1.23 (1.21–1.25) | 1 × 10−114 | 1.3 × 10−245 |
| 10q26.13 | (12) | FGFR2 | rs35054928 | G/GC | 0.4 | (102) | Overall | 1.27 (1.25–1.3) | 3.5 × 10−154 | 2.3 × 10−322 |
| 10q26.13 | (12) | FGFR2 | rs45631563 | A/T | 0.05 | (102) | Overall | 0.81 (0.78–0.85) | 9.1 × 10−21 | 7.3 × 10−37 |
| 2q35 | (46) | IGFBP5 | rs4442975 | G/T | 0.5 | (103) | ER+ | 0.89 (0.87–0.9) | 3.6 × 10−40 | 1.1 × 10−95 |
| 2q35 | (46) | IGFBP5 | rs34005590 | C/A | 0.05 | (104) | Overall | 0.82 (0.79–0.86) | 1.6 × 10−19 | 3.2 × 10−41 |
| 5p12 | (13) | FGF10/MRPS30 | rs10941679 | A/G | 0.25 | (13) | ER+ | 1.15 (1.13–1.18) | 6.2 × 10−43 | 5.6 × 10−73 |
| 3p24.1 | (16) | SLC4A7 | rs4973768 | C/T | 0.47 | (16) | Overall | 1.11 (1.09–1.13) | 1.7 × 10−28 | 4.8 × 10−57 |
| 17q22 | (16) | — | rs2787486 | A/C | 0.3 | (105) | Overall | 0.93 (0.91–0.94) | 1.2 × 10−14 | 5.6 × 10−29 |
| 22q12.1 | (106) | CHEK2 | rs17879961 | A/G | 0.01 | (22) | Overall | 1.26 (1.11–1.42) | 2.4 × 10−04 | 9.7 × 10−09 |
| 1p11.2 | (107) | EMBP1 | rs11249433 | A/G | 0.41 | (107) | Overall | 1.11 (1.09–1.13) | 2.2 × 10−31 | 1.8 × 10−52 |
| 14q24.1 | (107) | RAD51B | rs999737 | C/T | 0.23 | (107) | Overall | 0.91 (0.89–0.93) | 1.1 × 10−18 | 6.5 × 10−39 |
| 19p13.11 | (40) | — | rs67397200 | C/G | 0.3 | (108) | BRCA1 | 1.03 (1.01–1.05) | 4.2 × 10−03 | 1.6 × 10−08 |
| 9p21.3 | (20) | CDKN2A/CDKN2B | rs1011970 | G/T | 0.16 | (20) | Overall | 1.07 (1.04–1.09) | 1.4 × 10−07 | 1 × 10−15 |
| 10p15.1 | (20) | ANKRD16 | rs2380205 | C/T | 0.44 | (20) | Overall | 0.98 (0.96–0.99) | 1.1 × 10−02 | 1.7 × 10−04 |
| 10q22.3 | (20) | ZMZ1 | rs704010 | C/T | 0.38 | (20) | Overall | 1.07 (1.05–1.09) | 1.1 × 10−14 | 1.7 × 10−35 |
| 11q13.3 | (20) | CCND1 | rs554219 | C/G | 0.13 | (97) | ER+ | 1.21 (1.18–1.24) | 5.8 × 10−47 | 5.8 × 10−47 |
| 11q13.3 | (20) | CCND1 | rs75915166 | C/A | 0.06 | (97) | ER+ | 1.28 (1.24–1.33) | 4.1 × 10−42 | 4.1 × 10−95 |
| 6q25 | (20) | ESR1 | rs3757322 | T/G | 0.32 | (93) | ER- | 1.08 (1.06–1.1) | 1.1 × 10−16 | 3.3 × 10−41 |
| 6q25 | (20) | ESR1 | rs9397437 | G/A | 0.07 | (93) | ER- | 1.17 (1.14–1.21) | 6.3 × 10−21 | 4.8 × 10−54 |
| 6q25 | (20) | ESR1 | rs2747652 | C/T | 0.48 | (93) | ER- | 0.94 (0.92–0.960) | 1.2 × 10−11 | 1.3 × 10−26 |
| 10q21.2 | (109) | ZNF365 | rs10995201 | A/G | 0.16 | (110) | Overall | 0.9 (0.88–0.92) | 4.7 × 10−17 | 1.6 × 10−51 |
| 9q31.2 | (21) | — | rs10816625 | A/G | 0.06 | (111) | Overall | 1.11 (1.07–1.15) | 2.3 × 10−08 | 5 × 10−18 |
