Table 2. Associations with breast and ovarian cancer risk for SNPs found to be associated with risk at all 3 stages of the experiment.

SNP, Chr, Position, Allele1/Allele2	Stage	Number		Allele 2 Frequency		HR* (95% CI)
		Unaffected	Affected	Unaffected	Affected	Per Allele	Heterozygote	Homozygote	P-trend
Breast Cancer
rs2290854, 1q32, 202782648, G/A	Stage 1	1104	1283	0.30	0.34	1.19 (1.08–1.30)	1.28 (1.12–1.47)	1.31 (1.06–1.61)	4.2×10−4
	Stage 2	4681	4637	0.31	0.33	1.09 (1.03–1.16)	1.10 (1.02–1.19)	1.18 (1.03–1.35)	0.003
	Stages1+2	5785	5920	0.31	0.33	1.12 (1.06–1.17)	1.15 (1.07–1.23)	1.21 (1.08–1.36)	1.7×10−5
	Stage 3	1252	1393	0.30	0.33	1.19 (1.07–1.32)	1.24 (1.07–1.43)	1.36 (1.06–1.74)	0.0013
	Combined	7037	7313	0.31	0.33	1.13 (1.08–1.18)	1.16 (1.09–1.24)	1.24 (1.11–1.37)	1.4×10−7
rs6682208, 1q32, 202832806, G/A	Stage 1	1104	1283	0.32	0.35	1.14 (1.04–1.25)	1.24 (1.09–1.42)	1.20 (0.98–1.47)	0.0070
	Stage 2	4681	4637	0.32	0.34	1.10 (1.04–1.17)	1.09 (1.01–1.19)	1.21 (1.06–1.38)	0.0014
	Stages1+2	5785	5920	0.32	0.34	1.11 (1.05–1.17)	1.13 (1.05–1.21)	1.21 (1.08–1.35)	5.4×10−5
	Stage 3	1250	1394	0.30	0.34	1.19 (1.07–1.32)	1.31 (1.14–1.51)	1.28 (1.01–1.63)	8.6×10−4
	Combined	7035	7314	0.32	0.34	1.12 (1.07–1.17)	1.16 (1.09–1.23)	1.22 (1.11–1.35)	4.3×10−7
rs11196174, 10q25.3, 114724086, A/G	Stage 1	1103	1282	0.27	0.32	1.15 (1.05–1.27)	1.17 (1.03–1.34)	1.31 (1.05–1.63)	0.0038
	Stage 2	4681	4636	0.29	0.31	1.10 (1.04–1.17)	1.13 (1.04–1.23)	1.17 (1.01–1.35)	0.0017
	Stages1+2	5784	5918	0.28	0.31	1.12 (1.06–1.18)	1.14 (1.06–1.23)	1.21 (1.07–1.37)	3.1×10−5
	Stage 3	1251	1393	0.28	0.31	1.16 (1.05–1.29)	1.08 (0.93–1.25)	1.46 (1.15–1.85)	0.0057
	Combined	7035	7311	0.28	0.31	1.13 (1.07–1.18)	1.13 (1.06–1.21)	1.26 (1.13–1.40)	7.5×10−7
rs11196175, 10q25.3, 114726604, A/G	Stage 1	1101	1280	0.27	0.31	1.15 (1.05–1.27)	1.18 (1.03–1.35)	1.29 (1.03–1.62)	0.0043
	Stage 2	4674	4627	0.28	0.30	1.10 (1.03–1.17)	1.13 (1.04–1.22)	1.17 (1.01–1.35)	0.0020
	Stages1+2	5775	5907	0.28	0.30	1.12 (1.06–1.18)	1.14 (1.06–1.22)	1.21 (1.07–1.37)	3.9×10−5
	Stage 3	1251	1394	0.27	0.31	1.16 (1.04–1.29)	1.06 (0.91–1.22)	1.48 (1.17–1.87)	0.0075
	Combined	7026	7301	0.28	0.31	1.12 (1.07–1.18)	1.12 (1.05–1.20)	1.26 (1.13–1.41)	1.2×10−6
Ovarian Cancer
rs17631303, 17q21, 40872185, A/G	Stage 1	1797	574	0.19	0.25	1.46 (1.22–1.74)	1.36 (1.01–1.68)	2.46 (1.53–3.96)	1.3×10−5
	Stage 2	7996	1257	0.19	0.21	1.20 (1.07–1.35)	1.10 (0.96–1.26)	1.83 (1.34–2.48)	1.5×10−3
	Stages1+2	9793	1831	0.19	0.22	1.27 (1.16–1.40)	1.15 (1.03–1.29)	2.03 (1.16–2.61)	3.0×10−7
	Stage 3	2204	442	0.17	0.21	1.27 (1.07–1.51)	1.24 (0.99–1.56)	1.67 (1.07–2.62)	0.014
	Combined	11997	2273	0.19	0.22	1.27 (1.17–1.38)	1.17 (1.06–1.29)	1.95 (1.57–2.42)	1.4×10−8
rs183211, 17q21, 42143493, G/A	Stage 1	1812	575	0.22	0.28	1.45 (1.23–1.71)	1.37 (1.11–1.69)	2.29 (1.53–3.41)	2.5×10−5
	Stage 2	8054	1264	0.23	0.25	1.20 (1.07–1.33)	1.13 (0.99–1.28)	1.62 (1.22–2.14)	1.1×10−3
	Stages1+2	9866	1839	0.23	0.26	1.25 (1.15–1.37)	1.16 (1.04–1.29)	1.83 (1.46–2.28)	5.7×10−7
	Stage 3	2204	442	0.22	0.26	1.25 (1.06–1.48)	1.15 (0.92–1.44)	1.79 (1.21–2.67)	0.018
	Combined	12070	2281	0.23	0.26	1.25 (1.16–1.35)	1.16 (1.05–1.27)	1.82 (1.5–2.21)	3.1×10−8
rs4691139, 4q32.3, 166128171, A/G	Stage 1	1812	575	0.47	0.53	1.24 (1.08–1.42)	1.46 (1.13–1.88)	1.55 (1.16–2.05)	3.6×10−3
	Stage 2	8054	1264	0.48	0.52	1.18 (1.08–1.29)	1.29 (1.10–1.50)	1.40 (1.17–1.67)	1.3×10−4
	Stages1+2	9866	1839	0.48	0.52	1.20 (1.11–1.29)	1.33 (1.17–1.52)	1.44 (1.24–1.67)	1.1×10−6
	Stage 3	2204	441	0.47	0.52	1.20 (1.04–1.39)	1.19 (0.91–1.54)	1.44 (1.08–1.94)	9×10−3
	Combined	12070	2280	0.48	0.52	1.20 (1.17–1.38)	1.30 (1.16–1.46)	1.44 (1.26–1.65)	3.4×10−8

^*HRs estimated under the single disease risk models.