Characterization of non-coding variants associated with transcription factor binding through ATAC-seq-defined footprint QTLs in liver.

ABSTRACT: Non-coding variants discovered by genome-wide association studies (GWAS) are enriched in regulatory elements harboring transcription factor (TF) binding motifs, strongly suggesting a connection between disease association and the disruption of cis-regulatory sequences. Occupancy of a TF inside a region of open chromatin can be detected in ATAC-seq where bound TFs block the transposase Tn5, leaving a pattern of relatively depleted Tn5 insertions known as a "footprint". Here, we sought to identify variants associated with TF-binding, or "footprint quantitative trait loci" (fpQTLs) in ATAC-seq data generated from 170 human liver samples. We used computational tools to scan the ATAC-seq reads to quantify TF binding likelihood as "footprint scores" at variants derived from whole genome sequenci

SUBMITTER: Dudek MF 

PROVIDER: S-EPMC11463493 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature