Systemic lupus erythematosus variants modulate the function of an enhancer upstream of TNFAIP3

/A20 is a prominent autoimmune disease risk locus that is correlated with hypomorphic expression and exhibits complex chromatin architecture with over 30 predicted enhancers. This study aimed to functionally characterize an enhancer ∼55 kb upstream of the promoter marked by the systemic lupus erythematosus (SLE) risk haplotype index SNP, rs10499197. Allele effects of rs10499197, rs58905141, and rs9494868 were tested by EMSA and/or luciferase reporter assays in immune cell types. Co-immunoprecipitation, ChIP-qPCR, and 3C-qPCR were performed on patient-derived EBV B cells homozygous for the non-risk or SLE risk haplotype to assess haplotype-specific effects on transcription factor binding and chromatin regulation at the locus. This study found that the locus has a complex chromatin regulatory network that spans ∼1M bp from the promoter region of to the 3' untranslated region of . Functional dissection of the enhancer demonstrated co-dependency of the RelA/p65 and CEBPB binding motifs that, together, increase and expression and decreased expression in the context of the SLE risk haplotype through dynamic long-range interactions up- and downstream. Examination of SNPs in linkage disequilibrium ( = 1.0) with rs10499197 identified rs9494868 as a functional SNP with risk allele-specific increase in nuclear factor binding and enhancer activation . In summary, this study demonstrates that SNPs carried on the ∼109 kb SLE risk haplotype facilitate hypermorphic and expression, while suppressing expression, adding to the mechanistic potency of this critically important locus in autoimmune disease pathology.