Liver chromatin accessibility QTL from 138 individuals (Currin et al. 2025)
Warning: To download the data, please copy the link address and use wget or curl in the terminal. Clicking on the link to download will not work. Alternatively, the files can be downloaded from zenodo at the following link: Zenodo Currin et al. 2025. Contact Karen Mohlke (karen_mohlke@med.unc.edu) if you need help accessing the data.
Liver chromatin accessibility QTL in 138 individuals (Currin et al. 2025)
Supplemental data files for the liver caQTL study from Currin et al. 2025.
| File | Description | File size |
|---|---|---|
| supplementalData1_liver_ATAC_peaks.bed.gz | Liver ATAC peaks, including overlap with roadmap chromatin states, liver pilot peaks, and ENCODE ATAC peaks | 5.3Mb |
| liver_significant_caQTL_leadVariants_1kb_analysis_with_populationAlleleFrequencies.bed.gz | Significant caQTL lead variants from the 1kb analysis, including population allele frequencies from TOPMed | 3.5Mb |
| liver_significant_caQTL_leadVariants_1mb_analysis.bed.gz | Significant caQTL lead variants from the 1mb analysis | 1.7Mb |
| 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. | 5.1Gb |
| 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 | 926Mb |
| 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 | 1.5Kb |
| 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 | 4.3Mb |
| 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 | 14Mb |
| 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. | 1.2Mb |
| 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). | 1.8Mb |