HaploReg protocols

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HaploReg statistics

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Associated diseases

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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 No

Taxon


  • Primates
    • Homo sapiens

Publications for HaploReg

HaploReg in pipelines

 (32)
2018
PMCID: 5845532
PMID: 29559957
DOI: 10.3389/fendo.2018.00075

[…] functional elaboration of gwas results and predicted putative causal variants in haplotype blocks, likely cell types of action and candidate target genes of noncoding genome by using online haploreg v4.1 software (, ). a set of 25 query snps (p < 1 × 10−5) was submitted. the enrichments of cell-type enhancers with uncorrected p < 0.05 were reported., we performed gene-based tests […]

2017
PMCID: 5330487
PMID: 28245265
DOI: 10.1371/journal.pone.0172880

[…] λj; and (ii) including ranked variants until their cumulative posterior probability exceeds 0.99., the variants identified during fine mapping were annotated using a variety of tools, including haploreg, regulomedb and rsnpbase., the program eigensoft [] was used to perform a principal components analysis, after pruning markers showing short-range and long-range linkage disequilibrium using […]

2017
PMCID: 5470997
PMID: 28423715
DOI: 10.18632/oncotarget.16120

[…] several semi-automated bioinformatics tools were applied to assess whether snps or their linked genetic variants are associated with a putative function that might affect patient outcomes. haploreg [] v4 and the gtex database [] from the encode project [] were used to identify the regulatory potential of candidate functional variants. particular sites of interest were examined […]

2017
PMCID: 5517526
PMID: 28724990
DOI: 10.1038/s41467-017-00031-7

[…] in the gwas loci (gwas snps and snps in ld with the gwas snps) across 127 healthy human tissues/normal cell lines available in the encode project and the epigenetic roadmap project from the haploreg4 web browser using chromhmm. to evaluate whether replicated gwas loci were enriched with regulatory elements in skeletal muscle tissue, we performed a hypergeometric test. specifically […]

2017
PMCID: 5523840
PMID: 28671113
DOI: 10.3233/JAD-170049

[…] testing were then looked up in the igap to check for association with ad., snps surviving correction for multiple testing in association analyses were examined in silico. we used regulomedb [] and haploreg (version 4.1; ceu population code; http://www.broadinstitute.org/mammals/haploreg/) [] to explore whether any of the snps may affect gene expression. given the central role of hippocampus […]


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HaploReg in publications

 (427)
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 […]

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 […]

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, […]

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 […]

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 […]


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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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