Table 3.

Associations between SNPs reaching gene-wide significance with overall, ER+, and ER breast cancer risk in the AMBER consortium

GeneSNPFunctionRef/variant alleleMAFPLINK INFO scoreAll casesER+ER
Per allele OR (95% CI)Gene-wide PadjPer allele OR (95% CI)Gene-wide PadjPer allele OR (95% CI)Gene-wide Padj
All women
IL2RBrs228952IntronicG/T0.280.970.85 (0.79–0.92)0.0070.88 (0.80–0.96)0.9670.80 (0.71–0.90)0.051
POU2AF1rs145624147IntronicCAG/C0.241.010.85 (0.79–0.92)0.0080.88 (0.80–0.96)0.5490.82 (0.73–0.93)0.149
rs1815948IntronicG/C0.141.010.83 (0.75–0.92)0.0230.85 (0.76–0.96)0.8680.83 (0.71–0.93)1.000
rs76988807IntronicT/C0.081.000.80 (0.70–0.90)0.0350.79 (0.67–0.91)0.1800.86 (0.71–1.03)1.000
HLA-DQA1rs12722043Exonic syn SNVC/T0.250.980.85 (0.79–0.92)0.0100.86 (0.78–0.94)0.2870.83 (0.74–0.94)0.486
rs115976249IntronicG/A0.070.940.76 (0.66–0.87)0.0120.77 (0.65–0.91)0.3690.75 (0.61–0.92)1.000
TLR6rs141273518IntronicC/T0.050.861.39 (1.18–1.65)0.0171.33 (1.08–1.63)1.0001.63 (1.27–2.08)0.015
rs141628846UpstreamG/A0.020.971.68 (1.28–2.20)0.0241.61 (1.16–2.22)0.5562.02 (1.39–2.96)0.037
ATP6AP2rs115047524IntronicG/A0.090.980.80 (0.72–0.90)0.0250.82 (0.71–0.95)0.6390.80 (0.67–0.96)1.000
IL21rs76526843IntergenicG/T0.020.900.64 (0.49–0.83)0.0280.74 (0.54–1.00)1.0000.65 (0.42–0.98)1.000
CADM1rs73570052IntronicA/C0.040.971.43 (1.20–1.70)0.0521.41 (1.14–1.74)0.8431.58 (1.23–2.05)0.274
BCL3rs34698726IntergenicA/T0.320.911.16 (1.08–1.25)0.0101.19 (1.09–1.30)0.0131.11 (0.99–1.25)1.000
IL8rs188246983IntergenicT/C0.070.991.17 (1.03–1.34)0.9141.14 (0.97–1.34)1.0001.49 (1.23–1.81)0.002
rs113976067IntergenicT/C0.221.001.10 (1.01–1.19)1.0001.08 (0.98–1.19)1.0001.23 (1.09–1.39)0.047
MAP3K1rs863839IntronicA/G0.081.000.96 (0.84–1.09)1.0001.08 (0.93–1.25)1.0000.65 (0.53–0.81)0.003
rs191188130IntronicG/T0.090.871.03 (0.91–1.17)1.0000.95 (0.81–1.11)1.0001.32 (1.10–1.58)0.052
PRKDCrs148411126IntronicC/CT0.080.981.16 (1.03–1.32)1.0001.03 (0.89–1.19)1.0001.45 (1.22–1.72)0.003
rs8178033Exonic nonsyn SNVG/C0.081.001.15 (1.02–1.30)1.0001.02 (0.88–1.19)1.0001.41 (1.19–1.68)0.011
rs56411879IntronicT/C0.020.861.16 (0.91–1.48)1.0000.93 (0.69–1.26)1.0001.81 (1.31–2.50)0.039
Premenopausal
SLA2rs221310IntronicA/G0.73gtyped1.32 (1.16–1.51)0.0031.26 (1.08–1.48)0.3541.28 (1.06–1.56)0.949
CXCR4rs17848049IntergenicG/C0.091.000.65 (0.52–0.80)0.0040.59 (0.45–0.78)0.0090.74 (0.54–1.01)1.000
PRG3rs4411290IntergenicC/G0.471.000.79 (0.70–0.89)0.0070.76 (0.66–0.89)0.0160.84 (0.71–1.00)1.000
rs1867128IntergenicA/T0.511.000.81 (0.72–0.92)0.0390.78 (0.67–0.91)0.0430.86 (0.72–1.03)1.000
IL21rs115698762IntergenicC/T0.020.942.22 (1.45–3.41)0.0082.19 (1.33–3.60)0.0642.02 (1.07–3.79)0.934
rs143266239IntergenicG/A0.040.971.77 (1.29–2.43)0.0131.80 (1.25–2.60)0.0531.67 (1.06–2.65)0.914
HLA-DMArs580962IntergenicC/T0.78gtyped1.29 (1.12–1.49)0.0161.42 (1.19–1.70)0.0041.19 (0.96–1.46)1.000
LBPrs2232587IntronicT/C0.110.960.68 (0.56–0.83)0.0250.64 (0.50–0.82)0.0790.73 (0.55–0.98)1.000
