From: Common breast cancer risk variants in the post-COGS era: a comprehensive review
SNPa | Cyto-band | Gene/HGVS designation if applicableb | Breast cancer risk in first reported publication | RAF (EA) | Additional populations studied (other than EA)c | PRSd | References | |||
---|---|---|---|---|---|---|---|---|---|---|
A | B | C | D | |||||||
rs11249433 | 1p11.2 | Intergenic | 1.16 (1.09 to 1.24) | 0.39 | A, ER+ | * | * | * | Â | |
rs11552449 | 1p13.2 | DCLRE1B p.His61Tyr | 1.08 (1.02 to 1.14) | 0.17 | Â | Â | Â | Â | Â | [35] |
rs616488 | 1p36.22 | PEX14 c.84 + 10837A > G | 0.94 (0.90 to 0.98) | 0.33 | ER– |  |  |  |  | |
rs6678914 | 1q32.1 | LGR6 c.213-7375G > A | 1.10 (1.06 to 1.13) | 0.59 | ER– only |  |  |  |  | [39] |
rs2290854 | 1q32.1 | MDM4 c.903 + 20A > G | 1.13 (1.08 to 1.18) | 0.33 | B1+ only |  |  |  |  | [40] |
rs4245739 | 1q32.1 | MDM4 c.*32C > A | 1.14 (1.10 to 1.18) | 0.26 | ER– only |  |  |  |  | [39] |
rs6682208 | 1q32.1 | Intergenic | 1.12 (1.07 to 1.17) | 0.34 | B1+ only | Â | Â | Â | Â | [40] |
rs184577 | 2p22.2 | CYP1B1 antisense | 0.85 (0.79 to 0.91) | Â | B2+ only | Â | Â | Â | Â | [41] |
rs12710696 | 2p24.1 | Intergenic | 1.10 (1.06 to 1.13) | 0.36 | ER– only |  |  |  |  | [39] |
rs4849887 | 2q14.2 | Intergenic | 0.90 (0.84 to 0.96) | 0.10 | AA | Â | Â | Â | Â | |
rs2016394 | 2q31.1 | Intergenic | 0.95 (0.92 to 0.99) | 0.48 | Â | Â | Â | Â | Â | [35] |
rs1550623 | 2q31.1 | Intergenic | 0.91 (0.86 to 0.96) | 0.16 | Â | Â | Â | Â | Â | [35] |
rs1045485 e | 2q33.1 | CASP8 p.Asp302His | 0.89 (0.85 to 0.93) | 0.13 | AA e | Â | * | * | * | |
rs17468277f | 2q33.1 | ALS2CR12 c.1191G > A | 0.83 (0.70 to 0.98) | 0.09 |  | * |  |  |  | [44] |
rs13387042 | 2q35 | Intergenic | 1.20 (1.14 to 1.26) | 0.50 | H, Ag, AA, B1 + g | * | * | * | * | |
rs16857609 | 2q35 | DIRC3 noncoding transcript | 1.09 (1.05 to 1.14) | 0.26 | A, ER– |  |  |  |  | |
rs4973768 | 3p24.1 | SLC4A7 c.*2242G > A | 1.11 (1.08 to 1.13) | 0.46 | A, B2+ | * | * |  |  | |
rs12493607 | 3p24.1 | TGFBR2 c.95-3300G > C | 1.04 (1.00 to 1.09) | 0.35 |  |  |  |  |  | [35] |
rs6762644 | 3p26.1 | ITPR1 c.4509 + 651A > G | 1.06 (1.02 to 1.11) | 0.4 |  |  |  |  |  | [35] |
rs9790517 | 4q24 | TET2 c.-193 + 17535C > T | 1.09 (1.04 to 1.14) | 0.23 |  |  |  |  |  | [35] |
rs6828523 | 4q34.1 | ADAM29 c.-450-5711C > A | 0.89 (0.83 to 0.94) | 0.13 |  |  |  |  |  | |
rs4415084f | 5p12 | Intergenic | 1.16 (1.10 to 1.21) | 0.40 | B1 + f | * | * |  |  | |
rs10941679 | 5p12 | Intergenic | 1.19 (1.13 to 1.26) | 0.24 | AA, A, B2 + e | * | * |  |  | |
