Table 1.

Independent association signals identified for breast cancer risk in the 12p11 locus in women of European ancestry

Signal	SNPs	Position (hg 19)	Alleles	EAF	LD (r 2)b	Univariate analysis		Conditional analysis		SNPs retained for functional annotatione
						Per-allele OR (95 % CI)c	P-trend	Per-allele OR (95 % CI)d	P-trend
2	Indexa rs10771399	28155080	G*/A	0.12	-	0.85 (0.83–0.88)	5 × 10-25	-	-	-
1	rs7297051	28174817	T*/C	0.24	0.42	0.88 (0.86–0.90)	4 × 10-28	0.92 (0.89–0.94)	3 × 10-9	rs812020, chr12:28164044, rs2619434, rs2590275
2	rs805510	28139846	T*/C	0.12	0.88	0.85 (0.82–0.88)	10-25	0.93 (0.89–0.96)	2 × 10-5	74 SNPsf
3	rs1871152	28379826	G*/A	0.31	0.04	0.94 (0.92–0.96)	3 × 10-8	0.96 (0.94–0.98)	2 × 10-4	376 SNPsg

^*Effect alleles. ^aIdentified in the initial genome-wide association study conducted in women of European descent [1]. ^bLinkage disequilibrium (LD) with rs10771399 for women of European descent. ^cAdjusted for studies, and the top principal components and an additional principal component accounting for the Leuven Multidisciplinary Breast Centre (LMBC) study. ^dIncluded all three variants, and was adjusted for studies, and the top eight principal components as well as an additional principal component accounting for the LMBC study. ^eAssociated single nucleotide polymorphisms (SNPs) with a likelihood ratio >1/100 relative to the lead SNP in each signal. ^fSee Table S2 in Additional file 5. ^gSee Table S2 in Additional file 5. EAF effect allele frequency in controls, OR odds ratio, CI confidence interval