Bioinformatics selection of tagging polymorphisms for studying the functions of the VAV3 gene

Introduction. The VAV3 gene is promising for studying its role in the development of molecular mechanisms of pathology. The GWAS Catalog database contains 53 studies of 44 phenotypes, in which single nucleotide polymorphism variants of the VAV3 gene were identified with a statistical significance level of p-value<1 × 10-05. The purpose of the study is to form a sample of marker SNPs to test the hypotheses of the participation of VAV3 in the formation of phenotypic traits in representatives of the Russian ethnic group. Material and methods. To achieve this goal, we used bioinformatics methods, applying them to genotypic data from 1000 Genomes Project. Results. Number of 1000 Genomes Project (phase III) SNPs located within the boundaries of the VAV3 gene with a 5000 bp offset. from the 5´ and 3´ ends, and the MAF of at least 10% was 688. Grouping polymorphisms based on the distance between them takes into account the interaction between SNPs in a block. The number of polymorphisms marked by these tagSNPs did not exceed 4. The intersection of tagSNP lists obtained by two methods showed tagSNPs that were more effective. Tagger and TAGster identified a common marker SNP, rs345292, marking 16 highly linked SNPs. Tagger and Clustag identified rs12733154, which marked blocks of 39 polymorphisms. TAGster and Clustag pointed to rs71655926, which marks 10 polymorphisms. These tagSNPs are located in the introns of the gene of interest and can be considered candidates for association studies. Conclusion. Comparative analysis allowed us to identify three tagSNPs with at least 10 marked polymorphisms confirmed by two methods: rs345292, rs12733154, rs71655926. These polymorphisms may be candidates for studying the role of the VAV3 gene in the mechanisms of pathology development.