Stratification of instruments showed that robust associations were observed for MHC variants (IVW: MS OR=1.69, 95% CI=1.57–1.82, p=3.5×10−46; RA OR=1.30, 95% CI=1.23–1.37, p=4.7×10−21; SLE OR=1.74, 95% CI=1.55–1.94, p=1.9×10−22), while non-MHC variants showed no significant causal effects on any autoimmune disease, indicating that the MHC explains a large proportion of the inferred causality for these autoimmune diseases (Extended Data Fig. 9a). Here, HLA-C is linked to systemic lupus erythematosus.