Regional similarities in polymorphism in the human genome extend over many megabases

The human genome exhibits extensive regional variation both in base composition and in the synonymous and nonsynonymous substitution rates of protein-coding genes. If such regional variation is due to variation in mutation rates, then levels of polymorphism should also vary across the human genome. Building on recent advances in mapping the human genome, we demonstrate regional variation in single nucleotide polymorphism density extending over many megabases. The range of local similarity in polymorphism shown by our genome-wide study is similar to the range of local similarity in base composition, and occurs over much longer distances than the variation in polymorphism revealed by studies of linkage disequilibrium.