Table 2.

Nominally significant genes associated with overall, ER+, ER breast cancer risk in the AMBER Consortium

GeneChromosomal locationPathwayaN SNPsP
TotalPruned InAllER+ERER vs. ER+
All women
IL2RB22q13INTERLEUKIN BINDINGb3222200.0010.0740.0180.485
CADM111q23.2CYTOKINE PRODUCTION1,6056380.0030.0310.0060.957
ATP6AP2Xp11.4POSITIVE REGULATION OF CYTOKINE PRODUCTIONd283960.0060.1300.0910.689
TLR64p16.1CYTOKINE METABOLIC PROCESS4941410.0060.1420.0240.147
HLA-DQA16p21.3REACTOME PD1 SIGNALING [Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response]1,9861880.0070.0430.0790.361
POU2AF111q23.1HUMORAL IMMUNE RESPONSE244940.0090.0330.3380.881
TLR7Xp22.3BIOCARTA DC PATHWAY2511590.0090.3300.5630.949
CYP4F1119p13.1INFLAMMATORY RESPONSE3361220.0100.0680.2310.910
UBE2N12q22POSITIVE REGULATION OF IMMUNE RESPONSE227660.0980.0010.3780.345
IFNA19p22BIOCARTA INFLAM PATHWAY143770.0140.0020.1460.770
TRAF19q33-q34BIOCARTA TNFR2 PATHWAYc258620.3770.0030.7250.001
CALCA11p15.2CYTOKINE PRODUCTION129490.0340.0050.0150.124
MAP3K15q11.2BIOCARTA TNFR1 PATHWAY5441410.0960.0070.0150.007
BCL319q13.32CYTOKINE PRODUCTION2141310.0380.0070.2050.422
ICOSLG21q22.3REGULATION OF LYMPHOCYTE ACTIVATION2641480.0180.0090.5740.225
PRKDC8q11BIOCARTA TNFR1 PATHWAY4441090.1310.4880.0020.052
IL84q13-q21BIOCARTA INFLAM PATHWAY122490.3950.6440.0030.570
MAPK316p11.2KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY24190.6880.9530.0060.019
CARD117p22REGULATION OF CYTOKINE PRODUCTIONd1,4718280.0690.6650.0070.099
NFATC316q22INFLAMMATORY RESPONSE6601170.8980.9480.0080.147
Premenopusal women
IL214q26-q27POSITIVE REGULATION OF IMMUNE SYSTEM PROCESSb75320.0010.0190.4480.954
SLA220q11.23POSITIVE REGULATION OF IMMUNE SYSTEM PROCESSb220800.0010.0760.1220.704
TLR7Xp22.3CYTOKINE BIOSYNTHETIC PROCESS2511590.0030.0380.3110.500
CFHR11q32REGULATION OF IMMUNE SYSTEM PROCESSb5001230.0040.0340.2100.621
PRG311q12.1CYTOKINE BIOSYNTHETIC PROCESS93390.0060.0040.2720.211
CXCR42q21INFLAMMATORY RESPONSE90540.0080.0240.2280.060
HLA-DMA6p21.3REACTOME PD1 SIGNALING [Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response]c135400.0090.0020.6230.455
MAP3K15q11.2BIOCARTA TNFR2 PATHWAY5441410.1870.0030.5950.025
LBP20q11.23INFLAMMATORY RESPONSE3891960.0120.0060.6080.613
HLA-DOA6p21.3REACTOME PD1 SIGNALING [Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response]c3031360.0600.0080.2610.474
IL101q31-q32BIOCARTA CYTOKINE PATHWAYd114670.4420.4980.0010.021
IL84q13-q21KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY122490.3270.7320.0010.110
HELLS10q24.2LYMPHOCYTE ACTIVATION344770.8630.9820.0080.098
Postmenopausal women
IL2RB22q13INTERLEUKIN RECEPTOR ACTIVITYb3222200.0010.0230.0080.137
CYP4F1119p13.1INFLAMMATORY RESPONSE3361220.0010.0050.2130.985
IL214q26-q27REGULATION OF LYMPHOCYTE ACTIVATION75320.0040.2250.2370.912
CASP82q33-q34KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY2591220.0060.0140.1000.572
POU2AF111q23.1HUMORAL IMMUNE RESPONSE244940.0070.0120.3350.787
IRAK23p25.2INFLAMMATORY RESPONSE6453170.0080.4780.0010.631
XCR13p21.3-p21.1CYTOKINE BINDING95310.0860.0020.2960.988
CD2749p24.1REACTOME PD1 SIGNALING [Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response]130730.1130.0050.5240.532
UBE2N12q22POSITIVE REGULATION OF IMMUNE RESPONSE227660.0130.0060.4550.200
AOAH7p14.2INFLAMMATORY RESPONSE1,6087700.0300.0060.4650.911
IL1R12q12INTERLEUKIN RECEPTOR ACTIVITYb8583340.0220.0090.6300.874
CARD117p22REGULATION OF CYTOKINE PRODUCTION1,4718280.5540.9110.0040.011
SMAD315q21-q22CYTOKINE PRODUCTION8374480.0940.1160.0060.051
CD2471q24.2REACTOME PD1 SIGNALING [Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response]6823670.2840.2420.0080.238
  • NOTE: P-values for genes significant at P≤0.01 are indicated in bold text.

  • aPathway associated with the greatest statistical significance for gene as shown in Supplementary Tables S3–S5.

  • bPathway associated with overall breast cancer risk within study population specified (i.e., all women combined, premenopausal women, or postmenopausal women), as shown in Supplementary Tables S3–S5 (P < 0.05).

  • cPathway associated with risk of ER+ breast cancer risk within study population specified, as shown in Supplementary Tables S3–S5 (P < 0.05).

  • dPathway associated with ER breast cancer within study population specified, as shown in Supplementary Tables S3–S5 (P < 0.05).