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Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

GSE264684 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 477 samples Submitted 2025/02/01 Platform GPL20301Platform GPL20795
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 477 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
477 samples: 330 distinct titles, 70 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traitsGenome research · 2025
Summary (written by the submitters)
Chromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory elements that may underlie genetic effects on gene expression and clinical quantitative traits. However, caQTL discovery has been limited by the sample sizes of previous studies. Here, we mapped caQTL in liver tissue from 138 human donors and identified caQTL for 35,361 regulatory elements.
Read the full summary ↓
We identified 2,126 caQTL signals containing multiple regulatory elements, suggesting coordinated regulation of elements at these loci. CaQTL showed strong heritability enrichment and colocalization with genome-wide association study (GWAS) signals for traits relevant to liver function. We identified a colocalized caQTL at 667 GWAS signals for 17 traits, used multiple methods to predict target genes, and validated caQTL predictions at two loci using functional assays. These results demonstrate the power of caQTL to characterize gene regulation and predict regulatory mechanisms at GWAS loci.
Published in
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
Currin KW, Perrin HJ, Pandey GK et al. · Genome research 2025 · PMID 40393811 · doi:10.1101/gr.279741.124
This dataset
Open GSE264684 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE264684_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1103105 and SRA study SRP503267. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40393811) ↗
Study design
330 distinct titles, 70 of them repeated
liver_ATAC_122_l1_s ×2 liver_ATAC_162_l1_s ×2 liver_ATAC_172_l1_s ×2 liver_ATAC_174_l2_s ×2 liver_ATAC_174_l3_s ×2 liver_ATAC_177_l1_s ×2 liver_ATAC_177_l2_s ×2 liver_ATAC_200_l1_s ×2 +62 more

How we read this: Read from the first 400 of 477 sample titles: 330 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 437 more — browse all 477 samples with per-sample file links →

Datasets on a similar topic

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