Table 1.

The associations of each signal-representative SNP with tumor risk and mammographic density in the three contributing consortia

Signal	Representative SNP	Position	Alleles	Freq.	BCAC		CIMBA	BCAC ER−	MODE
					ER−	ER+	BRCA1 mutations	CIMBA BRCA1	Mammographic dense areaa
					OR (95% CI) Ptrend cOR (95% CI) Pcond	OR (95% CI) Ptrend cOR (95% CI) Pcond	HR (95% CI) P value cHR (95% CI) Pcond	Meta-analysis P value Pcond	β (95% CI) Ptrend cβ (95% CI) Pcond
1	rs3757322	151,942,194	GT	0.33	1.17 (1.12–1.21) 1.00 × 10−14	1.07 (1.04–1.09) 1.10 × 10−7	1.15 (1.10–1.20) 3.78 × 10−10	2.50 × 10−23	0.12 (0.07, 0.17) 1.82 × 10−6
					1.14 (1.10–1.19) 1.51 × 10−9	1.06 (1.04–1.09) 1.02 × 10−5	1.10 (1.06–1.14) 3.79 × 10−7	7.59 × 10−15	0.07 (0.01, 0.12) 0.017
2	rs9397437	151,952,332	AG	0.07	1.28 (1.19–1.37) 5.29 × 10−12	1.15 (1.10–1.20) 1.26 × 10−9	1.24 (1.15–1.33) 3.98 × 10−8	6.79 × 10−19	0.27 (0.18, 0.36) 2.36 × 10−9
					1.18 (1.11–1.26) 1.20 × 10−5	1.12 (1.07–1.17) 3.56 × 10−6	1.12 (1.05–1.19) 3.60 × 10−4	3.29 × 10−8	0.22 (0.12, 0.32) 1.66 × 10−5
3	rs851984	152,023,191	AG	0.41	1.04 (1.01–1.08) 0.024	1.06 (1.03–1.08) 1.97 × 10−6	1.05 (1.01–1.10) 0.015	9.14 × 10−4	−0.03 (−0.07, 0.02) 0.29
					NA	1.07 (1.05–1.10) 1.09 × 10−8	1.07 (1.03–1.10) 3.60 × 10−4	3.12 × 10−5	0.01 (−0.04, 0.06) 0.83
4	rs9918437	152,072,718	TG	0.07	1.18 (1.11–1.27) 6.20 × 10−7	1.08 (1.04–1.13) 1.04 × 10−4	1.17 (1.08–1.26) 1.30 × 10−4	1.48 × 10−10	0.03 (−0.05, 0.12) 0.45
					1.13 (1.06–1.20) 4.46 × 10−4	NA	1.10 (1.04–1.17) 0.0015	2.61 × 10−6	0.03 (−0.06, 0.12) 0.46
5	rs2747652	152,437,016	CT	0.54	1.12 (1.08–1.16) 1.83 × 10−9	1.05 (1.03–1.08) 9.49 × 10−6	1.00 (0.96–1.04) 0.95	1.44 × 10−5	−0.02 (−0.07, 0.03) 0.39
					1.12 (1.08–1.16) 2.32 × 10−9	1.05 (1.03–1.08) 6.60 × 10−6	1.00 (0.97–1.04) 0.86	5.97 × 10−5	−0.02 (−0.07, 0.03) 0.45

For each signal-representative SNP (the best associated genotyped SNP), odds ratios for the minor/major allele and conditional odds ratios (OR and cOR) together with 95% confidence intervals (CIs), hazard ratios (HR and cHR), β coefficients (β and cβ) and P values (P_cond) are from models including the other four signal-representative SNPs. Representative conditional odds ratios and confidence intervals could not be generated from the meta-analysis. NA indicates that the SNP was not included in conditional analysis because its individual effect was not significant at P > 1 × 10⁻⁴. Freq., frequency.

^aMammographic dense area was square-root transformed and adjusted for age, BMI, menopausal status, study and relevant principal components.