In this study, we explored the intrinsic genetic variants in gastric cancer prognosis individuals based on mGWAS and identified 32 genetic variant loci significantly associated with gastric cancer survival-related metabolites, corresponding to 7 genes, namely, VENTX, PCDH7, JAKMIP1, MIR202HG, MIR378D1, LINC02472, and LINC02310. Here, MIR378D1 is linked to gastric cancer.