Several known associations7,9,10,19–21 were replicated: both HLA-DQA1 and PLA2R1 were strongly associated with MN (p = 2.4 × 10−22 and p = 6.7 × 10−8, respectively), STAT4 was associated with SLE (p = 9.7 × 10−5) and HLA-DPB1 with GPA (p = 1.7 × 10−11, Table 2, Supplementary Table 2), supporting an appropriate selection of the control group. Here, STAT4 is linked to systemic lupus erythematosus.