Cast study 2: Search for a variant (rs334)

This case study assumes that you have a variant identifier that you want to learn more about, for example from the results of a variant calling analysis. In this example we will be using rs334, a dbSNP identifier.

One place you might search for the identifier is Ensembl. There, you can find the variant alleles and their source, along with links to further information, including population allele frequencies, sample genotypes, phenotypes that have been associated with the variant, and genes and proteins affected by the variant. rs334 has four observed alleles, where T is the reference (Figure 7).

Figure 7 Search for the rs334 variant in Ensembl (view in Ensembl).

In the genes and regulation section we can see that rs334 is a missense variant in HBB, a haemoglobin subunit. It is associated with sickle cell anaemia and malaria resistance, and that the phenotype-associated A allele is mostly found in African populations (you can see this in the Phenotype data and Population genetics sections). This is consistent with what we know about sickle cell anaemia; that it is caused by deformed haemoglobin protein resulting in sickled red blood cells. The same change in the protein structure also confers malarial resistance. This is advantageous to heterozygotes if they are exposed to malaria, so is most common in regions where malaria is endemic.