Variation summary

When you click on a variation ID (for example, rs1333049) from Ensembl views, the variation tab will open up (Figure 31).

The variation tab

Figure 31. 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 what genes might be affected by this variant
  • Population genetics. See allele frequencies across populations
  • Individual genotypes. Find out which alleles are carried by individuals
  • Linkage disequilibrium. View LD plots and export values
  • Phenotype data. See diseases and phenotypes associated with the variant
  • Phylogenetic context. Compare the nucleotide across species
  • Flanking sequence. View the sequence upstream and downstream of the variant



The top panel of the variation tab

Figure 32. The top panel of the variation tab provides a summary of information about this variant (in this example, a SNP).


NotesThe top panel shown in Figure 32 provides basic information about the variation. It is shown in all variation tab views. Specifically, you can find the following in this panel:
  • Variation class. The type (SNP), variant ID (rs4446534) 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 variation are shown.
  • Validation statusThis suggests the confidence level of the existance of the polymorphism.
  • HGVS name. A specific name from the HGVS project.