| 9q31.2 | (21) | — | rs13294895 | C/T | 0.18 | (111) | Overall | 1.06 (1.03–1.08) | 1.9 × 10−06 | 6.5 × 10−17 |
| 9q31.2 | (21) | — | rs676256 | T/C | 0.38 | (111) | Overall | 0.91 (0.9–0.93) | 1.9 × 10−21 | 3.5 × 10−53 |
| 5p15.33 | (47) | TERT | rs10069690 | C/T | 0.26 | (47) | ER- | 1.06 (1.04–1.08) | 2.5 × 10−08 | 7.8 × 10−17 |
| 12q24.21 | (19) | TBX3 | rs1292011 | A/G | 0.42 | (19) | Overall | 0.92 (0.9–0.94) | 2.4 × 10−19 | 4.4 × 10−39 |
| 21q21.1 | (19) | NRIP1 | rs2823093 | G/A | 0.27 | (19) | Overall | 0.94 (0.92–0.96) | 1.1 × 10−09 | 1.5 × 10−20 |
| 6q25.1 | (112) | TAB2 | rs9485372 | G/A | 0.19 | (112) | Overall | 0.96 (0.93–0.98) | 7.7 × 10−05 | 3.5 × 10−06 |
| 6q14.1 | (113) | — | rs17529111 | T/C | 0.22 | (113) | ER- | 1.02 (1–1.04) | 4.2 × 10−02 | 1.3 × 10−09 |
| 20q11.22 | (113) | RALY | rs2284378 | C/T | 0.32 | (113) | Overall | 1 (0.98–1.02) | 7.9 × 10−01 | 3.2 × 10−02 |
| 5p15.33 | (92) | TERT | rs3215401 | A/AG | 0.31 | (92) | Overall | 0.93 (0.91–0.95) | 7.1 × 10−13 | 1.1 × 10−20 |
| 1q32.1 | (48) | LGR6 | rs6678914 | G/A | 0.41 | (48) | Overall | 1 (0.99–1.02) | 7.3 × 10−01 | 3 × 10−01 |
| 1q32.1 | (48) | MDM4 | rs4245739 | A/C | 0.26 | (48) | Overall | 1.02 (1–1.04) | 2.5 × 10−02 | 1.3 × 10−04 |
| 2p24.1 | (48) | — | rs12710696 | C/T | 0.37 | (48) | Overall | 1.03 (1.01–1.04) | 6.6 × 10−03 | 1.3 × 10−08 |
| 16q12.2 | (48) | FTO | rs11075995 | T/A | 0.24 | (48) | Overall | 1.03 (1.01–1.06) | 1.3 × 10−03 | 8.7 × 10−09 |
| 6p24.3 | (114) | TFAP2A | rs9348512 | C/A | 0.33 | (114) | BRCA2 | 1 (0.99–1.02) | 6.4 × 10−01 | 8 × 10−01 |
| 22q13.1 | (60) | APOBEC3A/APOBEC3B | chr22:39359355 | I/D7 | 0.1 | (60) | Overall | 1.1 (1.07–1.14) | 6.1 × 10−09 | 4.9 × 10−12 |
| 1p36.22 | (22) | PEX14 | rs616488 | A/G | 0.33 | (22) | Overall | 0.94 (0.93–0.96) | 1.8 × 10−09 | 5 × 10−20 |
| 1p13.2 | (22) | DCLRE1B | rs11552449 | C/T | 0.17 | (22) | Overall | 1.04 (1.01–1.06) | 2.3 × 10−03 | 4.6 × 10−11 |
| 2q14.1 | (22) | — | rs4849887 | C/T | 0.1 | (22) | Overall | 0.91 (0.88–0.94) | 1.2 × 10−10 | 6.9 × 10−20 |
| 2q31.1 | (22) | DLX2-AS1 | rs2016394 | G/A | 0.47 | (22) | Overall | 0.95 (0.94–0.97) | 3.1 × 10−07 | 6.2 × 10−12 |
| 2q31.1 | (22) | CDCA7 | rs1550623 | A/G | 0.15 | (22) | Overall | 0.95 (0.93–0.98) | 8.8 × 10−05 | 5.4 × 10−10 |
| 2q35 | (22) | DIRC3 | rs16857609 | C/T | 0.26 | (22) | Overall | 1.06 (1.04–1.09) | 1.4 × 10−09 | 1.8 × 10−25 |
