LD plots were drawn using the R package “snp.plotter” (Luna et al., 2007) for the unrelated controls. We used r2 as the measure of LD strength. The haplotype association test was performed by WHAP (Purcell et al., 2007). WHAP calculates likelihood estimates, likelihood ratios and P-values, and takes into account the loss of information due to haplotype phase uncertainty and missing genotypes. To disentangle the correlation structure in the highly correlated regions, conditional haplotype analysis was performed using WHAP. To test the hypothesis that all significant associations surrounding a particular assumed “causal” SNP reflected the high correlation between each candidate SNP and the “causal” SNP, we performed a two-SNP haplotype analysis pairing the “causal” SNP with every other SNP one at a time and conditional on that SNP. Disappearance of the global haplotype association was interpreted to mean that the conditional SNP explained the entire association.
