Table 3.

Gene-wide significant tested SNPs for all breast cancer, ER+ tumors or ER− tumors

						All cases versus controls			ER+ cases versus controls			ER− cases versus Controls			P-heterogenerityf
Gene	SNP	Function	Allelesa	MAFb	Imputation r 2 c	OR (95% CI)d	Nominal P	P adj e	OR (95% CI)d	Nominal P	P adj	OR (95% CI)d	Nominal P	P adj
TSC2	rs181088346	Intron	G/A	0.06	0.909/0.802	0.77 (0.65–0.88)	2.7×10−4	0.035	0.73 (0.61–0.88)	0.0010	0.13	0.88 (0.70–1.09)	0.25	1.0	0.22
BRAF	rs114729114	Intron	C/T	0.03	0.728/0.950	1.53 (1.24–1.91)	1.1×10−4	0.012	1.44 (1.10–1.87)	0.0069	0.79	2.03 (1.50–2.76)	5.6 x 10-6	0.001	0.006
PGF	rs11542848	5′-UTR	C/T	0.08	0.983/0.923	1.14 (1.01–1.29)	0.035	1.0	1.13 (0.97–1.31)	0.08	1.0	1.38 (1.15–1.66)	4.5 x 10-4	0.049	0.22
PGF	rs61759375	Intron	C/T	0.11	0.975/0.884	1.11 (1.00–1.24)	0.051	1.0	1.07 (0.94–1.22)	0.29	1.0	1.34 (1.14–1.57)	2.9 x 10-4	0.032	0.06
MAPK3	rs78564187	Intron	G/A	0.18	Genotyped/0.966	1.07 (0.98–1.16)	0.13	1.0	1.03 (0.92–1.14)	0.63	1.0	1.26 (1.11–1.43)	3.4 x 10-4	0.006	0.004

^aMajor/minor alleles.

^bMinor allele frequency among controls.

^c r ² for imputed SNPs in the CBCS, WCHS and BWHS genotyping project/the MEC genotyping project.

^dAdditive model with each SNP coded as 0, 1 or 2 copies of the minor allele, adjusting for age, study, geographic location, DNA source and principal components of the genotypes.

^eBonferroni-corrected P values; bold P _adj are significant at the 0.05 level.

^fCalculated using a case–case only logistic regression model comparing ER− cases with ER+ cases.