Methods of identifying, diagnosing, and prognosing lupus, including certain subphenotypes of lupus, are provided, as well as methods of treating lupus, including certain subpopulations of patients. The methods provided are based on a set of alleles associated with systemic lupus erythematosus (SLE) risk loci including BLK, TNIP1, PRDM1, JAZF1, UHRF1BP1, IL1 O, IFIH1, CFB, CEC16A, IL12B and SH2B3 that contribute to SLE risk. Also provided are methods for identifying effective lupus therapeutic agents and predicting responsiveness to lupus therapeutic agents.
