A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
Abstract
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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The SNP Consortium built an initial map of 1.4 million SNPs; this has grown to more than 10 million SNPs and is estimated to contain 80% of all SNPs with frequencies of >10%.
“A public-private partnership, the SNP Consortium, built an initial map of 1.4 million SNPs (32); this has grown to more than 10 million SNPs (36) and is estimated to contain 80% of all SNPs with frequencies of >10% (37).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [32]
Humans have limited genetic variation: the heterozygosity rate for single-nucleotide polymorphisms (SNPs) is ~1 in 1000 bases.
“As predicted by classical theory (29), humans have limited genetic variation: The heterozygosity rate for single-nucleotide polymorphisms (SNPs) is ~1 in 1000 bases (30–32).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [32]
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- Authors
- The International SNP Map Working Group, Laboratories:, C. S. H., Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., National Center for Biotechnology Information:, Marth, G., Sherry, S., The Sanger Centre:, Mullikin, J. C., Mortimore, B. J., Willey, D. L., Hunt, S. E., Cole, C. G., Coggill, P. C., Rice, C. M., Ning, Z., Rogers, J., Bentley, D. R., Washington University in St. Louis:, Kwok, P.-Y., Mardis, E. R., Yeh, R. T., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R. H., McPherson, J. D., Whitehead/MIT Center for Genome Research:, Gilman, B., Schaffner, S., Van Etten, W. J., Reich, D., Higgins, J., Daly, M. J., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M. C., Linton, L., Lander, E. S., & Altshuler, D.
- Affiliations
- Wellcome Trust (GB)
- Massachusetts Institute of Technology (US)
- Massachusetts General Hospital (US)
- Harvard University (US)
- Corresponding author
- Bentley, David R.
- Altshuler, David
- ORCID
- Venue
- Nature
- Published
- 2001-02-15
- Volume
- 409
- Issue
- 6822
- Pages
- 928-933
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2061008984
- Cited by
- 2,977
- References
- 46
- Citations by year
- 2026: 23 · 2025: 37 · 2024: 39 · 2023: 51 · 2022: 55 · 2021: 58 · 2020: 64 · 2019: 70 · 2018: 77 · 2017: 79 · 2016: 92 · 2015: 81 · 2014: 112 · 2013: 99 · 2012: 109
- FWCI
- 155.07
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- single nucleotide polymorphisms, SNP map, exon coverage, nucleotide diversity, haplotype variation, population genetic models
- MeSH terms
- Chromosome Mapping, Genetics, Medical, Genetics, Population, Humans, Nucleotides, Genetic Variation, Genome, Human, Polymorphism, Single Nucleotide
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