We presently show that two T1D candidate genes (i.e. PTPN2 and BACH2) modulate STAT1 activation via two different pathways, namely the JAK/STAT, involved in the short-term phosphorylation of its tyrosine residue (Y701), and the MAPKs pathway, involved in the long-term phosphorylation of its serine residue (S727). Here, SOAT1 is linked to type 1 diabetes mellitus.