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. 2014 Jun 18;23(22):6096–6111. doi: 10.1093/hmg/ddu311

Table 2.

Summary results from COGS-BCAC for European women

Original SNP (nsC) Gene Surrogate SNPa Allelesb MAF pHWE OR (95% CI) P-valuec
 P-hetd I2 (%)d
Aa aa Per-a-allele
rs10415312 (E171K) OR7C1 AG 0.09 0.36 0.98 (0.95, 1.02) 0.31 1.02 (0.87, 1.17) 0.81 0.99 (0.96, 1.02) 0.43 0.38 5.05
rs10494217 (H50N) TBX15 CA 0.19 0.28 1.00 (0.97, 1.03) 0.94 0.98 (0.91, 1.05) 0.60 1.00 (0.97, 1.02) 0.81 0.06 27.7
rs10510592 (L513S) NEK10 AG 0.25 0.26 1.11 (1.08, 1.14) 1.4 × 10−12 1.18 (1.12, 1.25) 1.5 × 10−9 1.10 (1.07, 1.12) 5.1 × 10−17 0.53 0
rs1053338 (K264R) ATXN7 AG 0.13 0.53 1.07 (1.03, 1.10) 5.6 × 10−5 1.14 (1.04, 1.26) 0.0073 1.07 (1.04, 1.10) 2.9 × 10−6 0.23 13.7
rs11078738 (L621P) PFAS GA 0.24 0.41 1.01 (0.98, 1.03) 0.73 0.96 (0.90, 1.02) 0.15 0.99 (0.97, 1.01) 0.50 0.27 11.1
rs12051468 (S105G) CRISPLD2 AG 0.43 0.39 1.02 (0.99, 1.05) 0.25 1.01 (0.97, 1.05) 0.66 1.01 (0.99, 1.03) 0.53 0.34 7.10
rs12256835 (H1759Q) C10orf112 AC 0.18 0.25 1.01 (0.98, 1.04) 0.71 1.05 (0.97, 1.13) 0.25 1.01 (0.99, 1.04) 0.35 0.12 21.8
rs1265096 (E34K) PSORS1C1 GA 0.09 0.39 1.02 (0.98, 1.06) 0.26 0.86 (0.74, 1.01) 0.061 1.00 (0.97, 1.04) 0.80 0.84 0
rs12894584 (intronic) NAA30 GA 0.29 0.31 1.00 (0.97, 1.03) 0.96 0.98 (0.93, 1.03) 0.43 0.99 (0.97, 1.02) 0.60 0.65 0
rs13096522 (non-coding) ARL6 TA 0.20 0.31 1.02 (0.99, 1.05) 0.13 0.99 (0.92, 1.06) 0.79 1.01 (0.99, 1.04) 0.34 0.77 0
rs1801197 (L447P) CALCR rs2023778, r2 = 1.0 AG 0.24 0.30 1.02 (0.99, 1.04) 0.27 1.02 (0.96, 1.08) 0.53 1.01 (0.99, 1.04) 0.26 0.85 0
rs2107732 (V53I) CCM2 GA 0.09 0.48 0.99 (0.96, 1.03) 0.64 0.98 (0.84, 1.14) 0.80 0.99 (0.96, 1.02) 0.61 0.63 0
rs2230018 (T726K) KDM6A CA 0.12 0.43 0.98 (0.95, 1.01) 0.23 1.07 (0.96, 1.19) 0.23 0.99 (0.96, 1.02) 0.65 0.03 33.1
rs2272955 (M96T) WFDC8 AG 0.05 0.31 1.02 (0.98, 1.07) 0.36 0.82 (0.64, 1.05) 0.12 1.01 (0.97, 1.05) 0.72 0.34 7.30
rs2282542 (V1365M) CEP192 GA 0.12 0.42 0.97 (0.94, 1.01) 0.12 0.90 (0.80, 1.00) 0.050 0.97 (0.94, 1.00) 0.025 0.07 26.7
rs2285374e (K889R) VPS11 AG 0.39 0.32 0.99 (0.96, 1.02) 0.52 0.99 (0.95, 1.03) 0.67 0.99 (0.98, 1.01) 0.58 0.60 0
rs2286587 (R110H) MXRA7 AG 0.39 0.50 0.97 (0.95, 1.00) 0.083 0.97 (0.94, 1.02) 0.29 0.99 (0.97, 1.01) 0.15 0.08 25.7
rs2291533 (Q253H) NIF3L1BP1 rs7614311, r2 = 0.94 AC 0.19 0.34 1.03 (1.00, 1.06) 0.041 1.05 (0.98, 1.13) 0.14 1.03 (1.00, 1.05) 0.018 0.31 9.30
rs2298083 (V854I) SMG7 GA 0.11 0.17 0.99 (0.95, 1.02) 0.39 1.02 (0.90, 1.15) 0.78 0.99 (0.96, 1.02) 0.54 0.71 0
rs2735018 (intronic) HLA-G GC 0.10 0.32 0.97 (0.94, 1.01) 0.13 0.94 (0.82, 1.07) 0.36 0.97 (0.94, 1.00) 0.086 0.38 5.30
rs2822558 (S199N) ABCC13 GA 0.15 0.27 1.01 (0.98, 1.04) 0.52 1.01 (0.92, 1.10) 0.89 1.01 (0.98, 1.03) 0.56 0.60 0
rs2853699 (A27G) CCR8 rs12107527, r2 = 1.0 GA 0.30 0.37 1.01 (0.98, 1.04) 0.64 1.01 (0.97, 1.06) 0.60 1.01 (0.99, 1.03) 0.53 0.26 11.8
rs2856705 (non-coding) HLA-DQA2 GA 0.09 0.24 1.00 (0.96, 1.03) 0.87 1.07 (0.93, 1.22) 0.35 1.00 (0.97, 1.04) 0.79 0.07 26.5
