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Several Studies of substitution rate variation have indicated that the local mutation rate varies over the mammalian genome. In the present study, we show significant variation in substitution rates within the noncoding part of the human genome using 4.7 Mb of human-chimpanzee pairwise comparisons. Moreover, we rind a significant positive covariation of lineage-specific chimpanzee and human local Substitution rates, arid very similar mean substitution rates down the two lineages. The substitution rate variation is probably not Caused by selection or biased gene conversion, and so we conclude that mutation rates vary deterministically across the noncoding nonrepetitive regions of the human genome. We also show that noncoding substitution rates are significantly affected by G+C base composition, partly because the base composition is riot at equilibrium.