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. Author manuscript; available in PMC: 2019 Mar 1.
Published in final edited form as: Cancer Epidemiol Biomarkers Prev. 2018 Jan 16;27(3):321–330. doi: 10.1158/1055-9965.EPI-17-0434

Table 2.

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

Gene Chromosomal Location Pathwaya N SNPs
P-Value
Total Pruned In All ER+ ER− ER− vs ER+
All Women
IL2RB 22q13 INTERLEUKIN BINDINGb 322 220 0.001 0.074 0.018 0.485
CADM1 11q23.2 CYTOKINE PRODUCTION 1605 638 0.003 0.031 0.006 0.957
ATP6AP2 Xp11.4 POSITIVE REGULATION OF CYTOKINE PRODUCTIONd 283 96 0.006 0.130 0.091 0.689
TLR6 4p16.1 CYTOKINE METABOLIC PROCESS 494 141 0.006 0.142 0.024 0.147
HLA-DQA1 6p21.3 REACTOME PD1 SIGNALING (Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response) 1986 188 0.007 0.043 0.079 0.361
POU2AF1 11q23.1 HUMORAL IMMUNE RESPONSE 244 94 0.009 0.033 0.338 0.881
TLR7 Xp22.3 BIOCARTA DC PATHWAY 251 159 0.009 0.330 0.563 0.949
CYP4F11 19p13.1 INFLAMMATORY RESPONSE 336 122 0.010 0.068 0.231 0.910
UBE2N 12q22 POSITIVE REGULATION OF IMMUNE RESPONSE 227 66 0.098 0.001 0.378 0.345
IFNA1 9p22 BIOCARTA INFLAM PATHWAY 143 77 0.014 0.002 0.146 0.770
TRAF1 9q33-q34 BIOCARTA TNFR2 PATHWAYc 258 62 0.377 0.003 0.725 0.001
CALCA 11p15.2 CYTOKINE PRODUCTION 129 49 0.034 0.005 0.015 0.124
MAP3K1 5q11.2 BIOCARTA TNFR1 PATHWAY 544 141 0.096 0.007 0.015 0.007
BCL3 19q13.32 CYTOKINE PRODUCTION 214 131 0.038 0.007 0.205 0.422
ICOSLG 21q22.3 REGULATION OF LYMPHOCYTE ACTIVATION 264 148 0.018 0.009 0.574 0.225
PRKDC 8q11 BIOCARTA TNFR1 PATHWAY 444 109 0.131 0.488 0.002 0.052
IL8 4q13-q21 BIOCARTA INFLAM PATHWAY 122 49 0.395 0.644 0.003 0.570
MAPK3 16p11.2 KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY 24 19 0.688 0.953 0.006 0.019
CARD11 7p22 REGULATION OF CYTOKINE PRODUCTIONd 1471 828 0.069 0.665 0.007 0.099
NFATC3 16q22 INFLAMMATORY RESPONSE 660 117 0.898 0.948 0.008 0.147
Premenopusal Women
IL21 4q26-q27 POSITIVE REGULATION OF IMMUNE SYSTEM PROCESSb 75 32 0.001 0.019 0.448 0.954
SLA2 20q11.23 POSITIVE REGULATION OF IMMUNE SYSTEM PROCESSb 220 80 0.001 0.076 0.122 0.704
TLR7 Xp22.3 CYTOKINE BIOSYNTHETIC PROCESS 251 159 0.003 0.038 0.311 0.500
CFHR1 1q32 REGULATION OF IMMUNE SYSTEM PROCESSb 500 123 0.004 0.034 0.210 0.621
PRG3 11q12.1 CYTOKINE BIOSYNTHETIC PROCESS 93 39 0.006 0.004 0.272 0.211
CXCR4 2q21 INFLAMMATORY RESPONSE 90 54 0.008 0.024 0.228 0.060
HLA-DMA 6p21.3 REACTOME PD1 SIGNALING (Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response)c 135 40 0.009 0.002 0.623 0.455
MAP3K1 5q11.2 BIOCARTA TNFR2 PATHWAY 544 141 0.187 0.003 0.595 0.025
LBP 20q11.23 INFLAMMATORY RESPONSE 389 196 0.012 0.006 0.608 0.613
HLA-DOA 6p21.3 REACTOME PD1 SIGNALING (Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response)c 303 136 0.060 0.008 0.261 0.474
IL10 1q31-q32 BIOCARTA CYTOKINE PATHWAYd 114 67 0.442 0.498 0.001 0.021
IL8 4q13-q21 KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY 122 49 0.327 0.732 0.001 0.110
HELLS 10q24.2 LYMPHOCYTE ACTIVATION 344 77 0.863 0.982 0.008 0.098
Postmenopausal Women
IL2RB 22q13 INTERLEUKIN RECEPTOR ACTIVITYb 322 220 0.001 0.023 0.008 0.137
CYP4F11 19p13.1 INFLAMMATORY RESPONSE 336 122 0.001 0.005 0.213 0.985
IL21 4q26-q27 REGULATION OF LYMPHOCYTE ACTIVATION 75 32 0.004 0.225 0.237 0.912
CASP8 2q33-q34 KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY 259 122 0.006 0.014 0.100 0.572
POU2AF1 11q23.1 HUMORAL IMMUNE RESPONSE 244 94 0.007 0.012 0.335 0.787
IRAK2 3p25.2 INFLAMMATORY RESPONSE 645 317 0.008 0.478 0.001 0.631
XCR1 3p21.3-p21.1 CYTOKINE BINDING 95 31 0.086 0.002 0.296 0.988
CD274 9p24.1 REACTOME PD1 SIGNALING (Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response) 130 73 0.113 0.005 0.524 0.532
UBE2N 12q22 POSITIVE REGULATION OF IMMUNE RESPONSE 227 66 0.013 0.006 0.455 0.200
AOAH 7p14.2 INFLAMMATORY RESPONSE 1608 770 0.030 0.006 0.465 0.911
IL1R1 2q12 INTERLEUKIN RECEPTOR ACTIVITYb 858 334 0.022 0.009 0.630 0.874
CARD11 7p22 REGULATION OF CYTOKINE PRODUCTION 1471 828 0.554 0.911 0.004 0.011
SMAD3 15q21-q22 CYTOKINE PRODUCTION 837 448 0.094 0.116 0.006 0.051
CD247 1q24.2 REACTOME PD1 SIGNALING (Programmed death-1 (PD-1) is a cell surface molecule that regulates the adaptive immune response) 682 367 0.284 0.242 0.008 0.238
a

Pathway associated with the greatest statistical significance for gene as shown in Supplementary Tables 3, 4, or 5.

b

Pathway 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 3, 4, or 5, P<0.05.

c

Pathway associated with risk of ER+ breast cancer risk within study population specified, as shown in Supplementary Tables 3, 4, or 5, p<0.05.

d

Pathway associated with ER− breast cancer within study population specified, as shown in Supplementary Tables 3, 4, or 5, p<0.05.

P-values for genes significant at P≤0.01 are indicated in bold text.