To study how differences in LD patterns compare with the genome-wide average, we focused on the region immediately adjacent to the marker SNPs. For a window of 50 SNPs around the marker, we compared differences between Europeans and East Asians in LD patterns around replicated and non-replicated SNPs to genome-wide average differences for random SNPs. We used the permutation method included in varLD to assign an empirical p-value to the observed differences in LD for each analyzed window (see Materials and Methods). We considered three different sets of 50-SNP windows centered on each of the (i) 47 replicated SNPs, (ii) 64 non-replicated SNPs, and (iii) 100 groups of 47 SNPs randomly selected from across the genome. Because the two populations differ in their LD patterns, we observed a trend towards significant differences in LD (empirical P<0.05) for the three datasets. However, the proportion of significant windows was larger for non-replicated (78%) than for replicated (62%) and random genomic SNPs (66%). Figure 4 shows the cumulative distributions of empirical p-values for the three groups of SNPs. The cumulative distribution of p-values
