{"doi":"10.1016/j.xpro.2025.104148","title":"Protocol for discovering genetic variants associated with ATAC-seq footprint-inferred transcription factor binding","abstract":"Transcription factor (TF) binding is detectable in assay for transposase-accessible chromatin using sequencing (ATAC-seq) experiments, where bound TFs block transposase insertions, leaving a depletion of insertions known as a “footprint.” Here, we present a computational protocol for detecting genetic variants associated with footprint-inferred TF binding. We describe steps to run the PRINT footprinting software to quantify TF binding likelihood at variants across multiple genotyped ATAC-seq samples and then run regressions to measure genetic associations. This protocol can implicate causal variants in disease-associated loci. For complete details on the use and execution of this protocol, please refer to Dudek et al. 1","journal":"STAR Protocols","year":2025,"id":578387,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9555,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":596794,"name":"Brandon M. Wenz","orcid":null,"position":1,"is_corresponding":false},{"id":45188,"name":"Benjamin F. Voight","orcid":"0000-0002-6205-9994","position":2,"is_corresponding":false},{"id":24671,"name":"Laura Almasy","orcid":"0000-0002-9184-8124","position":3,"is_corresponding":false},{"id":40827,"name":"Struan F.A. Grant","orcid":"0000-0003-2025-5302","position":4,"is_corresponding":false},{"id":422827,"name":"Max F. Dudek","orcid":"0000-0001-8521-9543","position":0,"is_corresponding":true}],"reference_count":23,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:58:20.638044Z","pmid":"41108684","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}