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Protocols

HaploReg specifications

Information


Unique identifier OMICS_08323
Name HaploReg
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 4.1
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Publications for HaploReg

HaploReg citations

 (435)
library_books

Genome wide haplotype association analysis of primary biliary cholangitis risk in Japanese

2018
PMCID: 5958065
PMID: 29773854
DOI: 10.1038/s41598-018-26112-1

[…] cell types available in roadmap epigenomics.bbound protein: regulatory protein-binding chip-seq peak overlaps for specified proteins are provided for blood- or liver-related cell lines only (haploreg v4, ward and kellis).caltered motifs: the number of regulatory motifs predicted to be affected by the snp based on position weight matrices (pwm) score changes (haploreg v4, ward […]

library_books

Genetic variant for behavioral regulation factor of executive function and its possible brain mechanism in attention deficit hyperactivity disorder

2018
PMCID: 5956073
PMID: 29769613
DOI: 10.1038/s41598-018-26042-y

[…] we got the snps in ld with the significant snp (r2 > = 0.75) using the 1000 genomes project asn population data. the regulatory features related with these snps were searched in rvarbase, haploreg and roadmap washu epigenome browser. the eqtl data were searched in gtex portal, scan, seeqtl, smri human prefrontal cortex eqtl data, and braineac […]

library_books

Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

2018
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] grch38 human genome build using the software liftover, and extracted all gene transcription start sites that lie within the 1 mega-base (mb) on either side of a given variant., using the software haploreg (version 4.1) and regulomedb v1.1, we investigated regulatory annotations for variants in ld (r2 > 0.8, 1000 genomes ceu) with the cct-associated snps. to prioritize functional snps, […]

library_books

Evaluation of WISP1 as a candidate gene for bone mineral density in the Old Order Amish

2018
PMCID: 5940677
PMID: 29739999
DOI: 10.1038/s41598-018-25272-4

[…] variants of interest was performed using haploview version 4.2 (http://www.broadinstitute.org/haploview/). prediction of histone marks and dnase hypersensitivity sites was performed using haploreg v4.1, and the five snps were annotated in regulatory elements cataloged in encyclopedia of dna elements (encode) project according to ucsc genome bioinformatics website […]

library_books

A Bayesian Framework for Generalized Linear Mixed Modeling Identifies New Candidate Loci for Late Onset Alzheimer’s Disease

2018
PMCID: 5937180
PMID: 29507048
DOI: 10.1534/genetics.117.300673

[…] of prkar1b, and 21,254 and 21,059 bp upstream of pdgfa, respectively. to assess the functional relevance of the four variants, we queried the roadmap epigenomics () and encode () resources using haploreg () for chromatin state and protein binding annotations. we found that rs10490263 lies in promoter-associated histone marks in the hippocampus and circulating t cells, and that rs74944275 […]

library_books

Gene based analysis of genes related to neurotrophic pathway suggests association of BDNF and VEGFA with antidepressant treatment response in depressed patients

2018
PMCID: 5934385
PMID: 29725086
DOI: 10.1038/s41598-018-25529-y

[…] r version 3.0.2, plink version 1. 90b3.37 64-bit, and haploview version 4.1. additionally, to explore the potential roles of these six snps as expression quantitative trait locus (eqtl), we used haploreg (http://compbio.mit.edu/haploreg) to search gene regulation databases., among 428 subjects, 394 (92.06%) cases were observed at all four time points; 30 cases (7.02%) were missing […]


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HaploReg institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
HaploReg funding source(s)
National Institutes of Health (NIH) [R01-HG004037, RC1-HG005334, R01-HG008155]

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