Here, we aim to review the knowledge of functional consequences of T1D risk SNPs on the regulation, expression and function of linked risk genes and further contemplate how this may impact the functionality of the effector vs. regulatory T cells, changing the balance between immune activation and suppression in the pancreas that is critical to attenuate chronic inflammation and an uncontrolled damage of insulin producing β-cells. Here, INS is linked to type 1 diabetes mellitus.