Analogous patterns were observed when comparing the differences in LD. To assess differences in LD between populations, we computed the varLD score [31] in the same 50-SNP sliding windows we used for heterozygosity. As predicted, differences in LD were significantly larger for the windows centered in non-replicated than in replicated SNPs (varLD = 17.64 vs. 12.66, P<0.002). Indeed, varLD differences are only significant in the immediate vicinity of the associated SNP and they quickly cancel out as the distance for the associated allele increases (Figure 3 and Table S9). We obtained the same result when using only attempts with ≥80% statistical power and contrasting 39 replicated versus 14 non-replicated SNPs (varLD = 20.42 vs. 12.49, P = 0.045).
