Table 1.

Identification of two independent association signals for overall breast cancer risk among women of European ancestry.

Signal	SNPs	Position (hg 19)	Allelesb	RAF	LDc(r2)	Single Marker Analysis		Conditional Analysis
						OR (95% CI) d	P trendd	OR (95% CI)e	P trende
All cases (48,155 cases and 43,612 controls)
1f	rs9790517a	106084778	T/C	0.23	-	1.05(1.03–1.08)	5.44 × 10−6	1.04(1.02–1.07)	2.51 × 10−4
2g	rs77928427	106356761	A/C	0.24	0.04	1.05(1.03–1.08)	4.07 × 10−6	1.04(1.02–1.07)	1.86 × 10−4
ER (+) (28,038 cases and 43,612 controls)
1	rs9790517 a	106084778	T/C	0.23	-	1.06(1.03–1.09)	1.20 × 10−5	1.05(1.02–1.08)	2.49 × 10−4
2	rs77928427	106356761	A/C	0.24	0.04	1.05(1.02–1.08)	1.40×10−4	1.04(1.01–1.07)	3.07 × 10−3
ER (−) (7,786 cases and 43,612 controls)
1	rs9790517 a	106084778	T/C	0.22	-	1.04(0.99–1.08)	0.16	1.02(0.98–1.07)	0.3396
2	rs77928427	106356761	A/C	0.24	0.04	1.05(1.01–1.09)	0.03	1.04(1.00–1.09)	0.0508

Abbreviations: OR, odds ratio; CI, confidence interval; RAF, risk allele frequency

^aIndex SNP.

^bRisk/reference allele; risk alleles are shown in bold.

^cr² for linkage disequilibrium with the index SNP rs9790517.

^dAdjusted for age, study and the first six and an additional PC for LMBC study.

^eIncluded both top SNPs and adjusted for other top SNPs, age, study sites and the first six and an additional PC for LMBC study.

^fA total of 23 SNPs cannot be excluded using LR < 1/100 as candidate causal variants (see Supplementary table 1).

^gA total of 4 SNPs cannot be excluded using LR < 1/100 as candidate causal variants (see Supplementary table 1)