Table 2.

Breast Cancer Risk in Europeans by Haplotypes of Five iCHAV Representative SNPs

	Haplotypea
	h0	h1	h2	h3	h4	h5	h6
iCHAV1b	1	1	1	1	1	2	2
iCHAV2ac	1	1	1	2	2	1	2
iCHAV2bd	1	1	1	1	1	2	1
iCHAV2ce	1	2	1	1	2	1	2
iCHAV3f	1	1	2	1	1	1	1
Frequency	0.52	0.12	0.15	0.02	0.01	0.11	0.05
Overall Breast Cancer Risk
OR	–	1.01	0.95	1.08	1.05	1.16	1.31
95% CI	–	0.99–1.05	0.92–0.97	0.99–1.17	0.99–1.17	1.12–1.20	1.25–1.37
p value	–	4.50 × 10−1	2.08 × 10−4	7.57 × 10−2	3.81 × 10−1	2.00 × 10−20	1.66 × 10−29
ER+Breast Cancer Risk
OR	–	1.03	0.95	1.13	0.99	1.19	1.34
95% CI	–	0.99–1.07	0.92–0.99	1.02–1.24	0.87–1.13	1.14–1.23	1.27–1.42
p value	–	1.12 × 10−1	5.23 × 10−3	1.68 × 10−2	8.75 × 10−1	9.37 × 10−20	3.74 × 10−27
ER−Breast Cancer Risk
OR	–	1.04	1.04	1.08	1.17	1.1	1.15
95% CI	–	0.98–1.11	0.98–1.10	0.92–1.27	0.96–1.42	1.04–1.18	1.05–1.25
p value	–	2.08 × 10−1	1.67 × 10−1	3.45 × 10−1	1.12 × 10−1	1.82 × 10−3	3.64 × 10−3

1 represents major alleles, and 2 represents minor alleles in each SNP.

^ah₁–h₆ are compared to h₀ (the reference haplotype carrying the major alleles of all five SNPs).

^biCHAV1 represents 15 SNPs, of which rs62355902 is the best candidate.

^ciCHAV2a represents 90 SNPs that have r² ≥ 0.53 with rs113317823 and r² = 0.19–0.29 with rs62355902. rs113317823 is the best candidate.

^diCHAV2b represents 66 SNPs that have r² ≤ 0.01 with rs113317823 and r² = 0.59–0.62 with rs62355902; rs62355899 is the best candidate.

^eiCHAV2c represents 17 SNPs that have r² = 0.14–0.16 with rs113317823 and r² ≤ 0.01 with rs6235590; rs7721581 is the best candidate.

^fiCHAV3 represents five SNPs, of which rs11949391 is the best candidate.