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. 2017 Mar 31;13(3):e1006690. doi: 10.1371/journal.pgen.1006690

Table 3. SNPs nominally (p-value < 0.05) associated with breast cancer risk that contribute to expression of genes suggestively associated with breast cancer risk.

Proportion U4C UK Biobank Meta-analysis
SNP Allelesa of Weightb EAFc OR (95% CI) p-value EAFc OR (95% CI) p-value OR (95% CI) p-value
RCCD1 at 15q26.1 (Breast Tissue)
    rs3826033d G / A 0.13 0.32 0.92 (0.88, 0.98) 4.1x10-03 0.13 0.86 (0.79,0.93) 2.3x10-04 0.90 (0.86,0.94) 9.5x10-06
    rs2290202d G / T 0.24 0.3 0.93 (0.89, 0.98) 5.3x10-03 0.13 0.86 (0.79,0.93) 1.9x10-04 0.91 (0.88,0.95) 1.7x10-05
    rs4347602 A / C 0.025 0.72 0.94 (0.90,0.98) 6.5x10-03 0.77 0.96 (0.90,1.02) 0.16 0.94 (0.91,0.98) 2.4x10-03
    rs11207d C / T 0.030 0.35 0.97 (0.93, 1.02) 0.21 0.24 0.93 (0.87,0.98) 0.015 0.96 (0.93,0.99) 0.016
DHODH at 16q22.2 (Breast Tissue)
    rs3213422 C / A 0.56 0.42 0.92 (0.88,0.96) 2.8x10-05 0.48 0.95 (0.90,1.00) 0.039 0.93 (0.90,0.96) 4.5x10-06
    rs2240243 G / A 0.055 0.47 0.93 (0.89,0.97) 2.7x10-04 0.34 0.98 (0.93,1.04) 0.53 0.95 (0.92,0.98) 1.0x10-03
    rs12708928 C / A 0.019 0.47 0.93 (0.89,0.96) 2.5x10-04 0.34 0.99 (0.93,1.04) 0.59 0.95 (0.92,0.98) 1.2x10-03
ANKLE1 at 19p13.11 (Breast Tissue)
    rs34084277d A / G 0.23 0.19 1.09 (1.02,1.15) 7.1x10-03 0.19 1.11 (1.04,1.18) 2.0x10-03 1.10 (1.05,1.14) 4.7x10-05
    rs8170d G / A 0.26 0.19 1.08 (1.02,1.15) 7.2x10-03 0.19 1.11 (1.04,1.18) 2.6x10-03 1.09 (1.05,1.14) 6.3x10-05
RCCD1 at 15q26.1 (Whole Blood)
    rs3826033d G / A 0.33 0.32 0.92 (0.88,0.98) 4.1x10-03 0.13 0.86 (0.79,0.93) 2.3x10-04 0.90 (0.86,0.94) 9.5x10-06
    rs2290202d G / T 0.29 0.3 0.93 (0.89,0.98) 5.3x10-03 0.13 0.86 (0.79,0.93) 1.9x10-04 0.91 (0.88,0.95) 1.7x10-05
    rs7180016d G / A 0.012 0.49 0.97 (0.93,1.01) 0.13 0.16 0.90 (0.84,0.97) 5.7x10-03 0.95 (0.92,0.99) 7.3x10-03
    rs11073961 A / G 0.049 0.35 0.97 (0.93,1.01) 0.21 0.27 0.92 (0.87,0.98) 7.5x10-03 0.95 (0.93,0.99) 9.9x10-03
    rs11207d C / T 0.0092 0.35 0.97 (0.93,1.02) 0.21 0.24 0.93 (0.87,0.98) 0.015 0.96 (0.93,0.99) 0.016
    rs2285937d A / G 0.0064 0.46 0.98 (0.94,1.02) 0.31 0.16 0.90 (0.84,0.97) 4.9x10-03 0.96 (0.93,0.99) 0.023
    rs3809583 A / G 0.0035 0.36 0.97 (0.93,1.01) 0.12 0.32 0.96 (0.91,1.01) 0.15 0.96 (0.93,1.00) 0.035
ACAP1 at 17p13.1 (Whole Blood)
    rs35776863 A / G 0.49 0.85 1.08 (1.00,1.16) 0.045 0.77 1.11 (1.04,1.18) 0.15 1.10 (1.04,1.15) 1.4x10-04
    rs9892383 C / T 0.030 0.76 1.04 (0.98,1.09) 0.17 0.73 1.10 (1.03,1.18) 0.76 1.06 (1.02,1.11) 3.6x10-03
    rs5412 G / A 0.060 0.12 1.04 (0.97,1.12) 0.26 0.17 1.09 (1.02,1.17) 0.12 1.07 (1.02,1.12) 8.0x10-03
    rs4791423 A / C 0.0068 0.45 1.04 (1.00,1.09) 0.033 0.34 1.03 (0.98,1.09) 0.55 1.04 (1.01,1.08) 0.018
    rs35721044 T / C 0.031 0.84 1.11 (1.02,1.22) 0.012 0.76 1.03 (0.97,1.10) 0.16 1.06 (1.01,1.12) 0.019
LRRC25 at 19p13.11 (Whole Blood)
    rs11668719 C / T 0.25 0.5 1.06 (1.01,1.11) 0.011 0.54 1.10 (1.05,1.16) 1.87x10-04 1.08 (1.04,1.12) 1.2x10-05
    rs7257932d A / G 0.091 0.55 1.05 (1.01,1.10) 0.011 0.67 1.08 (1.02,1.14) 7.01x10-03 1.06 (1.03,1.10) 2.5x10-04
    rs13344313 A / G 0.16 0.68 1.06 (1.02,1.11) 6.6x10-03 0.71 1.04 (0.98,1.10) 0.20 1.05 (1.02,1.09) 3.2x10-03
    rs3795026 C / T <0.001 0.54 1.04 (1.00,1.08) 0.051 0.68 1.05 (0.99,1.11) 0.12 1.04 (1.01,1.08) 0.013
    rs7251067 A / G 0.031 0.85 1.00 (0.95,1.06) 0.94 0.86 1.14 (1.06,1.23) 6.70x10-04 1.05 (1.00,1.10) 0.041

Abbreviations: CI: confidence interval; EAF: effect allele frequency; OR: odds ratio; SNP: single nucleotide polymorphism; U4C: Up for a Challenge

a Reference allele / effect allele

b Proportion of total weight attributed to SNP in gene prediction model

c Effect allele frequency in controls

d Previously implicated in breast cancer or in high linkage disequilibrium (r2 > 0.5 in 1000 Genomes Phase 3 populations) with known risk variants