Breast Cancer Research

Table 3 Predicted haplotypes from the tagging SNPs for each gene and their association with breast cancer

From: Common variants in the ATM, BRCA1, BRCA2, CHEK2 and TP53 cancer susceptibility genes are unlikely to increase breast cancer risk

	Set 1					Sets 1 and 2
Gene	Haplotype	Frequency	P value	OR	95 percent CI	Haplotype	Frequency	P value	OR	95 percent CI
*ATM*
04,05,06,07,08,09,10,11,12	h010100100	0.30	0.2
	h000001000	0.28	0.7
	h000010000	0.14	0.05	0.9	0.78–0.99
	h100000000	0.09	0.6
	h010100101	0.07	0.9
	h010100110	0.05	0.2
	Combined rare		0.4
*BRCA1*
02,01,05,07,06	h00000	0.60	0.7
	h01101	0.14	0.3
	h01000	0.09	0.2
	h01011	0.09	0.2
	h10000	0.06	0.08	0.9	0.71–1.02
	Combined rare		0.5
*BRCA2*
Block 1: 01,02,03,04,05	h10000	0.42	0.6			h_0_00	0.42	0.5
	h01000	0.17	0.007	1.2	0.78–0.98	h_1_00	0.17	0.2
	h01010	0.17	0.02	0.9	0.78–0.98	h_1_10	0.17	0.3
	h00101	0.15	0.8			h_0_01	0.18	0.3
	Combined rare		0.4
Block 2: 07,09,10,22,11	h01010	0.27	0.8			h_1_10	0.27	0.9
	h01000	0.19	0.05	0.9	0.80–1.00	h_1_00	0.20	0.4
	h00100	0.18	0.9
	h10000	0.17	0.8			h_0_00	0.40	0.6
	h10001	0.07	0.07	1.2	0.99–1.37	h_0_01	0.11	0.2
	h00000	0.05	0.7
	Combined rare		0.4
Block 3: 13,14,16,18,19,21	h000010	0.27	0.6			h0____0	0.57	0.9
	h000001	0.21	0.1	0.9	0.83–1.02	h0____1	0.22	0.5
	h100000	0.15	0.04	1.1	1.01–1.27	h1____0	0.21	0.5
	h010000	0.15	0.2
	h011000	0.12	0.4
	h100100	0.06	0.1	1.2	0.98–1.35
	Combined rare		0.8
*CHEK2*
10,11,6,7,5,8,12,13,14,9	h0000000000	0.23	0.3			h_0______00	0.54	0.02	0.9	0.88–0.99
	h1000111000	0.20	0.5
	h0000000011	0.13	0.2			h_0______11	0.13	0.07	1.1	0.99–1.18
	h0111000010	0.07	0.08	0.9	0.74–1.02	h_1______10	0.07	0.1	0.9	0.81–1.02
	h0000111000	0.07	0.8
	h0011000010	0.06	0.6			h_0______10	0.25	0.06	1.1	0.99–1.15
	h0010000110	0.06	0.2
	h0000100010	0.04	0.05	1.3	1.00–1.56
	Combined rare		0.5			h_0______10 delC	0.004	0.003	2.7	1.40–5.05
*TP53*
03,01,02,06,07,08	h000000	0.42	0.8
	h000001	0.28	0.9
	h011000	0.11	0.3
	h001001	0.05	0.2
	Combined rare		0.4

All haplotypes with predicted frequencies of >0.05 in controls are shown individually. Rarer ones are combined. The single nucleotide polymorphism (SNP) IDs and their order are shown in the first column. CI, confidence interval; OR, odds ratio.

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