HaploReg statistics

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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

 (272)
library_books

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

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

[…] 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, we first […]

call_split

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

2018
Sci Rep
PMCID: 5940677
PMID: 29739999
DOI: 10.1038/s41598-018-25272-4
call_split See protocol

[…] surrounding 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 (http://genome.ucsc.ed […]

library_books

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

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

[…] ream 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 lies […]

call_split

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

2018
Sci Rep
PMCID: 5934385
PMID: 29725086
DOI: 10.1038/s41598-018-25529-y
call_split See protocol

[…] with 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. […]

library_books

Family Based Genome Wide Association Study of South Indian Pedigrees Supports WNT7B as a Central Corneal Thickness Locus

2018
PMCID: 5961220
DOI: 10.1167/iovs.17-23536

[…] ng equilibrium with rs9723267; r2 = 0.96 and 1.0 in the South Indian data set, 1000 Genomes (provided in the public domain, http://csg.sph.umich.edu/abecasis/MACH/download/1000G.2012-03-14.html), and Haploreg v.4.1 (provided in the public domain, http://www.broadinstitute.org/mammals/haploreg/haploreg.php), respectively, that disrupts a Rad21 binding motif and a CTCF (CCCTC-binding factor) binding […]

library_books

Mapping genetic variants for cranial vault shape in humans

2018
PLoS One
PMCID: 5919379
PMID: 29698431
DOI: 10.1371/journal.pone.0196148

[…] Lead SNPs at associated loci were queried using HaploReg [] to extract evidence of functional variation (promoter and enhancer histone marks, DNAse hypersensitivity, eQTL information) for all SNPs in LD (r2 > 0.8) with the lead SNPs. Genes of inter […]

Citations

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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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