ArticleNature2007
A second generation human haplotype map of over 3.1 million SNPs.
Article in Nature, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,459 papers, 5 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2,459 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- A contextual genomic perspective on physical activity and its relationship to health, well being and illness.Nature genetics · 2025Pooled it
- Potential Causal Association between Plasma Metabolites, Immunophenotypes, and Female Reproductive Disorders: A Two-Sample Mendelian Randomization Analysis.Biomolecules · 2024Pooled it
- East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease.Nature genetics · 2023Pooled it
- Cannabis use and the risk of primary open-angle glaucoma: a Mendelian randomization study.Scientific reports · 2023Pooled it
- A genome-wide association study for rheumatoid arthritis replicates previous HLA and non-HLA associations in a cohort from South Africa.Human molecular genetics · 2022Pooled it
- Allelic gene conversion softens selective sweeps.Genetics · 2026Article
- Western Hunter-Gatherer genetic ancestry contributes to human longevity in the Italian population.GeroScience · 2026Article
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- Reclaiming Data, Restoring Health: The Indigenous Biomedical Data Science Renaissance.Annual review of biomedical data science · 2026Review
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- Layers in the sand: The genetic imprint of migration, culture, and Indus craft in the Thar Desert.HGG advances · 2026Article
- Limited Selection on Neanderthal DNA in 30,780 Recently Admixed Genomes with African-like Ancestry.Molecular biology and evolution · 2026Article
- A transparent and generalizable deep-learning framework for genomic ancestry prediction.American journal of human genetics · 2026Article
- Inferring fine-scale rates of mutation and recombination in the coppery titi monkey (Plecturocebus cupreus).Heredity · 2026Article
- Popformer: Learning general signatures of positive selection with a self-supervised transformer.PLoS computational biology · 2026Article
- Understanding the effect of educational attainment on the risk of retinal detachment: a Mendelian randomization mediation analysis.International journal of retina and vitreous · 2026Article
- Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania.Science (New York, N.Y.) · 2026Article
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- Polygenic and single-locus selection on BMI during Polynesian expansion.Journal of human genetics · 2026Article
2,399 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
251 authors.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.