Variation summary

When you click on a variant ID (for example, rs1333049) from Ensembl views or a search, the variant tab will open up (Figure 28).

Figure 28. Information about rs1333049 is accessible through links in the left-hand menu, and through icons. Click on any link or icon to go to information such as population genetics, linkage disequilibrium, or phenotypes and diseases associated with this SNP.

 

Click on the icons to find information about this SNP. Specifically:

  • Genomic context. View the variant graphically on the genome
  • Genes and regulation. Find out which genes and regulatory features might be affected by this variant
  • Flanking sequence. View the sequence upstream and downstream of the variant
  • Population genetics. See allele frequencies across populations
  • Phenotype data. See diseases and phenotypes associated with the variant
  • Sample genotypes. Find out which alleles are carried by individuals
  • Linkage disequilibrium. View LD plots and export values
  • Phylogenetic context. Compare the nucleotide across species
  • Citations. Find open access papers that mention this variant

 

Figure 29. The top panel of the variant tab provides a summary of information about this variant (in this example, a SNP).

 

The top panel shown in Figure 29 is shown in all variant tab views. It provides basic information about the variant. 

  • Variant class. The type (SNP), variant ID (rs1333049) and link to dbSNP (if a record exists) are provided.
  • Alleles. The possible alleles are shown. The reference allele (the nucleotide in the reference sequence) is listed first. In this case the reference allele is 'G'. Note this may not be the major allele.
  • Synonyms. Any other IDs associated with this variant are shown.
  • Validation statusThis suggests the confidence level of the existance of the polymorphism.
  • HGVS name. A specific name from the HGVS project.