| 3p26.1 | (22) | EGPT/ITPR1 | rs6762644 | A/G | 0.38 | (22) | Overall | 1.05 (1.03–1.07) | 1.6 × 10−08 | 4 × 10−18 |
| 3p24.1 | (22) | TGFBR2 | rs12493607 | G/C | 0.34 | (22) | Overall | 1.05 (1.03–1.07) | 4.9 × 10−07 | 6.9 × 10−14 |
| 4q24 | (22) | TET2 | rs9790517 | C/T | 0.23 | (22) | Overall | 1.04 (1.01–1.06) | 1.1 × 10−03 | 5 × 10−11 |
| 4q34.1 | (22) | ADAM29 | rs6828523 | C/A | 0.12 | (22) | Overall | 0.91 (0.88–0.93) | 1.2 × 10−11 | 1.8 × 10−25 |
| 5q11.2 | (22) | RAB3C | rs10472076 | T/C | 0.38 | (22) | Overall | 1.03 (1.01–1.04) | 6.6 × 10−03 | 9.6 × 10−09 |
| 5q11.2 | (22) | PDE4D | rs1353747 | T/G | 0.09 | (22) | Overall | 0.96 (0.93–0.99) | 7.6 × 10−03 | 4.1 × 10−09 |
| 5q33.3 | (22) | EBF1 | rs1432679 | T/C | 0.43 | (22) | Overall | 1.08 (1.06–1.1) | 2.9 × 10−17 | 6.6 × 10−31 |
| 6p25.3 | (22) | FOXQ1 | rs11242675 | T/C | 0.37 | (22) | Overall | 1 (0.98–1.02) | 9.7 × 10−01 | 1 × 10−04 |
| 6p23 | (22) | RANBP9 | rs204247 | A/G | 0.44 | (22) | Overall | 1.04 (1.02–1.06) | 6.4 × 10−05 | 7.9 × 10−13 |
| 7q35 | (22) | NOBOX/ARHGEF6 | rs720475 | G/A | 0.25 | (22) | Overall | 0.96 (0.94–0.98) | 3 × 10−04 | 1.2 × 10−11 |
| 8p12 | (22) | — | rs9693444 | C/A | 0.32 | (22) | Overall | 1.06 (1.04–1.08) | 1.7 × 10−10 | 1.6 × 10−21 |
| 8q21.11 | (22) | — | rs6472903 | T/G | 0.17 | (22) | Overall | 0.94 (0.92–0.96) | 4.4 × 10−21 | 4.4 × 10−21 |
| 8q21.11 | (22) | HNF4G | rs2943559 | A/G | 0.08 | (22) | Overall | 1.1 (1.07–1.14) | 4.2 × 10−09 | 4 × 10−24 |
| 8q24.21 | (22) | MYC | rs11780156 | C/T | 0.17 | (22) | Overall | 1.05 (1.03–1.08) | 2.5 × 10−05 | 1.1 × 10−13 |
| 9q31.2 | (22) | — | rs10759243 | C/A | 0.29 | (22) | Overall | 1.06 (1.04–1.08) | 4.2 × 10−10 | 2.2 × 10−18 |
| 10p12.31 | (22) | DNAJC1 | rs7072776 | G/A | 0.29 | (22) | Overall | 1.05 (1.03–1.07) | 2.7 × 10−07 | 1.8 × 10−19 |
| 10p12.31 | (22) | DNAJC1 | rs11814448 | A/C | 0.02 | (22) | Overall | 1.12 (1.06–1.19) | 1.4 × 10−06 | 6.1 × 10−18 |
| 10q25.2 | (22) | TCFL2 | rs7904519 | A/G | 0.46 | (22) | Overall | 1.03 (1.01–1.05) | 8.6 × 10−04 | 1.5 × 10−13 |
| 10q26.12 | (22) | — | rs11199914 | C/T | 0.32 | (22) | Overall | 0.96 (0.94–0.98) | 2.1 × 10−05 | 6.5 × 10−12 |
| 11q13.1 | (22) | — | rs3903072 | G/T | 0.47 | (22) | Overall | 0.97 (0.95–0.97) | 9.1 × 10−04 | 2.3 × 10−12 |
| 11q24.3 | (22) | — | rs11820646 | C/T | 0.4 | (22) | Overall | 0.96 (0.94–0.98) | 2.5 × 10−05 | 2.1 × 10−14 |
| 12p13.1 | (22) | — | rs12422552 | G/C | 0.26 | (22) | Overall | 1.06 (1.04–1.08) | 3.2 × 10−08 | 3.6 × 10−15 |
