Recombination hotspots disrupt linkage disequilibrium

(top) Diagram of the distribution of SNPs and haplotypes for a chromosomal segment from 18 individuals. Haplotypes often occur in blocks (regions of lower recombination) separated from one another by recombination hotspots (different colors indicate haplotype blocks). (The column of S’s and D’s at the right are for Problem 19-4.) SNP8 (bold) controls a difference in trait values. (bottom) You can tell whether two SNPs show disequilibrium by noting the color of the square where the rows for the markers intersect. Within a haplotype block, SNPs show strong disequilibrium. SNPs in different haplotype blocks show weak or no disequilibrium.

[Data from David Altsftuler et al., Science 322, 2008, 881–888.]