MAP3K1rs252911IntergenicA/G0.830.991.22 (1.04–1.43)1.0001.45 (1.18–1.77)0.0431.03 (0.82–1.29)1.000
IL10chr1:206953202:IIntergenicT/TC0.110.921.21 (1.00–1.48)1.0001.06 (0.83–1.35)1.0001.73 (1.32–2.26)0.005
rs140929284IntergenicTC/T0.060.881.27 (0.98–1.63)1.0001.10 (0.80–1.52)1.0001.88 (1.35–2.63)0.015
rs74148793IntergenicC/T0.150.991.21 (1.02–1.42)0.9901.12 (0.92–1.37)1.0001.50 (1.19–1.88)0.035
IL8rs113976067IntergenicT/C0.211.001.20 (1.04–1.38)0.6601.15 (0.97–1.37)1.0001.50 (1.21–1.85)0.008
rs188246983IntergenicT/C0.070.991.25 (0.99–1.58)1.0001.20 (0.91–1.60)1.0001.78 (1.29–2.45)0.022
CADM1rs143193835IntronicG/C0.030.991.74 (1.22–2.47)0.0911.45 (0.94–2.23)1.0002.65 (1.69–4.17)0.016
HELLSrs200175744IntergenicACT/A0.320.961.11 (0.97–1.26)1.0001.03 (0.88–1.20)1.0001.43 (1.18–1.72)0.017
rs10882476IntronicT/G0.090.991.05 (0.85–1.30)0.9900.86 (0.66–1.13)1.0001.64 (1.23–2.17)0.049
rs11188009IntergenicA/G0.470.981.08 (0.96–1.22)1.0001.00 (0.87–1.16)1.0001.38 (1.16–1.66)0.032
Postmenopausal
POU2AF1rs75716067IntronicA/G0.031.020.53 (0.40–0.71)0.0020.46 (0.32–0.66)0.0030.60 (0.38–0.93)1.000
HLA-DQA1rs115976249IntronicG/A0.070.940.66 (0.54–0.80)0.0040.70 (0.56–0.88)0.3590.61 (0.45–0.83)0.332
IL21rs2390350IntronicA/G0.511.001.19 (1.08–1.30)0.0081.16 (1.04–1.29)0.2361.16 (1.00–1.33)1.000
rs17005895IntergenicA/T0.150.971.27 (1.11–1.44)0.0141.21 (1.03–1.41)0.3631.32 (1.08–1.61)0.160
CYP4F11rs4572524IntergenicA/G0.650.870.82 (0.73–0.90)0.0150.84 (0.74–0.95)0.5600.80 (0.68–0.93)0.659
IL2RBrs73406995IntergenicC/G0.160.970.78 (0.68–0.88)0.0210.77 (0.66–0.90)0.1860.71 (0.58–0.87)0.207
UBE2Nrs76506230IntergenicT/C0.020.772.12 (1.40–3.22)0.0262.52 (1.57–4.03)0.0082.13 (1.18–3.86)0.814
CASP8rs55637196IntronicG/A0.200.990.81 (0.72–0.91)0.0340.78 (0.68–0.90)0.0650.81 (0.67–0.97)1.000
IRAK2rs149858020IntronicC/T0.130.991.31 (1.14–1.50)0.0381.23 (1.05–1.45)1.0001.51 (1.24–1.85)0.017
CD274rs2890657IntronicG/C0.040.970.75 (0.59–0.95)1.0000.56 (0.42–0.76)0.0160.84 (0.59–1.20)1.000
rs10481593IntronicG/A0.24gtyped0.87 (0.78–0.97)0.6550.80 (0.70–0.91)0.0400.91 (0.77–1.07)1.000
CALCArs34587547Exonic nonsyn SNVC/G0.010.992.23 (1.26–4.29)0.1303.20 (1.67–6.16)0.0241.50 (0.54–4.13)1.000
XCR1rs2373148IntergenicT/C0.851.010.85 (0.75–0.96)0.3610.78 (0.67–0.90)0.0260.89 (0.73–1.07)1.000
rs2371UpstreamA/G0.910.980.82 (0.70–0.96)0.3820.73 (0.61–0.88)0.0330.85 (0.67–1.08)1.000
PRKDCrs8178153IntronicC/T0.080.961.26 (1.06–1.50)1.0001.09 (0.88–1.34)1.0001.60 (1.24–2.06)0.028
CD247rs12066323IntronicG/A0.130.981.12 (0.97–1.28)1.0000.98 (0.83–1.15)1.0001.49 (1.22–1.820.037
SMAD3rs2289259IntronicG/A0.341.001.08 (0.98–1.19)1.0001.00 (0.90–1.12)1.0001.34 (1.15–1.55)0.049
  • NOTE: P-values for SNPs with corrected gene-wide significance at P ≤ 0.05 are indicated in bold text.

  • Abbreviations: gtyped: genotyped; MAF, minor allele frequency; Ref: referent; nonsyn SNV: nonsynonymous single nucleotide variant; syn SNV: synonymous single nucleotide variant.