Table 1. Associations with breast and ovarian cancer risk for SNPs observed at p-trend<0.05 in stage II of the experiment.

BRCA1 carriers	SNP name	Gene	Unaffected (Number)	Affected (Number)	Unaffected (MAF)	Affected (MAF)	HR per allelea	HR heterozygoteb	HR homozygoteb	p-trendc	p-hetc	p-homc
Breast cancer	rs3847954d	UNG	7455	7797	0.18	0.19	1.05 (1.00–1.11)	1.09 (1.02–1.16)	0.99 (0.84–1.16)	0.04	0.011	0.713
Ovarian cancer	rs2072668	OGG1	12786	2461	0.22	0.23	1.09 (1.01–1.18)	1.16 (1.05–1.27)	1.03 (0.82–1.28)	0.016	3×10−3	0.77
	rs2269112	OGG1	12789	2461	0.17	0.18	1.11 (1.02–1.21)	1.11 (1.01–1.23)	1.21 (0.92–1.58)	0.013	0.014	0.268
	rs2304277	OGG1	12783	2462	0.2	0.21	1.12 (1.03–1.21)	1.19 (1.08–1.3)	1.01 (0.79–1.30)	4.8×10−3	6×10−4	0.69
	rs10161263	SMUG1	12790	2462	0.34	0.32	0.92 (0.86–0.99)	0.88 (0.80–0.97)	0.90 (0.78–1.04)	0.024	9×10−3	0.49

^aHazard Ratio per allele (1 df) estimated from the retrospective likelihood analysis.

^bHazard Ratio under the genotype specific models (2df) estimated from the retrospective likelihood analysis.

^cp-values were based on the score test.

^dHR per allele of 1.69 and p-trend of 1×10⁻⁴ for BRCA2 mutation carriers in stage I of the study.

^eHR per allele of 1.43 and p-trend of 0.01 for BRCA1 mutation carriers in stage I of the study.

^fHR per allele of 1.30 and p-trend of 0.03 for BRCA1 mutation carriers in stage I of the study.

^gHR per allele of 0.64 and p-trend of 0.057 for BRCA2 mutation carriers in stage I of the study.

^hHR per allele of 1.25 and p-trend of 0.04 for BRCA1 mutation carriers in stage I of the study.

ⁱHR per allele of 1.25 and p-trend of 0.058 for BRCA2 mutation carriers in stage I of the study.

^jrs3093926 did not yield results under the genotype specific model due to the low minor allele frequency.

Complete description of results from stage I are included in Supplementary Table S1.

Highlighted in bold are those SNPs showing strongest associations with breast or ovarian cancer risk (p<0.01).