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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.
16 Authors
John P. Ray
Carl G. de Boer
Charles P. Fulco
Caleb A. Lareau
Masahiro Kanai
Jacob C. Ulirsch
Ryan Tewhey
Leif S. Ludwig
Steven K. Reilly
Drew T. Bergman
Jesse M. Engreitz
Robbyn Issner
Hilary K. Finucane
Eric S. Lander
Aviv Regev
Nir Hacohen
Enabling scientific discoveries that improve human health