Composite plot of linkage disequilibrium as a function of distance. Two measures of linkage disequilibrium, absolute value of D' (A) and r2 (B) are shown as a function of distance for all loci examined. LD values between all pairs of SNP were plotted. Logarithmic trend line is included in plot (B). Of the 344 pairwise comparisons, 161 were significant at P < 0.01, with Bonferroni correction, and 126 were significant at P < 0.001 level.