{"doi":"10.1038/s41467-020-15022-4","title":"Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features","abstract":"Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we use seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in five disease-relevant immune cell lines, based on a set of features related to regulatory potential. Trait/disease-associated variants are enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 have at least one variant meeting one or both of these criteria, 5 of which are further supported by genetic fine-mapping. Our work provides a comprehensive strategy to characterize genetic variation at important disease-associated loci, and aids in the effort to identify trait causal genetic variants.","journal":"Nature Communications","year":2020,"id":320,"datarank":2.0391705702491,"base_score":4.406719247264253,"endowment":4.406719247264253,"self_citation_contribution":0.6610078870896381,"citation_network_contribution":1.3781626831594618,"self_endowment_contribution":0.6610078870896381,"citer_contribution":1.3781626831594618,"corpus_percentile":null,"corpus_rank":null,"citation_count":81,"citer_count":57,"citers_with_citation_signal":48,"citers_with_endowment":48,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.063,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-03-06","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":3029,"name":"Carl G. de Boer","orcid":"0000-0001-8935-5921","position":1,"is_corresponding":false},{"id":3030,"name":"Charles P. Fulco","orcid":"0000-0002-6592-1279","position":2,"is_corresponding":false},{"id":3031,"name":"Caleb A. Lareau","orcid":"0000-0003-4179-4807","position":3,"is_corresponding":false},{"id":3032,"name":"Masahiro Kanai","orcid":"0000-0001-5165-4408","position":4,"is_corresponding":false},{"id":3033,"name":"Jacob C. Ulirsch","orcid":"0000-0002-7947-0827","position":5,"is_corresponding":false},{"id":3034,"name":"Ryan Tewhey","orcid":"0000-0002-4607-8001","position":6,"is_corresponding":false},{"id":3035,"name":"Leif S. Ludwig","orcid":"0000-0002-2916-2164","position":7,"is_corresponding":false},{"id":3036,"name":"Steven K. Reilly","orcid":"0000-0003-3140-1483","position":8,"is_corresponding":false},{"id":3037,"name":"Drew T. Bergman","orcid":"0000-0002-8314-7088","position":9,"is_corresponding":false},{"id":3038,"name":"Jesse M. Engreitz","orcid":"0000-0002-5754-1719","position":10,"is_corresponding":false},{"id":861,"name":"Robbyn Issner","orcid":"0000-0003-4132-9219","position":11,"is_corresponding":false},{"id":3039,"name":"Hilary K. Finucane","orcid":"0000-0003-3864-9828","position":12,"is_corresponding":false},{"id":18887,"name":"Matthew E. Hurles","orcid":"0000-0002-2333-7015","position":13,"is_corresponding":false},{"id":29633,"name":"Prisca Liberali","orcid":"0000-0003-0695-6081","position":14,"is_corresponding":false},{"id":409,"name":"Nir Hacohen","orcid":"0000-0002-2349-2656","position":15,"is_corresponding":false},{"id":3040,"name":"John Ray","orcid":"0000-0001-7294-4260","position":16,"is_corresponding":false},{"id":3028,"name":"John P. Ray","orcid":null,"position":0,"is_corresponding":true}],"reference_count":73,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"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":[]}