These results suggest that the combined influence of the rs9494868 risk allele and other variants on the SLE risk haplotype increase the enhancer activity necessary for haplotype-specific expression of IL20RA and IFNGR1. Given the rarity of the SLE risk haplotype with the non-risk allele of rs9494868 in our cohort, we cannot definitively demonstrate the inverse of this experiment in the natural genomic context; however, the luciferase assays strongly suggest that the risk allele of rs9494868 drives the allele-specific enhancer activity. Here, IFNGR1 is linked to systemic lupus erythematosus.