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