Article Figures & Data
Figures
- Figure 1.
Allelic architecture of SNPs associated with ER-positive breast cancer. OR and effect allele frequency (EAF) for all SNPs associated with ER-positive breast cancer in the OncoArray meta-analysis (P < 5 × 10−8; ref. 24).
- Figure 2.
Allelic architecture of SNPs associated with ER-negative breast cancer. OR and effect allele frequency (EAF) for all SNPs associated with ER-negative breast cancer in the OncoArray meta-analysis (P < 5 × 10−8; refs. 24, 25).
Tables
- Table 1.
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.
April 2018
Volume 27, Issue 4
Volume 27, Issue 4
Common Genetic Variation and Breast Cancer Risk—Past, Present, and Future
Jump to section
- Article
- Abstract
- Introduction
- Initial Association Studies of Common Genetic Variants
- Earliest Breast Cancer GWAS (2007–2013)
- FGFR2: The First Consistently Replicated Hit
- Early Strategies to Identify Additional Susceptibility Loci
- SNP Discovery: COGS Era (2012–2015)
- SNP Discovery: OncoArray Era (2015–Present)
- Divide and Conquer: SNPs Associated with Breast Cancer Subtypes and Mutation Carriers
- Race/Ethnicity
- Putting It All Together—Polygenic Risk Scores
- Breast Cancer Gene–Environment Interactions/Associations with Other Risk Factors
- Understanding the Biology
- Conclusions
- Disclosure of Potential Conflicts of Interest
- Acknowledgments
- Footnotes
- References
- Figures & Data
- Info & Metrics
Advertisement