Annotating and prioritizing human non-coding variants with RegulomeDB v.2

[...]we included chromatin state annotations known as from chromHMM in EpiMap for 833 biosamples8. Transcription factor motifs and ChIP-seq data together provide evidence about how a variant is likely to affect phenotype in a cell-specific context. [...]rs72635708 is predicted as a regulatory varian...

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Published inNature genetics Vol. 55; no. 5; pp. 724 - 726
Main Authors Dong, Shengcheng, Zhao, Nanxiang, Spragins, Emma, Kagda, Meenakshi S, Li, Mingjie, Assis, Pedro, Jolanki, Otto, Luo, Yunhai, Cherry, J Michael, Boyle, Alan P, Hitz, Benjamin C
Format Journal Article
LanguageEnglish
Published United States Nature Publishing Group 01.05.2023
Subjects
Activator protein 1
Annotations
Chromatin
Consortia
Deoxyribonuclease
Experiments
Gene expression
Genetic Variation - genetics
Genomes
Genomics
Humans
Hypotheses
Liver
Phenotypes
Transcription factors
Ann Arbor Michigan
United States > US
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Summary:[...]we included chromatin state annotations known as from chromHMM in EpiMap for 833 biosamples8. Transcription factor motifs and ChIP-seq data together provide evidence about how a variant is likely to affect phenotype in a cell-specific context. [...]rs72635708 is predicted as a regulatory variant by RegulomeDB with a high probability of 0.91 due to its locus overlapping with DNase and ChIP-seq peaks, footprints, and it is an eQTL that associates with LINC01714 gene expression in the right lobe liver. Because rs72635708 lies in the FOS motif, it is likely to be a functional variant in the liver by modulating the binding of the AP-1 complex13.
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ISSN:1061-4036
1546-1718
DOI:10.1038/s41588-023-01365-3