| 12q22 | (22) | NTN4 | rs17356907 | A/G | 0.3 | (22) | Overall | 0.91 (0.9–0.93) | 6.6 × 10−20 | 1 × 10−39 |
| 13q13.1 | (22) | BRCA2 | rs11571833 | A/T | 0.01 | (22) | Overall | 1.35 (1.23–1.48) | 4 × 10−10 | 3.1 × 10−15 |
| 14q13.3 | (22) | PAX9 | rs2236007 | G/A | 0.21 | (22) | Overall | 0.93 (0.91–0.95) | 5.8 × 10−10 | 4.2 × 10−21 |
| 14q24.1 | (22) | RAD51B | rs2588809 | C/T | 0.17 | (22) | Overall | 1.06 (1.03–1.08) | 2.6 × 10−06 | 6.3 × 10−14 |
| 14q32.11 | (22) | CCDC88C | rs941764 | A/G | 0.35 | (22) | Overall | 1.03 (1.02–1.05) | 3.6 × 10−04 | 8.2 × 10−13 |
| 16q12.2 | (22) | FTO | rs17817449 | T/G | 0.41 | (22) | Overall | 0.95 (0.93–0.96) | 4.9 × 10−09 | 2.5 × 10−21 |
| 16q23.2 | (22) | CDYL2 | rs13329835 | A/G | 0.23 | (22) | Overall | 1.07 (1.05–1.09) | 8.3 × 10−11 | 8.8 × 10−27 |
| 18q11.2 | (22) | — | rs527616 | G/C | 0.38 | (22) | Overall | 0.97 (0.95–0.98) | 2.8 × 10−04 | 6.7 × 10−15 |
| 18q11.2 | (22) | CHST9 | rs1436904 | T/G | 0.4 | (22) | Overall | 0.95 (0.94–0.97) | 1.1 × 10−07 | 9.9 × 10−15 |
| 19p13.11 | (22) | ELL | rs4808801 | A/G | 0.34 | (22) | Overall | 0.93 (0.91–0.95) | 2 × 10−12 | 4.7 × 10−28 |
| 19q13.31 | (22) | KCCN4/LYPD5 | rs3760982 | G/A | 0.46 | (22) | Overall | 1.05 (1.03–1.07) | 2.1 × 10−08 | 1.4 × 10−16 |
| 22q12.2 | (22) | EM1D1 | rs132390 | T/C | 0.04 | (22) | Overall | 1.04 (0.99–1.09) | 8.1 × 10−02 | 1.2 × 10−08 |
| 22q13.1 | (22) | MKL1 | rs6001930 | T/C | 0.1 | (22) | Overall | 1.12 (1.09–1.16) | 5.7 × 10−16 | 4.4 × 10−34 |
| 1q32.1 | (72) | ZC3H11A | rs4951011 | A/G | 0.16 | (72) | Overall | 1.04 (1.02–1.07) | 5.4 × 10−04 | 1.3 × 10−05 |
| 5q14.3 | (72) | ARRDC3 | rs10474352 | C/T | 0.16 | (72) | Overall | 0.94 (0.92–0.97) | 4.5 × 10−11 | 4.5 × 10−11 |
| 15q26.1 | (72) | PRC1 | rs2290203 | G/A | 0.21 | (72) | Overall | 0.94 (0.92–0.96) | 1.8 × 10−07 | 8.07 × 10−10 |
| 3p14.1 | (115) | ATNX7 | rs1053338 | A/G | 0.14 | (115) | Overall | 1.05 (1.02–1.07) | 5 × 10−04 | 5.3 × 10−11 |
| 7q21.2 | (115) | AKAP9 | rs6964587 | G/T | 0.39 | (115) | Overall | 1.03 (1.02–1.05) | 2.2 × 10−04 | 9 × 10−11 |
| 7q34 | (116) | — | rs11977670 | G/A | 0.43 | (116) | Lobular | 1.06 (1.04–1.08) | 1.9 × 10−11 | 1 × 10−16 |
| 1q21.1 | (23) | RNF115 | rs12405132 | C/T | 0.37 | (23) | Overall | 0.97 (0.95–0.99) | 1 × 10−03 | 6.3 × 10−10 |
| 1q21.2 | (23) | OTUD7B | rs12048493 | A/C | 0.38 | (23) | Overall | 1.04 (1.02–1.06) | 9.4 × 10−06 | 8.6 × 10−14 |
