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Genetic effects on liver chromatin accessibility identify disease regulatory variants

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

PROVIDER: PRJNA692488 | ENA |

REPOSITORIES: ENA

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

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

| PRJNA692489 | ENA

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 [ATAC-seq]

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

| PRJNA692238 | ENA

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]

| PRJNA692245 | ENA

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

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

Chromatin accessibility profiling of human coronary arteries identifes disease regulatory variants

Project description:Coronary artery disease (CAD) is a complex inflammatory disease of the vessel wall and often leads to myocardial infarction. Genome-wide association studies (GWAS) have now identified over 200 genetic loci associated with CAD. The majority of CAD-associated variants are located in noncoding regions of the genome, many of which are predicted to regulate chromatin accessibility and gene expression. In this study, we performed ATAC-seq in human coronary artery patient samples to identify novel chromatin accessibility QTLs (caQTLs) and gain additional insights into CAD regulatory mechanisms in vivo.

2022-01-24 | GSE188422 | 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

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