To date, more than 100 genomic loci have been associated with SLE, many which map to non-coding regions (44,64) To illustrate different scenarios based on the application of our method, we pre-selected the genomic regions containing FAM167A-BLK, STAT4 and TNIP1 for fine-mapping because these regions showed robust single-SNP associations (P < 5 × 10−8) with SLE in at least two ancestries (FAM167A-BLK: EA and AA; STAT4: EA and HA; TNIP1: EA and HA) and the association signals are not refined to a single SNP, due in part to strong LD. The gene discussed is STAT4; the disease is systemic lupus erythematosus.