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Table 3 Extended information on SNPs identified in the major GWAS for breast cancer risk or SNPs used to generate published polygenic risk scores

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+ * * *   [30, 32, 3538]
rs11552449 1p13.2 DCLRE1B p.His61Tyr 1.08 (1.02 to 1.14) 0.17       [35]
rs616488 1p36.22 PEX14 c.84 + 10837A > G 0.94 (0.90 to 0.98) 0.33 ER–      [35, 39]
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      [40]
rs184577 2p22.2 CYP1B1 antisense 0.85 (0.79 to 0.91)   B2+ only      [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      [35, 42]
rs2016394 2q31.1 Intergenic 0.95 (0.92 to 0.99) 0.48       [35]
rs1550623 2q31.1 Intergenic 0.91 (0.86 to 0.96) 0.16       [35]
rs1045485 e 2q33.1 CASP8 p.Asp302His 0.89 (0.85 to 0.93) 0.13 AA e   * * * [23, 24, 32, 35, 42, 43]
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 * * * * [27, 30, 32, 33, 35, 40, 42, 4550]
rs16857609 2q35 DIRC3 noncoding transcript 1.09 (1.05 to 1.14) 0.26 A, ER–      [35, 37, 39]
rs4973768 3p24.1 SLC4A7 c.*2242G > A 1.11 (1.08 to 1.13) 0.46 A, B2+ * *    [3133, 35, 37, 41, 47, 48, 51, 52]
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       [35, 37]
rs4415084f 5p12 Intergenic 1.16 (1.10 to 1.21) 0.40 B1 + f * *    [28, 53]
rs10941679 5p12 Intergenic 1.19 (1.13 to 1.26) 0.24 AA, A, B2 +e * *    [30, 32, 33, 35, 37, 47, 50, 54],[55]
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+   *    [35, 42, 5759]
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 * * * * [25, 32, 35, 37, 48, 56, 6062]
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–      [35, 37, 39]
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)   B2+ only      [41]
rs11242675 6p25.3 Intergenic (3.9 kb 3′-FOXQ1) 0.97 (0.93 to 1.01) 0.39 A      [35, 37]
rs17530068 6q14.1 Intergenic 1.12 (1.08 to 1.16) 0.22 AA, ER     [35, 39, 63]
rs6569479f 6q22.33 RNF146 c.3-1173 T > C 1.39 (1.23 to 1.57) 0.21 AJ   *    [64, 65]
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- * *    [29, 32, 33, 35, 3740, 48, 6669]
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    *    [33, 70]
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      [35, 37]
rs6472903 8q21.11 Intergenic 0.88 (0.84 to 0.93) 0.18 A      [35, 37]
rs2943559 8q21.11 HNF4G c.-24 + 15494A > G 1.17 (1.09 to 1.26) 0.07 ER–      [35, 39]
rs4733664 8q24.21 Intergenic 1.10 (1.04 to 1.17) 0.41 B2+ only      [41]
rs13281615 8q24.21 Intergenic 1.08 (1.05 to 1.11) 0.40   * * * * [25, 33, 35, 47, 7173]
rs1562430 8q24.21 Intergenic 0.84 (0.78 to 0.90) 0.40    *    [32, 56]
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 * *    [32, 35, 39, 41, 74]
rs865686 9q31.2 Intergenic 0.90 (0.86 to 0.96) 0.39 AA, ER+ * *    [33, 35, 41, 7476]
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   * *    [32, 35]
rs16917302 10q21.2 ZNF365 c.981 + 41642A > C 0.75 (0.66 to 0.86) 0.11 B2 + e   *    [77, 78]
rs10995190 10q21.2 ZNF365 c.981 + 59126G > A 0.76 (0.82 to 0.91) 0.15 A, ER, B2 +f * *    [32, 35, 37, 39, 41, 74, 79]
rs704010 10q22.3 ZMIZ1 c.-337 + 12121 T > C 1.07 (1.03 to 1.11) 0.39 A, AA * *    [32, 35, 37, 41, 58, 80]
rs7904519 10q25.2 TCF7L2 c.382-25857A > G 1.06 (1.02 to 1.10) 0.46 ER–      [35, 39]
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+ * * * * [25, 26, 30, 32, 46, 48, 60, 62]
rs2420946f 10q26.13 FGFR2 c.109 + 1899A > G 1.24 (1.03 to 1.50) 0.38 B2+      [26, 41]
rs1219648 10q26.13 FGFR2 c.109 + 7033 T > C 1.23 (1.02 to 1.48) 0.39 AA, A, H      [26, 27, 37, 49, 62, 81, 82]
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+ * * * * [25, 32, 35, 37, 40, 41, 45, 48],[83]
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 * *    [32, 35, 37, 41, 80, 84, 85]
