Genes implicated in T cells, but not in FLS, showed a pattern of involvement in “canonical” T cell immunity, including CTLA4, CD28, IL2RA, and GATA3. Similarly, genes enriched in B cell-specific enhancers were involved in B cell biology, including IRF8, BLK, and TAB1. The stromal activation observed in RA joints was clearly reflected in the predicted function of the identified FLS-specific regulatory variants, many of which were previously associated with RA pathogenesis and are connected by functional networks. Here, GATA3 is linked to rheumatoid arthritis.