HaploReg pipeline

HaploReg specifications


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


  • Primates
    • Homo sapiens

Publications for HaploReg

HaploReg citations

PMCID: 5951816

[…] human genome build using the software liftover61,62 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)25 and regulomedb v1.122, we investigated regulatory annotations for variants in ld (r2 > 0.8, 1000 genomes ceu) with the cct-associated snps. to prioritize functional snps, […]

PMCID: 5476671

[…] 15) based on phase i of the 1000 genomes project. variants showing evidence of ld with associated an variants were explored for impact on gene function via regulatory function (including eqtls) by haploreg v4.1, which both collate data from the encyclopedia of dna elements (encode)14. we also referred to the genotype-tissue expression portal database (http://www.gtexportal.org) for eqtls […]

PMCID: 4350913

[…] after bonferroni correction was α = 0.0024. we analysed ld blocks in our sample using haploview [39]., functional annotation of significant snps was conducted using the following softwares: haploreg v2 [40] allows analysis of non-coding genetic variants in terms of their effect on the organization of chromatin regions and regulatory motifs; f-snp [41] is a tool which combines multiple […]

PMCID: 4042684

[…] consortium (http://www.ppmroadmap.com/) and the single nucleotide polymorphism database (dbsnp, https://www.ncbi.nlm.nih.gov/snp/), as implemented in haploreg (v2, www.broadinstitute.org/mammals/haploreg/; ernst et al., 2011) and regulomedb (www.regulomedb.org/; boyle et al., 2012)., variables are shown as number (n), and/or frequency (%), or mean ± standard deviation., table 1 shows […]

PMCID: 4127632

[…] the drive game-on consortium, http://epi.grants.cancer.gov/gameon/;, eigenstrat, http://genepath.med.harvard.edu/~reich/eigenstrat.htm;, encode: http://www.genome.gov/10005107;, haploreg, http://www.broadinstitute.org/mammals/haploreg/haploreg.php, hapmap project, http://hapmap.ncbi.nlm.nih.gov/;, humanexome beadchip: http://genome.sph.umich.edu/wiki/exome_chip_design;, […]

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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