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

Supplemental data files accompanying the liver chromatin accessibility quantitative trait locus (caQTL) study from Currin et al. 2025

Descriptions of files:

1. supplementalData1_liver_ATAC_peaks.bed.gz:
Liver ATAC peaks, including overlap with roadmap chromatin states, liver pilot peaks, and ENCODE ATAC peaks

2. liver_significant_caQTL_leadVariants_1kb_analysis_with_populationAlleleFrequencies.bed.gz:
Significant caQTL lead variants from the 1kb analysis, including population allele frequencies from TOPMed

3. liver_significant_caQTL_leadVariants_1mb_analysis.bed.gz:
Significant caQTL lead variants from the 1mb analysis

4. motifMatches_bestAllelicMatchPerTF_caQTL_variants.txt.gz:
Motifs overlapped by caQTL variants. Motif-variant pairs with pval_lr greater than or equal to 1 were classified as disrupted

5. motifMatches_bestAllelicMatchPerTF_non-caQTL_variants.txt.gz:
Motifs overlapped by non-caQTL variants. Motif-variant pairs with pval_lr greater than or equal to 1 were classified as disrupted

6. motifDisruptions_bestAllelicMatchPerTF_caQTL_variants_withCaQTLInfo.txt.gz:
Motifs classified as disrupted by caQTL variants, including caQTL peak and effect size. This file is useful for determining if the allele that matches the motif better is on the more or less accessible allele.

7.motifNames_atLeast20disruptions_motifWithMostDisruptionsPerTF_caQTL_variants.txt:

The IDs of motifs used in the logistic regression analysis that tested for association between caQTL status and motif disruption

8. caQTL_summaryStatistics_for_caPeaks_1kb_and_1mb_analyses.tar.gz:

CaQTL summary statistics for peaks with a significant caQTL (caPeaks) in the 1kb and 1Mb analyses. The tar archive contains files separated by chromosome.

9. liver_ATAC_peakCounts_DESeqDatasets_WASP-filtered_consensusPeaks_autosomalOnly_refinedBoundaries.RData:

DESeq2 datasets containing raw and normalized WASP-filtered read counts overlapping ATAC peaks in each donor. The “peaks.dds” variable contains raw and library-sized normalized counts and the “peaks.vst” variable contains variance-stabilized data

10. caQTL_variants_overlappingPeaks_LD-r2-0.8_withLead.bed.gz:

Variants overlapping caQTL peaks that are in strong LD (r2>=0.8) with the caQTL lead variant for that peak.

11. background_variants_overlapping_non-caPeaks.bed.gz:

Background variants overlapping peaks with no evidence of a caQTL (non-caQTL peaks, fastQTL beta-adjusted p-value > 0.5).