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HRC specifications


Unique identifier OMICS_14100
Name HRC
Alternative name Haplotype Reference Consortium
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 1.1
Maintained Yes


  • person_outline Jonathan Marchini

Publication for Haplotype Reference Consortium

HRC citations


Sex specific glioma genome wide association study identifies new risk locus at 3p21.31 in females, and finds sex differences in risk at 8q24.21

Sci Rep
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z
call_split See protocol

[…] principal components analysis in plink 1.9. Resulting files were imputed using Eagle 2 and Minimac3 as implemented on the Michigan imputation server ( using the Haplotype Reference Consortium Version r1.1 2016 as a reference panel–. Somatic characterization of TCGA cases was obtained from the final dataset used for the TCGA pan-glioma analysis, and classifica […]


Medical relevance of protein truncating variants across 337,205 individuals in the UK Biobank study

Nat Commun
PMCID: 5915386
PMID: 29691392
DOI: 10.1038/s41467-018-03910-9

[…] s and reference and alternate alleles of PTVs annotated in gnomAD to the UK Biobank positions and alleles for the UK Biobank data. We only considered PTVs in the HRC site list version 1.1 ( We removed 408 imputed PTVs that had an imputation score < 0.8, missingness > 1%, or whose MAF differed substantially from the non-Finnish European MAF in gno […]


One for all and all for One: Improving replication of genetic studies through network diffusion

PLoS Genet
PMCID: 5933817
PMID: 29684019
DOI: 10.1371/journal.pgen.1007306

[…] etic association analysis. Samples with outlier PC values >six standard deviations from the mean were excluded from subsequent analyses. Genotypes for a much larger set of SNPs were imputed using the Haplotype Reference Consortium panel release 1.1 [, ], which includes 64,976 haplotypes derived from 39,235,157 SNPs, and the Michigan Imputation Server ( runni […]


Identification of missing variants by combining multiple analytic pipelines

BMC Bioinformatics
PMCID: 5902939
PMID: 29661148
DOI: 10.1186/s12859-018-2151-0

[…] owing databases: dbSNP build 147, Exome Sequencing Project (ESP), ClinVar, the 1000 Genomes Project (1000G), The Exome Aggregation Consortium (ExAC), Kaviar Genomic Variant Database (Kaviar), and the Haplotype Reference Consortium (HRC). At a sample size of 1952, 77.53% of the BWA-unique and 76.7% of Novo-unique variants were found in public databases, suggesting that the majority of aligner-speci […]


The genetics of smoking in individuals with chronic obstructive pulmonary disease

PMCID: 5892035
PMID: 29631575
DOI: 10.1186/s12931-018-0762-7
call_split See protocol

[…] moved because they failed subsequent quality control, which resulted in a final sample of n = 4048 for the present analysis. Imputation was undertaken with the Michigan Imputation Server [] using the Haplotype Reference Consortium (HRC) [] panel. Variants were excluded if the imputation r2 was < 0.5 and if the minor allele frequency was < 1%. […]


Comparison of phasing strategies for whole human genomes

PLoS Genet
PMCID: 5903673
PMID: 29621242
DOI: 10.1371/journal.pgen.1007308

[…] inations of the following as input data for the relevant computations: the haplotype reference panels from the 1000 Genomes Project (1000GP) with 2.5k individuals or the haplotype references from the Haplotype Reference Consortium (HRC) with 23k individuals, conventional WGS reads generated from the Illumina or PacBio sequencing platforms, RNA-Seq reads, or parental genotype. […]


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HRC institution(s)
Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; [etc]
HRC funding source(s)
This work was supported by the ERC (grant n°617306) and the Wellcome Trust (grants n°WT097307 and WT090851).

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