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Background  Recent genome-wide association studies (GWAS) have identified many SNPs associated with type 2 diabetes mellitus (T2DM). However, the functional roles for most of the SNPs have not been elucidated. MicroRNAs (miRNAs) are key regulators of gene expression involved in the development and progression of various diseases including T2DM. In this study, we investigated whether commonly occurring SNPs modulate miRNA-directed regulation of gene expression, and whether such SNPs in miRNA-binding sites are associated with the susceptibility for T2DM.    Methods  Genotypes of eleven 3′ untranslated region (UTR) SNPs of seven susceptibility genes for T2DM were determined in 353 T2DM patients and 448 control subjects. In addition, the interactions of miRNAs with the 3′UTR in the hepatocyte nuclear factor 1β ( HNF1B ) gene were investigated using luciferase reporter assays.    Results  One 3′UTR SNP (rs2229295) in the  HNF1B  gene was significantly associated with T2DM, and the frequency of an A allele (rs2229295) in T2DM patients was decreased compared with that in controls. Luciferase reporter assays showed that the SNP (rs2229295) altered the binding of two miRNAs (hsa-miR-214-5p and hsa-miR-550a-5p).    Conclusions  We have detected the interactions of hsa-miR-214-5p/hsa-miR-550a-5p and the 3′UTR SNP of the  HNF1B  gene by  in vitro  luciferase reporter assays, and propose that the binding of such miRNAs regulates the expression of the  HNF1B  gene and the susceptibility of T2DM.    Electronic supplementary material  The online version of this article (doi:10.1186/s12881-015-0219-5) contains supplementary material, which is available to authorized users.

Polymorphism in microRNA-binding site in HNF1B influences the susceptibility of type 2 diabetes mellitus: a population based case–control study