Table 2.

Breast cancer index SNPs: original GWAS results and results from the BWHS

			Coded allele/reference	Coded allele	BWHS results: OR (95% CI), P value
Chromosome	SNP	GWAS OR	allele	frequency	All cases	ER+/PR+	ER−/PR−
1p11.2	rs11249433¹	1.16	C/T	0.13	0.97 (0.80–1.18), 0.76	1.15 (0.86–1.56), 0.35	0.76 (0.52–1.13), 0.17
2q35	rs13387042²	1.20	A/G	0.73	1.06 (0.93–1.20), 0.38	1.05 (0.85–1.30), 0.65	1.06 (0.83–1.35), 0.63
3p24.1	rs4973768³	1.11	T/C	0.37	0.92 (0.82–1.03), 0.16	0.98 (0.81–1.18), 0.82	0.89 (0.71–1.11), 0.31
5p12	rs4415084⁴	1.16	T/C	0.61	1.10 (0.98–1.22), 0.10	1.19 (0.98–1.43), 0.07	0.94 (0.76–1.16), 0.58
5p15.33 (ER−)	rs10069690⁵	1.18	T/C	0.57	1.05 (0.94–1.17), 0.34	1.02 (0.85–1.21), 0.86	1.29 (1.04–1.59), 0.02
5q11.2^a	rs16886165¹	1.23	G/T	0.29	1.02 (0.89–1.17), 0.79	1.20 (0.96–1.50), 0.10	0.94 (0.73–1.21), 0.63
5q11.2	rs889312⁶	1.13	C/A	0.32	1.03 (0.92–1.16), 0.61	1.08 (0.89–1.30), 0.43	0.94 (0.75–1.18), 0.61
6q22.33	rs2180341⁷	1.41	G/A	0.32	1.03 (0.90–1.18), 0.64	1.15 (0.93–1.42), 0.21	0.91 (0.71–1.17), 0.47
6q25.1	rs2046210⁸	1.29	A/G	0.61	1.10 (0.97–1.24), 0.13	1.16 (0.94–1.43), 0.17	1.12 (0.87–1.42), 0.38
8q24.21	rs13281615⁶	1.08	C/T	0.43	0.94 (0.85–1.05), 0.30	0.93 (0.77–1.11), 0.41	0.91 (0.74–1.13), 0.40
9p21.3	rs1011970⁹	1.09	T/G	0.34	1.01 (0.90–1.14), 0.81	0.96 (0.80–1.16), 0.67	0.90 (0.72–1.12), 0.35
9q31.2	rs865686¹⁰	0.89	G/T	0.47	1.11 (0.99–1.24), 0.07	1.11 (0.92–1.34), 0.29	1.10 (0.89–1.36), 0.40
10p15.1	rs2380205⁹	0.94	T/C	0.60	1.03 (0.91–1.15), 0.65	1.13 (0.92–1.38), 0.23	1.08 (0.86–1.36), 0.50
10q21.2^a	rs10995190⁹	0.86	A/G	0.16	0.98 (0.85–1.13), 0.81	0.91 (0.72–1.15), 0.44	1.01 (0.77–1.32), 0.96
10q22.3	rs704010⁹	1.07	A/G	0.10	1.24 (1.04–1.47), 0.01	1.27 (0.96–1.66), 0.09	1.52 (1.12–2.08), 0.01
10q26.13	rs2981579¹	1.17	T/C	0.60	1.04 (0.92–1.18), 0.48	1.28 (1.04–1.59), 0.02	1.08 (0.85–1.36), 0.56
10q26.13	rs1219648¹¹	1.32	G/A	0.42	1.01 (0.91–1.12), 0.82	1.07 (0.90–1.27), 0.44	0.99 (0.80–1.21), 0.89
10q26.13	rs2981582⁶	1.26	A/G	0.49	1.05 (0.92–1.19), 0.46	1.14 (0.90–1.45), 0.28	1.03 (0.80–1.31), 0.84
11p15.5	rs3817198⁶	1.07	C/T	0.11	1.21 (1.01–1.46), 0.04	1.22 (0.90–1.65), 0.21	1.18 (0.82–1.70), 0.37
11q13.3	rs614367⁹	1.15	T/C	0.14	1.04 (0.88–1.21), 0.66	0.92 (0.70–1.22), 0.58	0.97 (0.71–1.33), 0.85
14q24.1	rs999737¹	1.06	C/T	0.95	0.88 (0.68–1.13), 0.32	0.71 (0.48–1.06), 0.10	1.18 (0.68–2.06), 0.56
16q12.1	rs3803662⁶	1.20	T/C	0.51	0.96 (0.83–1.10), 0.54	0.99 (0.78–1.26), 0.94	0.95 (0.74–1.22), 0.69
17q23.2	rs6504950³	0.95	A/G	0.35	0.95 (0.85–1.07), 0.42	1.10 (0.92–1.33), 0.29	0.99 (0.79–1.23), 0.90
19p13.11 (ER−)	rs8170¹²	1.26	A/G	0.19	1.01 (0.88–1.16), 0.87	1.00 (0.80–1.25), 0.99	1.30 (1.01–1.68), 0.04

NOTE: ORs adjusted for age, geographic region of residence, and country of birth.

↵^aProxies: GWAS: rs16886165; Proxy: rs16886164 (r2 = 1.0 in HapMap YRI) and GWAS: rs10995190; Proxy: rs10995189 (r2 = 1.0 in HapMap YRI).