The association between VDR rs1544410 and the risk of progression to T1D in IA positive children differs by PTPN2 rs1893217 genotype. Black dots represent the hazard ratio for the VDR rs1544410 AA/AG genotype (with GG genotype as the referent). The solid lines represent the 95% confidence intervals for the hazard ratios. In children with the PTPN2 rs1893217 AA genotype (n = 79), the VDR rs1544410 AA/AG genotype (n = 54) was associated with a significantly lower risk of progressing to T1D compared to children with the VDR rs1544410 GG genotype (n = 25) (HR: 0.24, 95% CI: 0.11–0.53, p-value = 0.0004). In IA positive children with the PTPN2 rs1893217 GG/GA genotype (n = 43), the VDR rs1544410 AA/AG genotype (n = 27) was not associated with progression to T1D (HR: 1.32, 95% CI: 0.43, 4.06, p-value = 0.62).