ArticleNature communications2020
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
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- Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks.Nature genetics · 2025Article
- Defining three dimensional chromatin structures of pediatric and adolescent B cells using primary B cell and EBV-immortalized B cell reference genomes.BMC medical genomics · 2025Article
- Training deep learning models on personalized genomic sequences improves variant effect prediction.bioRxiv : the preprint server for biology · 2025Article
- STING pathways and Sjögren's syndrome: Exploration from mechanism to treatment.Frontiers in immunology · 2025Review
- Stratified shared genetic architecture of IBD and RA: an integrated analysis from polygenic overlap to directional heterogeneity.Frontiers in immunology · 2025Article
- CRISPR-Cas9 editing ofFrontiers in genome editing · 2025Article
- Systemic lupus erythematosus genetics: insights into pathogenesis and implications for therapy.Nature reviews. Rheumatology · 2024Review
- Massively parallel approaches for characterizing noncoding functional variation in human evolution.Current opinion in genetics & development · 2024Review
- A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes.BMC medical genomics · 2024Article
- Functional dissection of complex and molecular trait variants at single nucleotide resolution.bioRxiv : the preprint server for biology · 2024Article
- Functional genomics in stroke: current and future applications of iPSCs and gene editing to dissect the function of risk variants.BMC cardiovascular disorders · 2023Review
- Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases.American journal of human genetics · 2023Article
- Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay.Cell genomics · 2023Article
- Functional studies of lung cancer GWAS beyond association.Human molecular genetics · 2022Review
- Multiplexed functional genomic assays to decipher the noncoding genome.Human molecular genetics · 2022Article
- Functional inference of gene regulation using single-cell multi-omics.Cell genomics · 2022Article
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Authors and funding
16 authors.
Funding
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.
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