A haplotype map of the human genome

The International HapMap Consortium

doi:10.1038/nature04226

Cited by 5,858Genetic Associations and EpidemiologyForensic and Genetic ResearchGenetic Mapping and Diversity in Plants and Animals

A haplotype map of the human genome

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The International HapMap Consortium·2005·Nature

DOI 10.1038/nature04226PMC PMC1880871

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Abstract

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 tend to be somewhat shorter in African populations.
“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]
In the discussion of haplotype blocks in the ENCODE regions (page unavailable), the paper reports that 67% of sequence in the Yoruba (YRI) panel falls in blocks of four or more SNPs, versus 87% in the CEU panel. This supports a population difference in block structure, but the available passage does not establish that the blocks themselves are shorter; the study also cautions that its Yoruba sample does not represent all African populations. (LLM, conf=0.72)
Experimental — accuracy not yet measured
The frequency of the Asn (risk) allele varies considerably among populations (0%-60%).
“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]
The section ‘Allele frequency distributions within population samples’ reports differences in allele-frequency patterns among the population panels, supporting the general point that frequencies vary. It does not identify an Asn risk allele or give a 0%–60% frequency range for that allele (searched: Asn, risk allele, and 0%–60%). (LLM, conf=0.77)
Experimental — accuracy not yet measured
The first generation HapMap identified over 1 million SNPs in humans and characterized LD in 269 individuals from four ethnically different populations.
“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]
Studies in a different population than the discovery population, such as Mexican subjects, can assist in fine-mapping the actual susceptibility variants.
“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]
Patterns of linkage disequilibrium vary among populations with different demographic histories.
“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]

Linkage analyses in extended multiple sclerosis affected families validated the HLA association but showed no significant linkage to loci outside the MHC.
“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]
The Abstract lists HLA as a validated example in autoimmunity generally, but does not discuss multiple sclerosis affected families or their linkage results. Searches for multiple sclerosis linkage and linkage outside the MHC found no passage addressing whether those families showed significant linkage at other loci. (LLM, conf=0.76)
Experimental — accuracy not yet measured
The pairwise LD and the allele frequency of N342S are significantly different between European and Mexican populations.
“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]
The paper discusses pairwise linkage disequilibrium and allele-frequency differences among its analysis panels (sections on LD properties and population differentiation; page unavailable). Searches for N342S and for a European–Mexican comparison found no passage reporting the claimed differences or their statistical significance. (LLM, conf=0.76)
Experimental — accuracy not yet measured
Based on International HapMap data for the CEU sample, rs1800404 and rs1037208 are in modest linkage disequilibrium (R^2=0.35).
“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]
All three SNPs are essentially monomorphic in African and East Asian populations and thus are unlikely to contribute significantly to skin-pigmentation variation within those groups.
“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]
The alternate alleles of rs1426654 in human SLC24A5 are present at very different frequencies in populations of African and European ancestry.
“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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Research works printed but not linked: 3

Lechler, R. & Warrens, A. HLA in Health and Disease 2nd edn (Academic Press, San Diego, California, 2005).
McCarroll, S. et al. Common deletion variants in the human genome. Nature Genet. (in the press).
Lincoln D. Stein (Principal Investigator) 23 , Lalitha Krishnan 23 , Albert Vernon Smith 23 , Gudmundur A. Thorisson 23 ; Johns Hopkins University School of Medicine Aravinda Chakravarti (Principal Investigator) 24 , Peter E. Chen 24 , David J. Cutler 24 , Carl S. Kashuk 24 , Shin Lin 24 ; University of Michigan Gonc ¸alo R. Abecasis (Principal Investigator) 25 , Weihua Guan 25 , Heather M. Munro 25 , Zhaohui Steve Qin 25 , Daryl J. Thomas 26 ; University of Oxford Gilean McVean (Project Leader) 27 , Leonardo Bottolo 27 , Susana Eyheramendy 27 , Colin Freeman 27 , Jonathan Marchini 27 , Simon Myers 27 , Chris Spencer 27 , Matthew Stephens 28 , Peter Donnelly (Principal Investigator) 27 ; University of Oxford, Wellcome Trust Centre for Human Genetics Lon R. Cardon (Principal Investigator) 29 , Geraldine Clarke 29 , David M. Evans 29 , Andrew P. Morris 29 , Bruce S. Weir 30 ; RIKEN Tatsuhiko Tsunoda 20 ; US National Institutes of Health James C. Mullikin 31 , Stephen T. Sherry 32 , Michael Feolo 32 Community engagement/public consultation and sample collection groups: Beijing Normal University and Beijing Genomics Institute Houcan Zhang 33 , Changqing Zeng 3 , Hui Zhao 3 ; Health Sciences University of Hokkaido, Eubios Ethics Institute, and Shinshu University

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Authors: The International HapMap Consortium
Corresponding author: The International HapMap Consortium
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2005-10
Volume: 437
Issue: 7063
Pages: 1299-1320
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature04226
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

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A haplotype map of the human genome

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