Database SNP Criteria

Our database currently houses SNP locations and alleles extracted from dbSNP Build 137, as prepared by the R Bioconductor package SNPlocs.Hsapiens.dbSNP.20120608.

SNPs from dbSNP were filtered to keep only those satisfying the 3 following criteria:

  1. The SNP is a single-base substitution i.e. its type is "snp". Other types used by dbSNP are: "in-del", "mixed", "microsatellite", "named-locus", "multinucleotide-polymorphism", etc... All those SNPs were dropped.
  2. The SNP is marked as notwithdrawn.
  3. A single location on the reference genome (GRCh37.p5) is reported for the SNP, and this location is on chromosomes 1-22, X, Y, or MT.

Minor allele frequencies are drawn from the latest 1000 genomes reference population, as used on dbSNP as well.