| 1q43 | (23) | EXO1 | rs72755295 | A/G | 0.03 | (23) | Overall | 1.15 (1.09–1.2) | 8 × 10−08 | 1.7 × 10−14 |
| 3p21.31 | (23) | — | rs6796502 | G/A | 0.1 | (23) | Overall | 0.92 (0.89–0.95) | 2.5 × 10−08 | 5.5 × 10−15 |
| 5p15.1 | (23) | — | rs13162653 | G/T | 0.45 | (23) | Overall | 0.99 (0.97–1.010) | 1.8 × 10−01 | 5.4 × 10−07 |
| 5p13.3 | (23) | — | rs2012709 | C/T | 0.48 | (23) | Overall | 1.02 (1–1.04) | 2.1 × 10−02 | 1.2 × 10−08 |
| 5q14.2 | (23) | ATG10 | rs7707921 | A/T | 0.25 | (23) | Overall | 0.96 (0.94–0.98) | 1.2 × 10−04 | 1.7 × 10−12 |
| 6p22.1 | (23) | — | rs9257408 | G/C | 0.41 | (23) | Overall | 1.02 (1–1.040) | 5.5 × 10−02 | 6.9 × 10−08 |
| 7q32.3 | (23) | FLJ43663 | rs4593472 | C/T | 0.35 | (23) | Overall | 0.97 (0.95–0.99) | 7.9 × 10-04 | 1.8 × 10−11 |
| 8p11.23 | (23) | — | rs13365225 | A/G | 0.18 | (23) | Overall | 0.91 (0.89–0.93) | 1.2 × 10-15 | 1.4 × 10−20 |
| 8q23.3 | (23) | LINC00536 | rs13267382 | G/A | 0.36 | (23) | Overall | 1.03 (1.01–1.05) | 8.7 × 10−04 | 1.6 × 10−11 |
| 14q32.12 | (23) | RIN3 | rs11627032 | T/C | 0.25 | (23) | Overall | 0.96 (0.94–0.98) | 1.6 × 10−04 | 4.1 × 10−11 |
| 17q11.2 | (23) | ATAD5 | rs146699004 | GGT/G | 0.27 | (23) | Overall | 0.97 (0.95–0.99) | 1.3 × 10−03 | 2 × 10−09 |
| 17q25.3 | (23) | — | rs745570 | G/A | 0.5 | (23) | Overall | 1.03 (1.01–1.05) | 2.1 × 10−03 | 3.9 × 10−10 |
| 18q12.3 | (23) | SETBP1 | rs6507583 | A/G | 0.07 | (23) | Overall | 0.92 (0.89–0.96) | 9.5 × 10−06 | 2.2 × 10−12 |
| 2p23.2 | (10) | WDR43 | rs4577244 | C/T | 0.23 | (10) | ER-/BRCA1 | 1.01 (0.99–1.03) | 2.4 × 10−01 | 4.3 × 10−01 |
| 12p11.22 | (10) | — | rs7297051 | C/T | 0.24 | (10) | ER-/BRCA1 | 0.89 (0.87–0.91) | 2.9 × 10−27 | 3 × 10−60 |
| 13q22.1 | (10) | — | rs6562760 | G/A | 0.24 | (10) | ER-/BRCA1 | 0.95 (0.93–0.97) | 8.6 × 10−06 | 1.5 × 10−09 |
| 1p36.13 | (24) | KLHDC7A | rs2992756 | C/T | 0.49 | (24) | Overall | 1.06 (1.04–1.08) | 1.3 × 10−11 | 1.6 × 10−15 |
| 1p34.2 | (24) | — | rs4233486 | T/C | 0.36 | (24) | Overall | 0.97 (0.95–0.98) | 2.3 × 10−04 | 9.1 × 10−09 |
| 1p34.2 | (24) | HIVEP3 | rs79724016 | T/G | 0.03 | (24) | Overall | 0.93 (0.88–0.97) | 3.3 × 10−03 | 3.5 × 10−08 |
| 1p34.1 | (24) | PIK3R3, LOC101929626 | rs1707302 | G/A | 0.34 | (24) | Overall | 0.96 (0.95–0.98) | 1.4 × 10−04 | 3.0 × 10−08 |
| 1p32.3 | (24) | — | rs140850326 | I/D9 | 0.49 | (24) | Overall | 0.97 (0.95–0.99) | 3.4 × 10−04 | 3.9 × 10−08 |
