The initial HapMap Project data had a central role in the development of methods for the design and analysis of genome-wide association studies. These advances, alongside the release of commercial platforms for performing economically viable genome-wide genotyping, have led to a new phase in human medical genetics. Already, large-scale studies have identified novel loci involved in multiple complex diseases4,5. In addition, the HapMap data have led to novel insights into the distribution and causes of recombination hotspots3,6, the prevalence of structural variation7,8 and the identity of genes that have experienced recent adaptive evolution3,9. Because the HapMap cell lines are publicly available, many groups have been able to integrate their own experimental data with the genome-wide SNP data to gain new insight into copy-number variation10, the relationship between classical human leukocyte antigen (HLA) types and SNP variation11, and heritable influences on gene expression12-14. The ability to combine genome-wide data on such diverse aspects of genetic variation with molecular phenotypes collected in the same samples provides a powerful framework to study the connection of DNA sequence to function.
