The increased number of well-defined hotspots allows us to understand better the influence of genomic features on the distribution of recombination. Previous work identified specific DNA motifs that influence hotspot location6,37 as well as additional influences of local sequence context including the location of genes6 and base composition38. The Phase II HapMap provides the resolution to separate these influences. Figure 5a shows the distribution of recombination, hotspot motifs and base composition around genes. Within the transcribed region of genes there is a marked decrease in the estimated recombination rate. However, 5′ of the transcription start site is a peak in recombination rate with a corresponding local increase in the density of hotspot motifs. This region also shows a marked increase in G+C content, reflecting the presence of CpG islands in promoter regions. There is also an asymmetry in recombination rate across genes, with recombination rates 3′ of transcribed regions being elevated (as are motif density and G+C content) compared to regions 5′ of genes. Studies in yeast have previously suggested an association between promoter regions and recombination hotspots39. Our results