| 1p22.3 | (24) | — | rs17426269 | G/A | 0.15 | (24) | Overall | 1.05 (1.02–1.07) | 1.7 × 10−04 | 1.7 × 10−08 |
| 1p12 | (24) | — | rs7529522 | T/C | 0.23 | (24) | Overall | 1.06 (1.04–1.08) | 1.6 × 10−08 | 1.7 × 10−10 |
| 1q22 | (24) | TRIM46 | rs4971059 | G/A | 0.35 | (24) | Overall | 1.05 (1.03–1.07) | 3.9 × 10−08 | 4.8 × 10−11 |
| 1q32.1 | (24) | PHLDA3 | rs35383942 | C/T | 0.06 | (24) | Overall | 1.12 (1.08–1.17) | 12 × 10−09 | 3.8 × 10−13 |
| 1q41 | (24) | ESRRG | rs11117758 | G/A | 0.21 | (24) | Overall | 0.95 (0.93–0.97) | 7.7 × 10−07 | 3.9 × 10−09 |
| 2p25.1 | (24) | GRHL1 | rs113577745 | C/G | 0.1 | (24) | Overall | 1.08 (1.05–1.11) | 3.7 × 10−07 | 3.9 × 10−10 |
| 2p23.3 | (24) | ADCY3 | rs6725517 | A/G | 0.41 | (24) | Overall | 0.96 (0.94–0.98) | 7.5 × 10−06 | 2.9 × 10−12 |
| 2q13 | (24) | BCL2L11 | rs71801447 | CTTATGTT/C | 0.06 | (24) | Overall | 1.09 (1.05–1.13) | 7.7 × 10−06 | 3.7 × 10−08 |
| 2q36.3 | (24) | — | rs12479355 | A/G | 0.21 | (24) | Overall | 0.96 (0.94–0.98) | 4.7 × 10−04 | 2.4 × 10−08 |
| 3p13 | (24) | FOXP1 | rs6805189 | T/C | 0.48 | (24) | Overall | 0.97 (0.95–0.99) | 3.3 × 10−04 | 4.6 × 10−08 |
| 3p12.1 | (24) | VGLL3 | rs13066793 | A/G | 0.09 | (24) | Overall | 0.94 (0.91–0.97) | 1.5 × 10−04 | 1.0 × 10−09 |
| 3p12.1 | (24) | CMSS1, FILIP1L | rs9833888 | G/T | 0.22 | (24) | Overall | 1.06 (1.04–1.08) | 2.6 × 10−07 | 5.2 × 10−10 |
| 3q23 | (24) | ZBTB38 | rs34207738 | CTT/C | 0.41 | (24) | Overall | 1.06 (1.04–1.08) | 1.4 × 10−09 | 3.2 × 10−15 |
| 3q26.31 | (24) | — | rs58058861 | G/A | 0.21 | (24) | Overall | 1.06 (1.04–1.09) | 1.6 × 10−08 | 1.9 × 10−10 |
| 4p14 | (24) | — | rs6815814 | A/C | 0.26 | (24) | Overall | 1.06 (1.04–1.08) | 6.1 × 10−08 | 6.1 × 10−13 |
| 4q21.23 | (24) | HELQ | 4:84370124 | TA/TAA | 0.47 | (24) | Overall | 1.04 (1.02–1.05) | 1.7 × 10−04 | 2.2 × 10−09 |
| 4q22.1 | (24) | LOC105369192 | rs10022462 | C/T | 0.44 | (24) | Overall | 1.04 (1.02–1.06) | 9.4 × 10−06 | 1.6 × 10−09 |
| 4q28.1 | (24) | — | rs77528541 | G/T | 0.13 | (24) | Overall | 0.95 (0.92–0.97) | 4.8 × 10−05 | 1.4 × 10−09 |
| 5p15.33 | (24) | AHRR | rs116095464 | T/C | 0.05 | (24) | Overall | 1.06 (1.02–1.1) | 2.6 × 10−03 | 3.8 × 10−09 |
| 5q11.1 | (24) | — | rs72749841 | T/C | 0.16 | (24) | Overall | 0.93 (0.91–0.96) | 8.5 × 10−06 | 7.2 × 10−10 |
| 5q11.1 | (24) | — | rs35951924 | A/AT | 0.32 | (24) | Overall | 0.95 (0.93–0.97) | 4.0 × 10−07 | 1.3 × 10−11 |
| 5q22.1 | (24) | NREP | rs6882649 | T/G | 0.34 | (24) | Overall | 0.97 (0.95–0.99) | 2.7 × 10−03 | 3.7 × 10−09 |
