Pair-wise LD was measured by r2 for all SNPs less than 100 kb apart using the Haploview software [31]. A custom Perl script was used to categorize r2 according to inter-marker distance (0–5 kb, 5–10 kb etc.) and mean r2 was calculated for each category. The significance of the mean r2 values between cohorts was tested with the one-tailed t-test and p-value≤0.05 was considered as statistically significant.
