Scope Single nucleotide polymorphisms (SNP) in the fatty acid desaturase 1 (FADS1) gene is suggested as risk factor of metabolic diseases in genome‐wide association studies (GWAS). This study hypothesized that FADS1_rs174546T associates with serum triglycerides (TG) in Korean Genome and Epidemiology Study (KoGES). In addition, functional study of SNP genotypes in cultured cells is performed. Methods and results FADS1_rs174546T is associated with high level of serum TG (effect size of variant: 6.48 ± 1.84 mg dL−1) in Korean individuals (normotriglyceridemia, n = 5128; hypertriglyceridemia, n = 3714). Functional study in cells with FADS1_rs174546T, shows reduced transcriptional activity, when compared with rs174546C. MiR‐6728‐3p, which is predicted to bind with rs174546T, decreases transcriptional activity of rs174546T but not in rs174546C, and it is reversed by miR‐6728‐3p inhibitor. Formononetin is selected as binding molecule to 3′‐UTR of FADS1 and increases luciferase activity in both rs174546 (C/T). Moreover, formononetin compensates for the reduced luciferase activity by rs174546T and miR‐6728‐3p. Formononetin also increases endogenous FADS1 expression and long‐chain polyunsaturated fatty acid (LC‐PUFA) ratio. Conclusion FADS1_rs174546T is a crucial risk factor for hypertriglyceridemia in the Koreans potentially through the interaction with miR‐6728‐3p. Formononetin can be a potent dietary intervention to prevent and improve hypertriglyceridemia in both rs174546 (C/T) populations. The Korean Genome Epidemiology Study demonstrates that FADS1 rs174546T, minor allele, associated with high triglyceride levels. The luciferase assay after transient transfection of 3'‐UTR of FADS1 rs175446T shows reduced transcriptional activity. Moreover, FADS1 rs174546T serves a new target site for miR‐6728‐3p in hepatocytes and inhibitor of miR‐6728‐3p restores the reduced expression by rs174546T. Formononetin compensates for the adverse effects of miR‐6728‐3p on FADS1 rs174546T and possesses the potential for preventive medicine.