| 5q31.1 | (24) | HSPA4 | rs6596100 | C/T | 0.25 | (24) | Overall | 0.94 (0.92–0.96) | 5.2 × 10−08 | 7.7 × 10−09 |
| 5q35.1 | (24) | — | rs4562056 | G/T | 0.33 | (24) | Overall | 1.05 (1.03–1.07) | 4.1 × 10−07 | 4.7 × 10−10 |
| 6p22.3 | (24) | ATXN1 | rs3819405 | C/T | 0.33 | (24) | Overall | 0.96 (0.94–0.97) | 2.2 × 10−06 | 1.7 × 10−08 |
| 6p22.3 | (24) | CDKAL1 | rs2223621 | C/T | 0.38 | (24) | Overall | 1.04 (1.02–1.06) | 1.0 × 10−04 | 3.0 × 10−10 |
| 6p22.2 | (24) | — | rs71557345 | G/A | 0.07 | (24) | Overall | 0.92 (0.88–0.96) | 8.4 × 10−05 | 3.9 × 10−10 |
| 6q14.1 | (24) | — | rs12207986 | A/G | 0.47 | (24) | Overall | 0.97 (0.95–0.98) | 2.0 × 10−04 | 1.5 × 10−09 |
| 6q23.1 | (24) | L3MBTL3 | rs6569648 | T/C | 0.24 | (24) | Overall | 0.94 (0.92–0.96) | 4.8 × 10−08 | 3.0 × 10−12 |
| 7p15.3 | (24) | DNAH11, CDCA7L | rs7971 | A/G | 0.35 | (24) | Overall | 0.96 (0.94–0.98) | 1.4 × 10−05 | 1.9 × 10−08 |
| 7p15.1 | (24) | CREB5 | rs17156577 | T/C | 0.11 | (24) | Overall | 1.05 (1.02–1.08) | 3.8 × 10−04 | 4.3 × 10−09 |
| 7q21.3 | (24) | — | rs17268829 | T/C | 0.28 | (24) | Overall | 1.05 (1.03–1.07) | 1.3 × 10−06 | 4.5 × 10−13 |
| 7q22.1 | (24) | CUX1 | rs71559437 | G/A | 0.12 | (24) | Overall | 0.93 (0.91–0.96) | 9.1 × 10−07 | 5.1 × 10−12 |
| 8q22.3 | (24) | — | rs514192 | T/A | 0.32 | (24) | Overall | 1.05 (1.03–1.07) | 3.7 × 10−06 | 5.6 × 10−09 |
| 8q23.1 | (24) | ZFPM3 | rs12546444 | A/T | 0.1 | (24) | Overall | 0.93 (0.91–0.96) | 5.8 × 10−06 | 7.5 × 10−11 |
| 8q24.13 | (24) | — | rs58847541 | G/A | 0.15 | (24) | Overall | 1.08 (1.05–1.1) | 7.3 × 10−09 | 5.5 × 10−13 |
| 9q33.1 | (24) | ASTN2 | rs1895062 | A/G | 0.41 | (24) | Overall | 0.94 (0.92–0.95) | 6.9 × 10−13 | 1.1 × 10−14 |
| 9q33.3 | (24) | LMX1B | rs10760444 | A/G | 0.43 | (24) | Overall | 1.03 (1.02–1.05) | 2.8 × 10−04 | 9.1 × 10−09 |
| 9q34.2 | (24) | ABO | rs8176636 | I/D10 | 0.2 | (24) | Overall | 1.03 (1.01–1.06) | 3.2 × 10−03 | 1.4 × 10−08 |
| 10p14 | (24) | — | rs67958007 | TG/T | 0.12 | (24) | Overall | 1.09 (1.06–1.12) | 1.8 × 10−09 | 1.7 × 10−10 |
| 10q23.33 | (24) | — | rs140936696 | C/CAA | 0.18 | (24) | Overall | 1.04 (1.02–1.07) | 7.4 × 10−04 | 4.2 × 10−08 |
| 11p15 | (24) | PIDD1 | rs6597981 | G/A | 0.48 | (24) | Overall | 0.96 (0.94–0.97) | 5.7 × 10−07 | 1.4 × 10−12 |
| 12q21.31 | (24) | — | rs202049448 | T/C | 0.34 | (24) | Overall | 0.95 (0.93–0.97) | 2.5 × 10−07 | 2.7 × 10−08 |
