Table 2.

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

Gene	Chromosomal location	Pathway^a	N SNPs		P
			Total	Pruned In	All	ER⁺	ER⁻	ER⁻ vs. ER⁺
All women
IL2RB	22q13	INTERLEUKIN BINDING^b	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 PRODUCTION^d	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 PATHWAY^c	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 PRODUCTION^d	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 PROCESS^b	75	32	0.001	0.019	0.448	0.954
SLA2	20q11.23	POSITIVE REGULATION OF IMMUNE SYSTEM PROCESS^b	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 PROCESS^b	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 PATHWAY^d	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 ACTIVITY^b	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 ACTIVITY^b	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).