Aim Single nucleotide polymorphisms (SNP) occurring in the precursor or mature sequences of microRNA or in their binding sites on 3′ untranslated region of target genes may participate in the occurrence and development of many diseases, such as tumor, nervous system diseases, muscle hypertrophy, cardiovascular diseases and so on. In this study, bioinformatics technology was used to analyze the biological processes and signal pathways that may be affected by SNP rs386585341 A＞G located at the fourth position of miR-499a-3p seed sequence. Methods RNAfold database was used to predict whether rs386585341 A＞G would affect the secondary structure of pre-miR-499a. Pre-miR-499a-A and pre-miR-499a-G overexpression plasmids were constructed respectively to detect whether rs386585341 A＞G would affect the expression of mature miR-499a. Gene expression microarray and bioinformatics were used to analyze the effect of rs386585341 A＞G on the function of miR-499a-3p, then take the intersection of differential gene expression profile and TargetScan target gene, and analyze the divergence of target genes of miR-499a-3p with different alleles of rs386585341A＞G.Results rs386585341 A＞G did not affect the secondary structure of pre-miR-499a, nor the expression levels of mature miR-499a-5p and miR-499a-3p, but affected the target gene network regulated by mature miR-499a-3p. The results of GO and pathway analysis of differentially expressed genes (DEG) showed that miR-499a-3p-A and miR-499a-3p-G showed different biological functions. The downstream gene network of miR-499a-3p-A was mainly enriched in immune regulation, while the downstream gene network of miR-499a-3p-G was mainly enriched in angiogenesis. The 4 target genes of miR-499a-3p-A including Spry2, Pcnx, Ndufa5 and Tcf7l2, were obtained by intersect analysis of down-regulated genes and TargetScan target genes, but the direct target genes of miR-499a-3p-G were not obtained. It indicated that after the miR-499a-3p seed region fourth was converted from A to G by rs386585341, the target gene formula of miR-499a-3p could be transformed from the degradation of target gene mRNA to the protein translation that only inhibits target genes.Conclusion rs386585341 A＞G may play important roles in immune differentiation and angiogenesis by affecting the downstream network of miR-499a-3p.