Both type 2 diabetes (two at SND1–PAX4 locus and one at GAST locus) and GC (EFNA1, PTGER4 and PSCA loci) shared three significant variants after Bonferroni’s correction (P < 8.6 × 10−6) with PUD or its subtypes (Supplementary Fig. 16). Here, EFNA1 is linked to type 2 diabetes mellitus.