rs7716600f | 5p12 | Intergenic, 54 kb 3′-MRPS30 | 1.24 (1.14 to 1.34) | 0.23 | A |  |  | * |  | [56] |
rs10069690 | 5p15.33 | TERT c.1951-205G > A | 1.18 (1.13 to 1.25) | 0.27 | AA, ER+, ER–, B1+ |  | * |  |  | |
rs16886113 | 5q11.2 | Intergenic, 5′ to MAP3K1 | 1.24 (1.11 to 1.38) | 0.06 | B2+ only |  |  |  |  | [41] |
rs889312 | 5q11.2 | Intergenic, 5′ to MAP3K1 | 1.13 (1.10 to 1.16) | 0.28 | A | * | * | * | * | |
rs10472076 | 5q11.2 | Intergenic, 5′ to MAP3K1 | 1.06 (1.02 to 1.11) | 0.38 |  |  |  |  |  | [35] |
rs1353747 | 5q11.2 | PDE4D c.809-2683A > C | 0.90 (0.84 to 0.96) | 0.10 |  |  |  |  |  | [35] |
rs1432679 | 5q33.3 | EBF1 c.778 + 6101G > A | 1.06 (1.02 to 1.10) | 0.43 | A, ER– |  |  |  |  | |
rs204247 | 6p23 | Intergenic (11 kb 5′-RANBP9) | 1.06 (1.02 to 1.10) | 0.43 |  |  |  |  |  | [35] |
rs9348512 | 6p24.3 | Intergenic | 0.85 (0.80 to 0.90) | Â | B2+ only | Â | Â | Â | Â | [41] |
rs11242675 | 6p25.3 | Intergenic (3.9 kb 3′-FOXQ1) | 0.97 (0.93 to 1.01) | 0.39 | A |  |  |  |  | |
rs17530068 | 6q14.1 | Intergenic | 1.12 (1.08 to 1.16) | 0.22 | AA, ER– |  |  |  |  | |
rs6569479f | 6q22.33 | RNF146 c.3-1173 T > C | 1.39 (1.23 to 1.57) | 0.21 | AJ |  | * |  |  | |
rs2253407 | 6q25.1 | SYNE1 c.23020-466C > A | 0.92 (0.86 to 0.98) | 0.47 | B2+ only |  |  |  |  | [41] |
rs9485372 | 6q25.1 | Intergenic, 5′ tp TAB2 | 0.89 (0.84 to 0.94) |  | A only |  |  |  |  | [37] |
rs3757318 | 6q25.1 | CCDC170 c.1294-129G > A | 1.30 (1.17 to 1.46) | 0.07 | ER- | * | * |  |  | |
rs2046210 | 6q25.1 | Intergenic, 6 kb 3'- CCDC170 | 1.29 (1.21 to 1.37) | 0.35 | A, ER–, B1+ | * | * |  |  | |
rs9383938f | 6q25.1 | Intergenic, 5′ to ESR1 | 1.18 (1.10 to 1.27) | 0.08 |  |  | * |  |  | |
rs720475 | 7q35 | ARHGEF5 c.4531 + 646G > A | 0.93 (0.89 to 0.98) | 0.25 |  |  |  |  |  | [35] |
rs9693444 | 8p21 | Intergenic | 1.07 (1.03 to 1.12) | 0.32 | A | Â | Â | Â | Â | |
rs6472903 | 8q21.11 | Intergenic | 0.88 (0.84 to 0.93) | 0.18 | A | Â | Â | Â | Â | |
rs2943559 | 8q21.11 | HNF4G c.-24 + 15494A > G | 1.17 (1.09 to 1.26) | 0.07 | ER– |  |  |  |  | |
rs4733664 | 8q24.21 | Intergenic | 1.10 (1.04 to 1.17) | 0.41 | B2+ only | Â | Â | Â | Â | [41] |
rs13281615 | 8q24.21 | Intergenic | 1.08 (1.05 to 1.11) | 0.40 | Â | * | * | * | * | |
rs1562430 | 8q24.21 | Intergenic | 0.84 (0.78 to 0.90) | 0.40 | Â | Â | * | Â | Â | |
rs11780156 | 8q24.21 | Intergenic (32 kb 3′-MIR1208) | 1.13 (1.07 to 1.19) | 0.16 |  |  |  |  |  | [35] |
rs10965163 | 9p21.3 | MTAP c.561C > T | 0.84 (0.77 to 0.93) | 0.10 | B2+ only |  |  |  |  | [41] |
