We performed the interaction effect analysis of miRNA polymorphism and gene polymorphisms and found three SNP-SNP pairs associated with diseases, of which the interaction of one pair (pri-let-7a-1 rs10739971–ERCC6 rs1917799) was associated with gastric cancer risk, and the interactions of the other two pairs (pri-let-7a-1 rs10739971–PGC rs65458238, and pri-let-7a-1 rs10739971–PGC rs9471643) were associated with atrophic gastritis risk. The gene discussed is PGC; the disease is chronic atrophic gastritis.