A second generation human haplotype map of over 3.1 million SNPs
Open accessAbstract
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.
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The fine-scale pattern of LD in humans confirms that the human genome is comprised of haplotype blocks within which most or all SNPs are in high LD.
“The fine-scale pattern of LD in humans confirms that the human genome is comprised of haplotype blocks within which most or all SNPs are in high LD21.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [21]
In “New insights into linkage disequilibrium structure” (page unavailable), the paper describes short stretches of strong LD, or haplotype blocks, but explicitly calls this a simplified view. It does not confirm that the genome is uniformly organized into such blocks or that most or all SNPs within them are in high LD; it also reports SNPs with almost no LD with other SNPs. (LLM, conf=0.87)
Experimental — accuracy not yet measuredThe second generation HapMap characterized 3.1 million SNPs in the same group of individuals.
“The second generation HapMap published recently characterized 3.1 million SNPs in the same group of individuals21.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [21]
The number of inferred ancestral recombination events per genomic window agrees with a previously published population recombination map (Spearman's rho = 0.46; P < 2.2 × 10−16).
“that the number of inferred ancestral recombination events per genomic window agrees with a previously published population recombination map (17) (fig. S20B; Spearman’s rho = 0.46; P < 2.2 × 10−16), as expected.”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [17]
Tag SNP allele frequencies in the samples mirrored previously described distributions in major geographic groups.
“As expected, the tag SNP allele frequencies in our samples mirrored previously described distributions in major geographic groups (Lamason et al. 2005;Yuasa et al. 2006;Frazer et al. 2007;Miller et al. 2007;Norton et al. 2007;Soejima and Koda 2007) (table 1).”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Frazer et al. 2007
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 [21]
The section on recent common ancestry and segmental sharing describes haplotype blocks and mentions population differences in linkage-disequilibrium patterns, but gives no comparison of block lengths between African and non-African populations. Searches for shorter blocks in African populations and for YRI–non-African comparisons found no passage establishing the claimed direction. (LLM, conf=0.72)
Experimental — accuracy not yet measured
Previous studies using several population samples from different continents have shown that, unlike SLC45A2, derived alleles at SLC24A5, TYRP1, and KITLG are present at low frequencies in some sub-Saharan populations.
“Previous studies using several population samples from different continents have shown that, unlike SLC45A2, derived alleles at SLC24A5, TYRP1, and KITLG are present at low frequencies in some sub-Saharan populations (table 1, see also Yuasa et al. 2006;Frazer et al. 2007;Norton et al. 2007;Soejima and Koda 2007;Coop et al. 2009;Pickrell et al. 2009).”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Frazer et al. 2007
The Natural selection section discusses derived-allele frequencies across SNPs generally, and the Advances made possible by the Phase I haplotype map section identifies geographically diverse samples. Neither reports low-frequency derived alleles at SLC24A5, TYRP1, or KITLG in sub-Saharan populations or contrasts them with SLC45A2 (searched those gene names and pigmentation-related allele frequencies). (LLM, conf=0.72)
Experimental — accuracy not yet measured
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- Authors
- The International HapMap Consortium
- Venue
- Nature
- Published
- 2007-10
- Volume
- 449
- Issue
- 7164
- Pages
- 851-861
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2689609
- OpenAlex
- W2119279196
- Cited by
- 4,438
- References
- 59
- Citations by year
- 2026: 53 · 2025: 67 · 2024: 77 · 2023: 71 · 2022: 114 · 2021: 129 · 2020: 111 · 2019: 133 · 2018: 150 · 2017: 153 · 2016: 162 · 2015: 232 · 2014: 275 · 2013: 317 · 2012: 412
- FWCI
- 270.06
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Deep Blue (University of Michigan) (submittedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Leicester Research Archive (University of Leicester) (submittedVersion)
- Funders
- W. M. Keck Foundation
- Genome Canada
- Wellcome Trust (081682, 077011, 077008, 077046)
- Ministry of Education, Culture, Sports, Science and Technology
- 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
- Engineering and Physical Sciences Research Council
- 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
- 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
- single nucleotide polymorphisms, linkage disequilibrium, SNP genotyping, imputation, recombination hotspots, recombination rate, genetic differentiation, natural selection, non-synonymous SNPs, genetic ancestry, genome-wide association study, Lassa virus, skin pigmentation, hair follicle development
- MeSH terms
- Female, Haplotypes, Homozygote, Humans, Male, Recombination, Genetic, Selection, Genetic, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Racial Groups
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.
What counts as a claim ›How we measure confidence ›How we check this ›
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