Nominally significant genes associated with overall, ER+, ER− breast cancer risk in the AMBER Consortium
Gene | Chromosomal location | Pathwaya | N SNPs | P | ||||
---|---|---|---|---|---|---|---|---|
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 | 1,605 | 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] | 1,986 | 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 | 1,471 | 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 | 1,608 | 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 | 1,471 | 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 |
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).