Table 2.

Breast cancer index SNPs: original GWAS results and results from the BWHS

Coded allele/referenceCoded alleleBWHS results: OR (95% CI), P value
ChromosomeSNPGWAS ORallelefrequencyAll casesER+/PR+ER−/PR−
1p11.2rs1124943311.16C/T0.130.97 (0.80–1.18), 0.761.15 (0.86–1.56), 0.350.76 (0.52–1.13), 0.17
2q35rs1338704221.20A/G0.731.06 (0.93–1.20), 0.381.05 (0.85–1.30), 0.651.06 (0.83–1.35), 0.63
3p24.1rs497376831.11T/C0.370.92 (0.82–1.03), 0.160.98 (0.81–1.18), 0.820.89 (0.71–1.11), 0.31
5p12rs441508441.16T/C0.611.10 (0.98–1.22), 0.101.19 (0.98–1.43), 0.070.94 (0.76–1.16), 0.58
5p15.33 (ER−)rs1006969051.18T/C0.571.05 (0.94–1.17), 0.341.02 (0.85–1.21), 0.861.29 (1.04–1.59), 0.02
5q11.2ars1688616511.23G/T0.291.02 (0.89–1.17), 0.791.20 (0.96–1.50), 0.100.94 (0.73–1.21), 0.63
5q11.2rs88931261.13C/A0.321.03 (0.92–1.16), 0.611.08 (0.89–1.30), 0.430.94 (0.75–1.18), 0.61
6q22.33rs218034171.41G/A0.321.03 (0.90–1.18), 0.641.15 (0.93–1.42), 0.210.91 (0.71–1.17), 0.47
6q25.1rs204621081.29A/G0.611.10 (0.97–1.24), 0.131.16 (0.94–1.43), 0.171.12 (0.87–1.42), 0.38
8q24.21rs1328161561.08C/T0.430.94 (0.85–1.05), 0.300.93 (0.77–1.11), 0.410.91 (0.74–1.13), 0.40
9p21.3rs101197091.09T/G0.341.01 (0.90–1.14), 0.810.96 (0.80–1.16), 0.670.90 (0.72–1.12), 0.35
9q31.2rs865686100.89G/T0.471.11 (0.99–1.24), 0.071.11 (0.92–1.34), 0.291.10 (0.89–1.36), 0.40
10p15.1rs238020590.94T/C0.601.03 (0.91–1.15), 0.651.13 (0.92–1.38), 0.231.08 (0.86–1.36), 0.50
10q21.2ars1099519090.86A/G0.160.98 (0.85–1.13), 0.810.91 (0.72–1.15), 0.441.01 (0.77–1.32), 0.96
10q22.3rs70401091.07A/G0.101.24 (1.04–1.47), 0.011.27 (0.96–1.66), 0.091.52 (1.12–2.08), 0.01
10q26.13rs298157911.17T/C0.601.04 (0.92–1.18), 0.481.28 (1.04–1.59), 0.021.08 (0.85–1.36), 0.56
10q26.13rs1219648111.32G/A0.421.01 (0.91–1.12), 0.821.07 (0.90–1.27), 0.440.99 (0.80–1.21), 0.89
10q26.13rs298158261.26A/G0.491.05 (0.92–1.19), 0.461.14 (0.90–1.45), 0.281.03 (0.80–1.31), 0.84
11p15.5rs381719861.07C/T0.111.21 (1.01–1.46), 0.041.22 (0.90–1.65), 0.211.18 (0.82–1.70), 0.37
11q13.3rs61436791.15T/C0.141.04 (0.88–1.21), 0.660.92 (0.70–1.22), 0.580.97 (0.71–1.33), 0.85
14q24.1rs99973711.06C/T0.950.88 (0.68–1.13), 0.320.71 (0.48–1.06), 0.101.18 (0.68–2.06), 0.56
16q12.1rs380366261.20T/C0.510.96 (0.83–1.10), 0.540.99 (0.78–1.26), 0.940.95 (0.74–1.22), 0.69
17q23.2rs650495030.95A/G0.350.95 (0.85–1.07), 0.421.10 (0.92–1.33), 0.290.99 (0.79–1.23), 0.90
19p13.11 (ER−)rs8170121.26A/G0.191.01 (0.88–1.16), 0.871.00 (0.80–1.25), 0.991.30 (1.01–1.68), 0.04

NOTE: ORs adjusted for age, geographic region of residence, and country of birth.

  • aProxies: GWAS: rs16886165; Proxy: rs16886164 (r2 = 1.0 in HapMap YRI) and GWAS: rs10995190; Proxy: rs10995189 (r2 = 1.0 in HapMap YRI).