Table 6.

CFH haplotype analysis using a substracting approach

Number of SNPs	SNPs in best model	Haplotypes	Case Freq	Control Freq	Chi square	P-value	OR (95 % IC)
	Protective Haplotypes
7	rs3766404 rs1329421 rs1831282 rs12144939 rs2284664 rs1329428 rs1065489	CAGTGAG	0.091	0.186	24215.00	8.61×10−07	0.44 (0.57 – 0.33)
		TAGGAAG	0.100	0.164	11208.00	8×10−04	0.57 (0.74 – 0.43)
		TAGTGAG	0.030	0.070	10.89	0.001	0.41 (0.63 – 0.26)
6	rs1329421 rs1831282 rs12144939 rs2284664 rs1329428 rs1065489	AGTGAG	0.121	0.254	37.17	1.08×10−09	0.4 (0.51 – 0.32)
		AGGAAG	0.101	0.162	10.42	0.0012	0.58 (0.76 – 0.45)
5	rs1329421 rs1831282 rs2284664 rs1329428 rs1065489	AGGAG	0.121	0.257	39.00	4.31×10−10	0.39 (0.5 – 0.31)
		AGAAG	0.101	0.162	10.43	0.0012	0.58 (0.75 – 0.44)
4	rs1329421 rs1831282 rs1329428 rs1065489	AGAG	0.222	0.419	56.84	4.74×10−14	0.39 (0.48 – 0.32)
3	rs1329421 rs1831282 rs1065489	AGG	0.225	0.421	56.04	7.10×10−14	0.4 (0.48 –0.33)
2	rs1831282 rs1065489	GG	0.225	0.420	55.12	1.13×10−13	0.4 (0.49–0.33)
	Risk Haplotypes
7	rs3766404 rs1329421 rs1831282 rs12144939 rs2284664 rs1329428 rs1065489	TTTGGGG	0.512	0.345	35165.00	3.03×10−09	1.99 (2.38 – 1.66)
6	rs3766404 rs1329421 rs1831282 rs12144939 rs2284664 rs1329428	TTTGGG	0.517	0.345	37.01	1.17×10−09	2.03 (2.43 – 1.70)
5	rs3766404 rs1329421 rs1831282 rs2284664 rs1329428	TTTGG	0.517	0.343	38.26	6.18×10−10	2.05 (2.45 -1.71)
4	rs3766404 rs1329421 rs2284664 rs1329428	TTGG	0.516	0.343	38.13	6.61×10−10	2.04 (2.45-1.71)
3	rs3766404 rs2284664 rs1329428	TGG	0.771	0.581	52.61	4.07×10−13	2.43 (2.95 – 2)
2	rs2284664 rs1329428	GG	0.773	0.581	53.73	2.31×10−09	2.45 (2.98 – 2.02)

OR= Odds ratios