*2.5. Linkage Disequilibrium (LD) Analysis*

We performed linkage disequilibrium analysis for all possible pairs of SNPs with a minor allele frequency (MAF) greater than 0.01 in a dataset. To determine the degree of resolution achieved in the association analysis, both the genome and chromosome-wide LDs were estimated [56].

LD blocks were viewed using Haploview4.2, which uses permutation tests to determine the *p*-values for each pairwise correlation. The LD decay was calculated with PopLDdecay [57,58]. The physical distance of the LD decay plot was determined based on the *D'* values and distances between each pair of SNPs on each chromosome using a nonlinear model [59].

The standard descriptive LD parameter D' was estimated as previously described by [60,61]. The average D' value was calculated for each chromosome using Haploview software [60].
