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A haplotype map of the human genome
Open accessAbstract
Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.
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“Haplotype blocks vary somewhat among human populations — they tend to be somewhat shorter in African populations15,20,21.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [20]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The frequency of the Asn (risk) allele varies considerably among populations (0%-60%) (10,14).”
From The N342S MYLIP polymorphism is associated with high total cholesterol and increased LDL receptor degradation in humans (2011) · cites this paper as [10]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“which in its first generation identified over 1 million SNPs in humans and characterized the LD in 269 individuals in four ethnically different populations (European, Han Chinese, Japanese and Yoruban)20.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [20]
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“As patterns of linkage disequilibrium (LD) vary among populations with different demographic histories (10), studies in a different population than the discovery population, such as Mexican subjects, can assist in fine-mapping the actual susceptibility variants (i.e., trans-ethnic fine-mapping).”
From The N342S MYLIP polymorphism is associated with high total cholesterol and increased LDL receptor degradation in humans (2011) · cites this paper as [10]
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“As patterns of linkage disequilibrium (LD) vary among populations with different demographic histories (10), studies in a different population than the discovery population, such as Mexican subjects, can assist in fine-mapping the actual susceptibility variants (i.e., trans-ethnic fine-mapping).”
From The N342S MYLIP polymorphism is associated with high total cholesterol and increased LDL receptor degradation in humans (2011) · cites this paper as [10]
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“These validated the HLA association but showed no significant linkage to loci outside the MHC.”
From Genome‐wide association studies of multiple sclerosis (2018) · cites this paper as [25]
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In the citing paper
“Accordingly, the pairwise LD and the allele frequency of N342S are significantly different between European and Mexican populations (10).”
From The N342S MYLIP polymorphism is associated with high total cholesterol and increased LDL receptor degradation in humans (2011) · cites this paper as [10]
Experimental — accuracy not yet measuredIn the citing paper
“On the basis of International HapMap data for the CEU sample (Utah residents with ancestry from northern and western Europe), 29 these two SNPs are in modest linkage disequilibrium with one another ( ).Al-2 R p 0.35”
From A Genomewide Association Study of Skin Pigmentation in a South Asian Population (2007) · cites this paper as [29]
In the citing paper
“All three of the SNPs are essentially monomorphic in African and East Asian populations and thus are unlikely to contribute significantly to skin-pigmentation variation within those groups.13,25,29,30”
From A Genomewide Association Study of Skin Pigmentation in a South Asian Population (2007) · cites this paper as [29]
In the citing paper
“Using data from the human HapMap project (8), they observed that the alternate alleles of the nsSNP (rs1426654) in human SLC24A5 were present at very different frequencies in populations of African and European ancestry.”
From SLC24A5 encodes a trans-Golgi network protein with potassium-dependent sodium-calcium exchange activity that regulates human epidermal melanogenesis (2008) · cites this paper as [8]
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Metadata
- Authors
- The International HapMap Consortium
- Corresponding author
- The International HapMap Consortium
- Venue
- Nature
- Published
- 2005-10
- Volume
- 437
- Issue
- 7063
- Pages
- 1299-1320
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC1880871
- OpenAlex
- W2217809488
- Cited by
- 5,858
- References
- 105
- Citations by year
- 2026: 41 · 2025: 53 · 2024: 67 · 2023: 83 · 2022: 80 · 2021: 150 · 2020: 123 · 2019: 166 · 2018: 148 · 2017: 144 · 2016: 175 · 2015: 223 · 2014: 245 · 2013: 238 · 2012: 360
- FWCI
- 369.10
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion, public-domain)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Leicester Research Archive (University of Leicester) (submittedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- Funders
- W. M. Keck Foundation
- Genome Canada
- Wellcome Trust
- University of Oxford
- National Natural Science Foundation of China
- University Grants Committee
- Chinese Academy of Sciences
- Beijing Normal University
- Ministry of Science and Technology of the People's Republic of China
- Innovation and Technology Commission
- National Institutes of Health
- University of California, San Francisco
- Engineering and Physical Sciences Research Council
- RIKEN
- National Institute on Alcohol Abuse and Alcoholism
- National Institute on Aging
- National Institute of Mental Health
- National Institute on Drug Abuse
- National Human Genome Research Institute (R01HG001720)
- National Eye Institute
- National Cancer Institute
- National Institute on Deafness and Other Communication Disorders
- National Institute of General Medical Sciences
- National Institute of Allergy and Infectious Diseases
- National Institute of Diabetes and Digestive and Kidney Diseases
- National Institute of Neurological Disorders and Stroke
- National Institute of Environmental Health Sciences
- National Institute of Arthritis and Musculoskeletal and Skin Diseases
- National Institute of Biomedical Imaging and Bioengineering
- National Institute of Dental and Craniofacial Research
- National Center for Research Resources
- 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 › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- HapMap, single nucleotide polymorphisms, common genetic variants, linkage disequilibrium, recombination hotspots, haplotype diversity, genetic association studies, structural variants, natural selection, human evolution, population genomics
- MeSH terms
- DNA, Mitochondrial, Gene Frequency, Haplotypes, Humans, Recombination, Genetic, Selection, Genetic, Linkage Disequilibrium, Genome, Human, Polymorphism, Single Nucleotide, Chromosomes, Human, Y
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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