databases > DOI:10.25504/FAIRsharing.x18jh7
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ready HaploReg

General Information
HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Homepage http://compbio.mit.edu/HaploReg

Countries that developed this resource United States

Created in 2011

Taxonomic range

Subjects 





How to cite this record FAIRsharing.org: HaploReg; HaploReg; DOI: https://doi.org/10.25504/FAIRsharing.x18jh7; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jul 31 2021 1:56 p.m.


Record updated: Sept. 26, 2016, 10:19 a.m. by The FAIRsharing Team.

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Support

General

online documentation http://archive.broadinstitute.org/mammal ...

Additional Information

Contact Manolis Kellis

Tools

    No tools defined


Access / Retrieve Data

Conditions of Use


Data Versioning

access to historical files available No link recorded

Data Release

ad-hoc release No link recorded

Data Curation

manual curation No link recorded

Data Access

file download(txt) No link recorded



Publications

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease.

Ward LD,Kellis M
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants.

Ward LD,Kellis M
Nucleic Acids Res 2011

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

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Related Databases

No related databases defined


Implementing Policies

This record is not implemented by any policy.


Credit

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Funds

Undefined

Grant Number(s)

  • 0644282 (National Science Foundation (NSF), USA)

  • R01-HG004037 (ELIXIR Italy)

  • R01-HG008155 (ELIXIR Italy)

  • RC1-HG005334 (ELIXIR Italy)