Table 3.

Associations between SNPs and risk of breast cancer by ER status among European American or African American women.

Gene	SNP	Coded/ reference allele	Race	Estrogen receptor status	Allele frequency in cases	Allele frequency in controls	Heterozygotes OR(95%CI)a	Homozygotes OR(95%CI)a	Per allele OR(95%CI)a	P for trend	Pcc
CYP17A1	rs12413409	A/G	EA	+	0.10	0.10	0.95 (0.66–1.36)	1.89 (0.54–6.61)	1.04 (0.75–1.43)	0.83	1.00
				−	0.15	0.10	2.01 (1.15–3.54)	2.55 (0.28–23.31)	1.92 (1.15–3.21)	0.01	0.05
			AA	+	0.05	0.05	1.01 (0.64–1.60)	N/Ab	0.99 (0.63–1.55)	N/Ab	N/Ab
				−	0.05	0.05	0.90 (0.48–1.71)	N/Ab	0.89 (0.47–1.67)	N/Ab	N/Ab
CYP1A2	rs2470893	A/G	EA	+	0.25	0.26	1.03 (0.78–1.37)	0.61 (0.33–1.13)	0.91 (0.73–1.14)	0.40	1.00
				−	0.21	0.26	0.89 (0.53–1.50)	0.33 (0.07–1.45)	0.76 (0.49–1.16)	0.20	0.90
			AA	+	0.08	0.05	1.78 (1.14–2.79)	2.80 (0.52–14.99)	1.76 (1.17–2.64)	0.006	0.03
				−	0.05	0.05	0.72 (0.33–1.59)	N/Ab	0.67 (0.31–1.45)	N/Ab	N/Ab
ESR1	rs1801132	C/G	EA	+	0.24	0.17	1.34 (1.00–1.80)	2.69 (1.38–5.23)	1.46 (1.16–1.85)	0.002	0.01
				−	0.23	0.17	1.25 (0.73–2.14)	2.69 (0.92–7.89)	1.42 (0.84–2.16)	0.10	0.45
			AA	+	0.11	0.11	0.96 (0.68–1.35)	0.85 (0.20–3.68)	0.95 (0.69–1.31)	0.76	1.00
				−	0.12	0.11	0.99 (0.61–1.58)	2.62 (0.61–11.29)	1.11 (0.73–1.69)	0.61	1.00
ESR1	rs2046210	A/G	EA	+	0.41	0.35	1.11 (0.82–1.49)	1.74 (1.14–2.67)	1.26 (1.03–1.55)	0.02	0.09
				−	0.40	0.35	0.82 (0.48–1.42)	1.62 (0.79–3.32)	1.16 (0.80–1.67)	0.44	1.00
			AA	+	0.63	0.64	1.49 (0.96–2.30)	1.08 (0.69–1.70)	0.95 (0.77–1.16)	0.59	1.00
				−	0.64	0.64	0.75 (0.44–1.30)	0.84 (0.49–1.45)	0.96 (0.74–1.25)	0.75	1.00
ESR1	rs3020314	G/A	EA	+	0.36	0.28	1.46 (1.10–1.95)	1.88 (1.18–3.00)	1.40 (1.14–1.72)	0.001	0.005
				−	0.36	0.28	2.01 (1.19–3.39)	1.78 (0.71–4.48)	1.55 (1.07–2.25)	0.02	0.09
			AA	+	0.72	0.72	0.98 (0.57–1.69)	1.02 (0.59–1.74)	1.02 (0.82–1.28)	0.84	1.00
				−	0.71	0.72	0.76 (0.38–1.52)	0.77 (0.39–1.52)	0.93 (0.70–1.25)	0.63	1.00
HSD17B2	rs4445895	A/G	EA	+	0.41	0.41	1.03 (0.76–1.39)	1.00 (0.67–1.50)	1.01 (0.83–1.22)	0.96	1.00
				−	0.29	0.41	0.41 (0.24–0.71)	0.54 (0.26–1.12)	0.62 (0.43–0.90)	0.01	0.05
			AA	+	0.36	0.31	1.23 (0.92–1.66)	1.54 (0.99–2.40)	1.24 (1.01–1.52)	0.04	0.18
				−	0.29	0.31	1.08 (0.74–1.59)	0.71 (0.35–1.47)	0.94 (0.71–1.25)	0.67	1.00
UGT1A9	rs6714486	A/T	EA	+	0.06	0.05	1.35 (0.87–2.1)	N/Ab	1.24 (0.81–1.89)	N/Ab	N/Ab
				−	0.03	0.05	0.47 (0.16–1.41)	N/Ab	0.45 (0.16–1.33)	N/Ab	N/Ab
			AA	+	0.13	0.17	0.70 (0.50–0.98)	0.70 (0.31–1.56)	0.75 (0.57–0.98)	0.04	0.18
				−	0.16	0.17	1.08 (0.71–1.63)	0.14 (0.02–1.14)	0.85 (0.60–1.22)	0.39	1.00

Abbreviations: OR, odds ratio; 95%CI, 95% confidence interval; EA, European American; AA, African American; Code allele/reference allele, the minor allele of each SNP in EA controls is defined as coded allele, whereas the other allele is defined as reference allele; Allele frequency, allele frequencies of the coded alleles; P for trend, p value for linear trend. Detailed information on number of subjects, ORs and 95% CIs for all 49 SNPs analyzed are shown in Supplementary Table 3.

^aAdjusted for age at diagnosis (continuous), education (less than high school, high school, college and graduate school), family history of breast cancer (yes, no), history of benign breast disease (yes, no), menopausal status (premenopausal, postmenopausal), number of full pregnancies (continuous), breast feeding (yes, no, nulliparous), Hormone Replacement Therapy (HRT, yes, no), body mass index (continuous), proportion of European ancestry (continuous) and “estrogen months” (continuous). P values corrected for multiple comparisons using a modified FDR method.

^bOR, 95% CI and corresponding P for trend were not calculated due to the small number of breast cancer cases in the category.

^cP values corrected for multiple testing using a modified FDR method.