Table 2.

Results of stepwise haplotype association analysis

		SNPs			ΔLRT	P
rs2274700					135.42	<0.0001
rs2274700	rs1280514				53.27	<0.0001
rs2274700	rs1280514	rs412852			30.66	<0.0001
rs2274700	rs1280514	rs412852	rs11582939		96.81	<0.0001
rs2274700	rs1280514	rs412852	rs11582939	rs1048663	19.22	0.0104

Empirical P value was adjusted for multiple testing and was assessed using 10,000 permutations. A permutated sample was obtained by permuting disease affection status among affected individuals and controls while preserving evidence for association among SNPs selected in the previous step. Specifically, at each step, we grouped individuals according to genotype patterns at previously selected SNPs, and then permuted the disease affection status within each group of individuals with the same genotype pattern. Haplotype association was evaluated using a likelihood ratio test to compare haplotype frequencies between cases and controls. The likelihood ratio statistic was calculated with FUGUE-CC²⁸. ΔLRT, difference in the likelihood ratio statistic between the current step and the previous step.