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The Haplotype Reference Consortium

The Haplotype Reference Consortium (HRC) will create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts. By combining together multiple cohorts, the reference panels produced by the project will be as large as possible in terms of both number of haplotypes, and numbers of variants. This will increase the accuracy of the genotype imputation, especially at low-frequency variants, and the number of imputable variants, thus increasing the power of GWAS.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001002729 11227
Publications Citations
A reference panel of 64,976 haplotypes for genotype imputation.
Nat Genet 48: 2016 1279-1283
Comparison of phasing strategies for whole human genomes.
PLoS Genet 14: 2018 e1007308
A One-Penny Imputed Genome from Next-Generation Reference Panels.
Am J Hum Genet 103: 2018 338-348
Detecting the dominance component of heritability in isolated and outbred human populations.
Sci Rep 8: 2018 18048
Sequencing and imputation in GWAS: Cost-effective strategies to increase power and genomic coverage across diverse populations.
Genet Epidemiol 44: 2020 537-549
A genotype imputation method for de-identified haplotype reference information by using recurrent neural network.
PLoS Comput Biol 16: 2020 e1008207
Genotype imputation using the Positional Burrows Wheeler Transform.
PLoS Genet 16: 2020 e1009049
Genome-wide association study of Alzheimer's disease CSF biomarkers in the EMIF-AD Multimodal Biomarker Discovery dataset.
Transl Psychiatry 10: 2020 403
A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility.
Cancer Res 81: 2021 1695-1703
Generalized Structured Component Analysis in candidate gene association studies: applications and limitations.
Wellcome Open Res 4: 2019 142
Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries.
Nat Commun 12: 2021 1258
The impact of non-additive genetic associations on age-related complex diseases.
Nat Commun 12: 2021 2436
Identifying genetic modifiers of age-associated penetrance in X-linked dystonia-parkinsonism.
Nat Commun 12: 2021 3216
Rapid genotype imputation from sequence with reference panels.
Nat Genet 53: 2021 1104-1111
A fast Data-Driven method for genotype imputation, phasing, and local ancestry inference: MendelImpute.jl.
Bioinformatics 37: 2021 4756-4763
Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability.
Genes (Basel) 12: 2021 1228
Privacy-preserving genotype imputation in a trusted execution environment.
Cell Syst 12: 2021 983-993.e7
Validity and Prognostic Value of a Polygenic Risk Score for Parkinson's Disease.
Genes (Basel) 12: 2021 1859
Genetic Dissection of Temperament Personality Traits in Italian Isolates.
Genes (Basel) 13: 2021 4
GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing.
Nucleic Acids Res 50: 2022 2464-2479
Mapping genomic loci implicates genes and synaptic biology in schizophrenia.
Nature 604: 2022 502-508
Borderline personality disorder and the big five: molecular genetic analyses indicate shared genetic architecture with neuroticism and openness.
Transl Psychiatry 12: 2022 153
The genomic origins of the world's first farmers.
Cell 185: 2022 1842-1859.e18
Polygenic Resilience Modulates the Penetrance of Parkinson Disease Genetic Risk Factors.
Ann Neurol 92: 2022 270-278
Variation in CFHR3 determines susceptibility to meningococcal disease by controlling factor H concentrations.
Am J Hum Genet 109: 2022 1680-1691
EagleImp: fast and accurate genome-wide phasing and imputation in a single tool.
Bioinformatics 38: 2022 4999-5006
Rapid, Reference-Free human genotype imputation with denoising autoencoders.
Elife 11: 2022 e75600
Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes.
Nat Neurosci 25: 2022 1559-1568
Accuracy of haplotype estimation and whole genome imputation affects complex trait analyses in complex biobanks.
Commun Biol 6: 2023 101
The HUNT study: A population-based cohort for genetic research.
Cell Genom 2: 2022 100193
The female protective effect against autism spectrum disorder.
Cell Genom 2: 2022 100134
Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus.
Neuro Oncol 25: 2023 1709-1720
Polygenetic risk scores and phenotypic constellations of obsessive-compulsive disorder in clozapine-treated schizophrenia.
Eur Arch Psychiatry Clin Neurosci 274: 2024 181-193
Regulator of G-Protein Signalling 9: A New Candidate Gene for Sweet Food Liking?
Foods 12: 2023 1739
Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.
Nat Genet 55: 2023 1243-1249
Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes.
Nat Genet 55: 2023 1088-1090
Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses.
Nat Med 29: 2023 1832-1844
Assessing transcriptomic reidentification risks using discriminative sequence models.
Genome Res 33: 2023 1101-1112
Proteomic analysis of 92 circulating proteins and their effects in cardiometabolic diseases.
Clin Proteomics 20: 2023 31
Evidence for a shared genetic contribution to loneliness and borderline personality disorder.
Transl Psychiatry 13: 2023 398
The correlates of neonatal complement component 3 and 4 protein concentrations with a focus on psychiatric and autoimmune disorders.
Cell Genom 3: 2023 100457
How local reference panels improve imputation in French populations.
Sci Rep 14: 2024 370
Analysis of rare Parkinson's disease variants in millions of people.
NPJ Parkinsons Dis 10: 2024 11
Clenching the Strings of Bruxism Etiopathogenesis: Association Analyses on Genetics and Environmental Risk Factors in a Deeply Characterized Italian Cohort.
Biomedicines 12: 2024 304
A resampling-based approach to share reference panels.
Nat Comput Sci 4: 2024 360-366