The program Haploview (v4.2) was used to delineate haplotype blocks (Barrett et al., 2005). Haploview calculates linkage disequilibrium (D′ or r2) between each pair of SNPs. We used the method of confidence intervals to assign haplotype blocks (Gabriel et al., 2002). For SNPs within the same haplotypic block, haplotypes were reconstructed using the program PHASE2 (Stephens et al., 2001), which employs an iterative stochastic-sampling strategy and the pseudo-Gibbs sampler for assignment of haplotype phases. Based on the haplotype frequency estimation, we assumed a dominant genetic model in Haplotype association analysis. The tests were two sided with a 0.05 significance level.
