What resources are used for SNP annotation?

  • In the SNP module, three options are provided for SNP annotation, including HaploReg, PhenoScanner, and VEP by using the Application Programming Interface (API) service of each database.
  • In the gene module, VEP nearest gene mapping pipeline is used to provide the genomic annotation (chromosome location, nearest genes, and most severe consequence) using a 50kb window size based on homo_sapiens_vep_104_GRCh38. The nearest gene mapping retrieves the gene with the nearest transcription start site (TSS) for the input SNP. Note the nearest TSS may not belong to a gene that overlaps the input SNP.