A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms


We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

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Figure 1: Distribution of SNP coverage across intervals of finished sequence.
Figure 2: Distribution of heterozygosity.


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The SNP Consortium, the Wellcome Trust and the National Human Genome Research Institute funded SNP discovery and data management at Cold Spring Harbor Laboratories, The Sanger Centre, Washington University in St. Louis, and the Whitehead/MIT Center for Genome Research. Work in P.Y.K.'s laboratory is supported in part by grants from the SNP Consortium and the National Human Genome Research Institute. P.Y.K. thanks Q. Li, M. Minton, R. Donaldson and S. Duan for technical assistance. D.M.A. was supported during a phase of this work under a Postdoctoral Fellowship for Physicians from the Howard Hughes Medical Institute. For full list of contributors to TSC programme, see http://www.snp.cshl.org.

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Correspondence to David R. Bentley or David Altshuler.

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