The 2p16 region exhibited a novel SLE association at rs1432296 (OR=1.18, P=1.34 × 10−8) near PAPOLG-LINC01185, which includes REL. A linkage region at 4p16 (ref. 21) contained a strong novel association for rs3733345 (OR=0.89, P=1.83 × 10−11); EA dominated the association, but with significant support from HA and AA. Here, PAPOLG is linked to systemic lupus erythematosus.