rs2879097 (R79C) CISD3 GA 0.22 0.50 1.00 (0.97, 1.03) 0.83 0.97 (0.91, 1.04) 0.38 0.99 (0.97, 1.01) 0.49 0.20 15.7
rs315675 (L396H) ZCCHC4 rs13149511, r2 = 1.0 AG 0.11 0.37 1.00 (0.97, 1.03) 0.96 0.97 (0.85, 1.10) 0.61 1.00 (0.97, 1.03) 0.79 0.99 0
rs365990 (V1101A) MYH6 AG 0.35 0.20 1.04 (1.01, 1.07) 0.014 1.04 (1.00, 1.09) 0.052 1.03 (1.01, 1.05) 0.012 0.13 20.4
rs3742801 (E368K) ABCD4 GA 0.36 0.21 1.00 (0.97, 1.02) 0.76 1.02 (0.98, 1.06) 0.37 1.01 (0.99, 1.03) 0.57 0.10 23.2
rs3815768 (A298T) ELL2 GA 0.26 0.38 1.00 (0.97, 1.03) 0.90 1.04 (0.98, 1.10) 0.16 1.01 (0.99, 1.03) 0.40 0.47 0
rs3873283 (non-coding) HCG9 rs9260734, r2 = 1.0 GA 0.15 0.28 0.99 (0.96, 1.02) 0.51 0.95 (0.87, 1.04) 0.24 0.98 (0.96, 1.01) 0.25 0.54 0
rs3891175 (non-coding) HLA-DQB1 GA 0.21 0.32 0.99 (0.96, 1.02) 0.64 0.97 (0.91, 1.03) 0.30 0.99 (0.97, 1.01) 0.34 0.22 14.2
rs3997854 (non-coding) HLA-DQA2 AC 0.13 0.31 0.98 (0.95, 1.02) 0.33 0.93 (0.84, 1.03) 0.18 0.98 (0.95, 1.01) 0.14 0.73 0
rs4128458 (K323E) LAD1 AG 0.50 0.27 0.99 (0.96, 1.03) 0.75 0.97 (0.94, 1.01) 0.18 0.99 (0.97, 1.01) 0.18 0.10 23.7
rs4986790 (D299G) TLR4 AG 0.06 0.41 0.98 (0.94, 1.02) 0.38 0.96 (0.77, 1.20) 0.73 0.98 (0.94, 1.02) 0.35 0.40 4.12
rs5744751 (A252V) POLE GA 0.11 0.29 1.01 (0.98, 1.04) 0.57 1.02 (0.91, 1.15) 0.75 1.01 (0.98, 1.04) 0.52 0.87 0
rs6032538 (H36D) WFDC3 rs399672, r2 = 1.0 AG 0.28 0.11 1.00 (0.97, 1.03) 0.82 0.98 (0.93, 1.03) 0.49 0.99 (0.97, 1.01) 0.55 0.11 22.0
rs6964587 (M463I) AKAP9 GT 0.39 0.29 1.04 (1.01, 1.07) 0.0098 1.11 (1.06, 1.15) 1.6 × 10−6 1.05 (1.03, 1.07) 1.7 × 10−6 0.18 16.7
rs7158731 (L118P) ZNF839 AG 0.18 0.33 1.00 (0.97, 1.03) 0.89 1.01 (0.94, 1.10) 0.71 1.00 (0.98, 1.03) 0.75 0.16 18.7
rs7454108 (non-coding) HLA-DQA2 AG 0.11 0.26 0.96 (0.93, 1.00) 0.034 0.98 (0.87, 1.10) 0.73 0.97 (0.94, 1.00) 0.047 0.71 0
rs7863265 (F10L) STRBP GC 0.34 0.40 1.01 (0.98, 1.04) 0.48 1.00 (0.96, 1.05) 0.98 1.00 (0.98, 1.02) 0.75 0.43 2.42
rs8059973 (intronic) MGC3101 GA 0.16 0.18 1.00 (0.97, 1.03) 0.83 1.00 (0.92, 1.08) 0.92 1.00 (0.98, 1.03) 0.91 0.55 0
rs9891699 (P19S) PFAS AG 0.19 0.48 1.01 (0.98, 1.04) 0.59 0.99 (0.92, 1.07) 0.87 1.00 (0.98, 1.03) 0.75 0.61 0

COGS, Collaborative Oncological Gene-environment Study; BCAC, Breast Cancer Association Consortium; nsC, non-synonymous amino acid change; MAF, minor allele frequency for controls; pHWE, P-value for compliance with Hardy–Weinberg equilibrium for controls; OR, odds ratio, where A is the common allele, a is the rare allele and both Aa and aa are compared with AA genotypes; CI, confidence interval; P-het, P-value for between-study homogeneity.

aSNP genotyped as a surrogate for the original SNP when the latter failed on design; r2 value given is that for LD between the surrogate and the original SNP; results in columns to the right are for the surrogate SNP.

bMinor allele listed second.

cBased on the Wald statistic for the genotype-specific estimates; based on the likelihood ratio test for the per-allele estimate.

dApplying the per-allele (log-additive) model.

ers2285374 has been merged into rs15818.