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dc.contributor.authorWard, Lucas D.
dc.contributor.authorKellis, Manolis
dc.date.accessioned2016-01-04T15:05:30Z
dc.date.available2016-01-04T15:05:30Z
dc.date.issued2015-12
dc.date.submitted2015-11
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.urihttp://hdl.handle.net/1721.1/100576
dc.description.abstractMore than 90% of common variants associated with complex traits do not affect proteins directly, but instead the circuits that control gene expression. This has increased the urgency of understanding the regulatory genome as a key component for translating genetic results into mechanistic insights and ultimately therapeutics. To address this challenge, we developed HaploReg (http://compbio.mit.edu/HaploReg) to aid the functional dissection of genome-wide association study (GWAS) results, the prediction of putative causal variants in haplotype blocks, the prediction of likely cell types of action, and the prediction of candidate target genes by systematic mining of comparative, epigenomic and regulatory annotations. Since first launching the website in 2011, we have greatly expanded HaploReg, increasing the number of chromatin state maps to 127 reference epigenomes from ENCODE 2012 and Roadmap Epigenomics, incorporating regulator binding data, expanding regulatory motif disruption annotations, and integrating expression quantitative trait locus (eQTL) variants and their tissue-specific target genes from GTEx, Geuvadis, and other recent studies. We present these updates as HaploReg v4, and illustrate a use case of HaploReg for attention deficit hyperactivity disorder (ADHD)-associated SNPs with putative brain regulatory mechanisms.en_US
dc.description.sponsorshipNational Institutes of Health (U.S.) (R01-HG004037)en_US
dc.description.sponsorshipNational Institutes of Health (U.S.) (RC1-HG005334)en_US
dc.description.sponsorshipNational Institutes of Health (U.S.) (R01-HG008155)en_US
dc.language.isoen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttp://dx.doi.org/10.1093/nar/gkv1340en_US
dc.rightsCreative Commons Attributionen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en_US
dc.sourceOxford University Pressen_US
dc.titleHaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and diseaseen_US
dc.typeArticleen_US
dc.identifier.citationWard, Lucas D., and Manolis Kellis. “HaploReg V4: Systematic Mining of Putative Causal Variants, Cell Types, Regulators and Target Genes for Human Complex Traits and Disease.” Nucleic Acids Research (December 10, 2015): gkv1340.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratoryen_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Electrical Engineering and Computer Scienceen_US
dc.contributor.mitauthorWard, Lucas D.en_US
dc.contributor.mitauthorKellis, Manolisen_US
dc.relation.journalNucleic Acids Researchen_US
dc.eprint.versionFinal published versionen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dspace.orderedauthorsWard, Lucas D.; Kellis, Manolisen_US
dc.identifier.orcidhttps://orcid.org/0000-0002-8017-809X
mit.licenseOPEN_ACCESS_POLICYen_US


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