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Genetic effects on liver chromatin accessibility identify disease regulatory variants [genotypes]

ABSTRACT: Genetic effects on liver chromatin accessibility identify disease regulatory variants [genotypes]

PROVIDER: PRJNA692489 | ENA |

REPOSITORIES: ENA

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Genetic effects on liver chromatin accessibility identify disease regulatory variants [genotypes]

Project description:Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. The caQTL variants are enriched in liver tissue promoter and enhancer states and frequently disrupt binding motifs of transcription factors expressed in liver. We predicted target genes for 861 caQTL peaks using proximity, chromatin interactions, correlation with promoter accessibility or gene expression, and colocalization with expression QTL. Using GWAS signals for 19 liver function and/or cardiometabolic traits, we identified 110 colocalized caQTL and GWAS signals, 56 of which contained a predicted caPeak target gene. At the LITAF LDL-cholesterol GWAS locus, we validated that a caQTL variant showed allelic differences in protein binding and transcriptional activity. These caQTL contribute to the epigenomic characterization of human liver and help identify molecular mechanisms and genes at GWAS loci.

2021-05-01 | GSE164938 | GEO

Genetic effects on liver chromatin accessibility identify disease regulatory variants

Project description:Genetic effects on liver chromatin accessibility identify disease regulatory variants

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Genetic effects on liver chromatin accessibility identify disease regulatory variants [ATAC-seq]

Project description:Genetic effects on liver chromatin accessibility identify disease regulatory variants [ATAC-seq]

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Genetic effects on liver chromatin accessibility identify disease regulatory variants [RNA-seq]

Project description:Genetic effects on liver chromatin accessibility identify disease regulatory variants [RNA-seq]

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2021-05-01 | GSE164876 | GEO

Genetic effects on liver chromatin accessibility identify disease regulatory variants [ATAC-seq]

2021-05-01 | GSE164870 | GEO

Genetic effects on liver chromatin accessibility identify disease regulatory variants.

Project description: Not available

| S-EPMC8323023 | biostudies-literature

Genetic effects on liver chromatin accessibility identify disease regulatory variants

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-05-01 | GSE164942 | GEO

Genetic determinants of chromatin accessibility in T cell activation across human individuals [RNA-seq]

Project description:We analyzed 105 chromatin accessibility (ATAC-seq) profiles in activated primary CD4+ T cells from healthy donors to identify genetic variants associated with variability in chromatin accessibility (ATAC-QTLs).we analyzed 105 chromatin accessibility (ATAC-seq) profiles in activated primary CD4+ T cells from healthy donors to identify genetic variants associated with variability in chromatin accessibility (ATAC-QTLs)

2018-07-12 | GSE86887 | GEO

Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq

Project description:Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at cell type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) and genotyping in peripheral blood mononuclear cells from 13 individuals. Clustering chromatin accessibility profiles of 96,002 total nuclei identified 17 immune cell types and sub-types. We mapped chromatin accessibility QTLs (caQTLs) in each immune cell type and sub-type which identified ~6,000 total caQTL peaks, including those obscured from assays of bulk tissue such as with divergent effects on different cell types. For ~3,000 caQTLs we further annotated putative target genes of variant activity using single cell co-accessibility, and caQTL variants were significantly correlated with the accessibility level of linked gene promoters. We fine-mapped loci associated with 16 complex immune traits and identified immune cell caQTLs, including those with cell type-specific effects. At the 6q15 locus associated with type 1 diabetes, in line with previous reports, variant rs72928038 was a naïve CD4+ T cell caQTL linked to BACH2 and we validated the allelic effects of this variant on regulatory activity in Jurkat T cells. These results highlight the utility of snATAC-seq for mapping genetic effects on accessible chromatin in specific cell types and provide a resource for annotating complex immune trait loci.

2023-01-10 | GSE199253 | GEO

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