rs1011970 | 9p21.3 | CDK2NB antisense RNA | 1.09 (1.04 to 1.14) | 0.17 | ER– | * | * |  |  | |
rs865686 | 9q31.2 | Intergenic | 0.90 (0.86 to 0.96) | 0.39 | AA, ER+ | * | * | Â | Â | |
rs10759243 | 9q31.2 | Intergenic (53 kb 5′-KLF4) | 1.07 (1.02 to 1.12) | 0.39 | A |  |  |  |  | [35] |
rs7072776 | 10p12.31 | Intergenic (382 bp 3′-MLLT10) | 1.11 (1.07 to 1.16) | 0.29 |  |  |  |  |  | [35] |
rs11814448 | 10p12.31 | Intergenic (23 kb 5′-DNAJC1) | 1.35 (1.17 to 1.56) | 0.02 |  |  |  |  |  | [35] |
rs2380205 e | 10p15.1 | Intergenic , 2.6 kb 5′- GDI2 | 0.94 (0.91 to 0.98) | 0.43 |  | * | * |  |  | |
rs16917302 | 10q21.2 | ZNF365 c.981 + 41642A > C | 0.75 (0.66 to 0.86) | 0.11 | B2 + e |  | * |  |  | |
rs10995190 | 10q21.2 | ZNF365 c.981 + 59126G > A | 0.76 (0.82 to 0.91) | 0.15 | A, ER–, B2 + f | * | * |  |  | |
rs704010 | 10q22.3 | ZMIZ1 c.-337 + 12121 T > C | 1.07 (1.03 to 1.11) | 0.39 | A, AA | * | * |  |  | |
rs7904519 | 10q25.2 | TCF7L2 c.382-25857A > G | 1.06 (1.02 to 1.10) | 0.46 | ER– |  |  |  |  | |
rs11196174 | 10q25.2 | TCF7L2 c.381 + 22730A > G | 1.13 (1.07 to 1.18) | 0.31 | B1+ only |  |  |  |  | [40] |
rs11199914 | 10q26.12 | Intergenic (77 kb 5′-7SK) | 0.94 (0.89 to 0.98) | 0.32 |  |  |  |  |  | [35] |
rs2981582f | 10q26.13 | FGFR2 c.109 + 906 T > C | 1.26 (1.23 to 1.28) | 0.39 | AA, H, B2+ | * | * | * | * | |
rs2420946f | 10q26.13 | FGFR2 c.109 + 1899A > G | 1.24 (1.03 to 1.50) | 0.38 | B2+ |  |  |  |  | |
rs1219648 | 10q26.13 | FGFR2 c.109 + 7033 T > C | 1.23 (1.02 to 1.48) | 0.39 | AA, A, H |  |  |  |  | |
rs2981579 | 10q26.13 | FGFR2 c.110-12117 T > C | 1.27 (1.24 to 1.29) | 0.40 |  |  |  |  |  | [35] |
rs3817198 | 11p15.5 | LSP1 c.*13 + 200 T > C | 1.07 (1.04 to 1.11) | 0.30 | A, B1 + d, B2+ | * | * | * | * | |
rs909116f | 11p15.5 | TNNT3 c.-19 + 954 T > C | 1.17 (1.10 to 1.24) | 0.53 |  |  | * |  |  | [32] |
rs3903072 | 11q13.1 | Intergenic (7.4 kb 3′-CFL1) | 0.92 (0.89 to 0.96) | 0.47 |  |  |  |  |  | [35] |
rs614367 | 11q13.3 | Intergenic | 1.15 (1.10 to 1.20) | 0.15 | A, ER+, B2 + e | * | * |  |  | |
rs11820646 | 11q24.3 | Intergenic (139 kb 3′-BARX2) | 0.93 (0.90 to 0.97) | 0.41 | A, ER– |  |  |  |  | |
rs27633 | 12p11.22 | PTHLH c.-266 + 555A > C | 1.14 (1.07 to 1.21) | 0.39 | B2+ only |  |  |  |  | [41] |
rs10771399 | 12p11.22 | Intergenic, 29 kb 5′- PTHLH | 0.85 (0.83 to 0.88) | 0.12 | A, B1+, B2 + e, ER– | * |  |  |  | |
rs12422552 | 12p13.1 | Intergenic (11 kb 5′-U6) | 1.11 (1.05 to 1.16) | 0.26 | A |  |  |  |  | |
rs17356907 | 12q22 | Intergenic (16 kb 3′-Y_RNA) | 0.89 (0.85 to 0.93) | 0.3 | A, ER– |  |  |  |  | |
