In three glycosylation loci, we found evidence for pleiotropy (PSMR ≤ 9.1 × 10−4, PHEIDI ≥ 0.05) between at least one IgG glycan and eight other diseases or traits [Crohn’s disease (CD), IBD, UC, RA, primary biliary cirrhosis (PBC), asthma, high-density lipoprotein (HDL) cholesterol, and Parkinson’s disease (PD)] and expression of GSDMB and ORMDL3 in B and T cells and IKZF3 and SLC22A4 in peripheral blood. Here, ORMDL3 is linked to primary biliary cholangitis.