Specifically, our meta-analysis identified 38 genetic variants shared among subsets of the diseases under study, five of which, including PADI4, NAB1, COBL, CCL21, and GATA3, represent new shared genetic risk loci. Moreover, ten of the 38 pleiotropic variants showed opposite allelic effects across phenotypes contributing to the association signal, thus indicating the complexity of the molecular mechanisms by which SNPs affect autoimmune diseases. Here, PADI4 is linked to autoimmune disease.