rs1292011 | 12q24.21 | Intergenic | 0.92 (0.91 to 0.94) | 0.41 | A, B2 + e |  |  |  |  | |
rs11571833 | 13q13.1 | BRCA2 p.Lys3326Ter | 1.39 (1.13 to 1.71) | 0.01 | ER– |  |  |  |  | |
rs2236007 | 14q13.3 | PAX9 c.631 + 41G > A | 0.88 (0.83 to 0.93) | 0.21 | A |  |  |  |  | |
rs2588809 | 14q24.1 | RAD51B c.757-98173 T > C | 1.07 (1.01 to 1.13) | 0.16 |  |  |  |  |  | [35] |
rs999737 | 14q24.1 | RAD51B c.1037-43041C > T | 0.94 (0.88 to 0.99) | 0.24 | AA, ER–, B1 + d | * | * | * |  | |
rs941764 | 14q32.11 | CCDC88C c.271-15014 T > C | 1.05 (1.00 to 1.09) | 0.34 |  |  |  |  |  | [35] |
rs3803662 | 16q12.1 | Intergenic , 5′ to TOX3 | 1.20 (1.16 to 1.24) | 0.25 | A, AA, B1 + e, B2+, MBC, ER– | * | * | * | * | |
rs4784227 | 16q12.1 | Intergenic, 5' to TOX3 | 1.27 (1.22 to 1.32) | 0.25 | A | Â | Â | Â | Â | [37] |
rs17817449 | 16q12.2 | FTO c.-215-30685 T > G | 0.95 (0.91 to 0.99) | 0.4 | ER– |  |  |  |  | |
rs13329835 | 16q23.2 | CDYL2 c.1007 + 3855 T > C | 1.14 (1.09 to 1.19) | 0.22 | AA |  |  |  |  | |
rs2075555f | 17q21.33 | COL1A1 c.804 + 80A > C | No association | 0.14 |  |  | * |  |  | [86] |
rs6504950 | 17q22 | STXBP4 c.-156-6504G > A | 0.95 (0.92 to 0.97) | 0.27 | ER– | * | * |  |  | |
rs527616 | 18q11.2 | Intergenic | 0.91 (0.87 to 0.95) | 0.38 | Â | Â | Â | Â | Â | [35] |
rs1436904 | 18q11.2 | CHST9 c.202 + 33413A > C | 0.93 (0.9 to 0.97) | 0.4 |  |  |  |  |  | [35] |
rs8170 e | 19p13.1 | BABAM1 c.837G > A | 1.26 (1.17 to 1.35) | 0.20 | AA, B1+, ER– | * |  |  |  | |
rs4808801 | 19p13.11 | ELL c.744 + 1247 T > C | 0.94 (0.90 to 0.98) | 0.35 | AA, ER– |  |  |  |  | |
rs1982073f | 19q13.2 | TGFB1 p.Pro10Leu | 1.08 (1.04 to 1.11) | 0.38 | Â | Â | Â | Â | Â | |
rs3760982 | 19q13.31 | Intergenic (1.1 kb 5′-KCNN4) | 1.06 (1.02 to 1.10) | 0.46 |  |  |  |  |  | [35] |
rs2284378f | 20q11 | RALY c.-93 + 6158 T > C | 1.08 (1.05 to 1.12) | 0.35 |  |  |  |  |  | [63] |
rs13039229 | 20q13.33 | Intergenic (2.1 kb 3′ of PTK6) | 0.90 (0.84 to 0.97) | 0.21 | B2+ only |  |  |  |  | [41] |
rs311499f | 20q13.33 | Intergenic (1.4 kb 3′-GMEB2) | 0.72 (0.61 to 0.85) | 0.07 | B2+ only |  |  |  |  | [78] |
rs2823093 | 21q21 | Intergenic (5′ to NRIP1 ) | 0.94 (0.92 to 0.96) | 0.27 |  |  |  |  |  | |
rs132390 | 22q12.2 | EMID1 c.403 + 272C > T | 1.36 (1.19 to 1.54) | 0.04 |  |  |  |  |  | [35] |
rs6001930 | 22q13.1 | MKL1 c.-59-16944A > G | 1.17 (1.11 to 1.25) | 0.11 | ER– |  |  |  |  | [39] |
rs619373 | Xq27.1 | FGF13 c.50-73946C > T | 1.30 (1.17 to 1.45) | 0.03 | B2+ only |  |  |  |  | [41] |