| 12q24.31 | (24) | — | rs206966 | C/T | 0.16 | (24) | Overall | 1.05 (1.02–1.07) | 2.7 × 10−04 | 3.8 × 10−08 |
| 14q32.33 | (24) | ADSSL1 | rs10623258 | C/CTT | 0.45 | (24) | Overall | 1.04 (1.02–1.06) | 2.7 × 10−05 | 2.3 × 10−08 |
| 16q12.2 | (24) | — | rs28539243 | G/A | 0.49 | (24) | Overall | 1.05 (1.03–1.07) | 3.6 × 10−08 | 9.1 × 10−15 |
| 16q13 | (24) | AMFR | rs2432539 | G/A | 0.4 | (24) | Overall | 1.03 (1.02–1.05) | 3.1 × 10−04 | 4.0 × 10−08 |
| 16q24.2 | (24) | — | rs4496150 | C/A | 0.25 | (24) | Overall | 0.96 (0.94–0.98) | 3.4 × 10−05 | 8.1 × 10−09 |
| 17q21.2 | (24) | CNTNAP1 | rs72826962 | C/T | 0.01 | (24) | Overall | 1.2 (1.11–1.3) | 5.1 × 10−06 | 4.6 × 10−09 |
| 17q21.31 | (24) | KANSL1 | rs2532263 | G/A | 0.19 | (24) | Overall | 0.95 (0.93–0.97) | 4.7 × 10−06 | 6.9 × 10−13 |
| 18q12.1 | (24) | GAREM1 | rs117618124 | T/C | 0.05 | (24) | Overall | 0.89 (0.85–0.92) | 4.5 × 10−08 | 5.5 × 10−12 |
| 19p13.13 | (24) | NFIX1 | rs78269692 | T/C | 0.05 | (24) | Overall | 1.09 (1.04–1.13) | 3.9 × 10−05 | 1.9 × 10−09 |
| 19p13.12 | (24) | — | rs2594714 | G/A | 0.23 | (24) | Overall | 0.97 (0.95–0.99) | 6.7 × 10−03 | 1.1 × 10−08 |
| 19p13.11 | (24) | GATAD2A, MIR640 | rs2965183 | G/A | 0.35 | (24) | Overall | 1.04 (1.02–1.06) | 9.6 × 10−06 | 6.3 × 10−12 |
| 19q13.22 | (24) | GIPR | rs71338792 | A/AT | 0.23 | (24) | Overall | 1.05 (1.03–1.07) | 8.1 × 10−06 | 3.5 × 10−09 |
| 20p12.3 | (24) | MCM8 | rs16991615 | G/A | 0.06 | (24) | Overall | 1.1 (1.06–1.14) | 1.4 × 10−07 | 1.9 × 10−09 |
| 20q13.13 | (24) | — | rs6122906 | A/G | 0.18 | (24) | Overall | 1.05 (1.03–1.07) | 2.9 × 10−05 | 2.5 × 10−10 |
| 22q13.1 | (24) | PLA2G6 | rs738321 | C/G | 0.38 | (24) | Overall | 0.95 (0.93–0.97) | 2.7 × 10−08 | 1.0 × 10−13 |
| 22q13.2 | (24) | XRCC6 | rs73161324 | C/T | 0.06 | (24) | Overall | 1.06 (1.02–1.09) | 3.8 × 10−03 | 2.0 × 10−09 |
| 22q13.31 | (24) | — | rs28512361 | G/A | 0.11 | (24) | Overall | 1.05 (1.02–1.08) | 5.7 × 10−04 | 2.3 × 10−08 |
↵aRisk locus was originally discovered in the associated reference.
↵bMAF reported in OncoArray controls.
↵cReference for the refined SNP of interest.
↵dBreast cancer subtype in which the refined SNP was evaluated.
↵eORs reported for overall breast cancer OncoArray analysis.
↵f95% confidence interval (CI) reported for overall breast cancer OncoArray analysis.
↵gP values reported for overall breast cancer OncoArray analysis.
↵hCombined meta-analysis P values reported for overall breast cancer.