rs11820646 11q24.3 Intergenic (139 kb 3′-BARX2) 0.93 (0.90 to 0.97) 0.41 A, ER–      [35, 37, 39]
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 *     [34, 35, 37, 39, 40, 74]
rs12422552 12p13.1 Intergenic (11 kb 5′-U6) 1.11 (1.05 to 1.16) 0.26 A      [35, 37]
rs17356907 12q22 Intergenic (16 kb 3′-Y_RNA) 0.89 (0.85 to 0.93) 0.3 A, ER–      [35, 37, 39]
rs1292011 12q24.21 Intergenic 0.92 (0.91 to 0.94) 0.41 A, B2 +e      [34, 35, 37, 80]
rs11571833 13q13.1 BRCA2 p.Lys3326Ter 1.39 (1.13 to 1.71) 0.01 ER–      [35, 39]
rs2236007 14q13.3 PAX9 c.631 + 41G > A 0.88 (0.83 to 0.93) 0.21 A      [35, 37]
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 * * *   [30, 32, 35, 36, 40, 42, 47, 66],[70]
rs941764 14q32.11 CCDC88C c.271-15014 T > C 1.05 (1.00 to 1.09) 0.34       [35]
rs3803662 16q12.1 Intergenic , 5to TOX3 1.20 (1.16 to 1.24) 0.25 A, AA, B1 +e, B2+, MBC, ER– * * * * [25, 27, 32, 35, 37, 39, 41, 46],[55, 60, 66, 70, 73, 78]
rs4784227 16q12.1 Intergenic, 5' to TOX3 1.27 (1.22 to 1.32) 0.25 A      [37]
rs17817449 16q12.2 FTO c.-215-30685 T > G 0.95 (0.91 to 0.99) 0.4 ER      [35, 39]
rs13329835 16q23.2 CDYL2 c.1007 + 3855 T > C 1.14 (1.09 to 1.19) 0.22 AA      [35, 42]
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– * *    [31, 39, 41, 87]
rs527616 18q11.2 Intergenic 0.91 (0.87 to 0.95) 0.38       [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– *     [35, 3942, 58, 66, 77]
rs4808801 19p13.11 ELL c.744 + 1247 T > C 0.94 (0.90 to 0.98) 0.35 AA, ER      [35, 39, 42]
rs1982073f 19q13.2 TGFB1 p.Pro10Leu 1.08 (1.04 to 1.11) 0.38       [23, 24, 44]
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 (5to NRIP1 ) 0.94 (0.92 to 0.96) 0.27       [34, 35]
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]
  1. COGS, Collaborative Oncological Gene–environment Study; EA, European descent; ER, estrogen receptor; GWAS, genome-wide association studies; PRS, polygenic risk score; RAF, risk allele frequency; SNP, single nucleotide polymorphism. aBold SNPs are considered the established breast cancer loci pre-COGS. All SNPs listed are in independent linkage disequilibrium blocks as determined using HaploReg with r2 >0.8, with the exception of the 2q33.1 SNPs rs1045485 and rs17468277. Two SNPs in linkage disequilibrium with listed SNP were tested in other populations; that is, rs76972116 at 4q34, and rs7107217 at 11q24. bHuman Genome Variation Society (HGVS) names are given for variants found with the coding region of a gene using the designation for transcript variant #1 as per the Ensembl/UCSC GRCh37/hg19 human genome assembly. cAll SNPs have been identified in populations of European descent (EA) and unselected for ER status; if other populations have been studied, this is noted. If a SNP has been identified only in a subpopulation, it is denoted with 'only’. A, Asian; AA, African-American; AJ, Ashkenazi Jewish; B1+, BRCA1-positive; B2+, BRCA2-positive; H, Hispanic; ER+, estrogen receptor-positive breast cancer; ER–, estrogen receptor-negative breast cancer; MBC, male breast cancer. SNP association listed for population subtype if reported P <10–3.
  2. dPolygenic risk scores are from: model A, Sawyer and colleagues [88]; model B, Husing and colleagues [89]; model C, Wacholder and colleagues [90]; model D, Gail [91]. eSNPs showing borderline association with breast cancer risk in COGS; if population specific, this is indicated in the Additional populations studied column. fSNPs that were not studied in any COGS study [35, 37, 3942]; if population specific, this is indicated in the Additional populations studied column. gSNPs showing no association with breast cancer risk in COGS; if population specific, this is indicated in the Additional populations studied column.