varTFBridge — processed FOODIE footprints and variant–TF binding–gene linkage tables

Processed datasets accompanying the manuscript Genome-wide maps of transcription factor footprints identify noncoding variants rewiring gene regulatory networks (Lin, Dong, Zhang, Xie, Jing, Zhao, Ma, Kang, Jiang, Xie & Zhao; Changping Laboratory). varTFBridge is an integrative framework that combines high-resolution FOODIE (single-molecule deaminase footprinting) transcription-factor footprints with UK Biobank whole-genome sequencing to identify causal noncoding variants and elucidate the regulatory mechanisms by which they rewire gene regulatory networks. Applied to 490,640 UK Biobank genomes across 13 erythroid traits, varTFBridge prioritises 113 high-confidence regulatory variants (104 common, 9 rare), encompassing 2,173 variant–TF binding–gene–trait linkages across 64 TFs and 108 genes, and recapitulates the causal variant rs112233623 acting through disruption of a GATA1/TAL1 co-binding motif at a CCND3 enhancer. Analysis code is publicly available at https://github.com/JasonLinjc/varTFBridge under the MIT License. This Zenodo deposit contains all processed datasets generated and used in the study: FOODIE footprints for K562 (188,484 footprints, median 19 bp) and GM12878 cell lines on GRCh38, plus matched ATAC-/DNase-derived footprints used as benchmark annotations. Common-variant pipeline outputs: per-trait variant–footprint overlap tables, VAR2TFBS predictions (Create / Disrupt / Increase / Decrease classifications), ABC-FP-Max variant-to-gene assignments, and AlphaGenome TF-ChIP scores for PIP > 0.7 variants. Rare-variant pipeline outputs: leave-one-variant-out (LOO) driver variant tables for footprint-wide significant burden hits, VAR2TFBS predictions, and ABC-FP-Max gene assignments. Final high-confidence variant–TF binding–gene–trait resource (113 variants, 2,173 linkages) together with interactive Plotly HTML reports for novel-mechanism discovery scoring. S-LDSC heritability enrichment tables for K562 FOODIE, DNase, and ATAC annotations across 28 UK Biobank blood traits. Trait metadata for the 13 erythroid traits and full set of manuscript Supplementary Data files (Supplementary Data 1–6, Supplementary Tables 1–2). See README.md and FILE_MANIFEST.md (rendered on this page and also included inside the archive) for a per-file description, provenance, and reproduction instructions.