Variant Query and Visualization

In this section, users can query genetic variants using two main criteria: by rsID (e.g., rs1805005) or through a combination of chromosome and position (e.g., 16:89919436). The visualizations provided include a geographical map displaying sample coordinates and interpolating allele frequencies, with layers representing individuals as well as their parents and grandparents. Additionally, charts are presented that indicate the samples in GAL carrying the reference allele vs. those with the alternative allele, showcasing the genotypic composition of individuals. A representation of allele variant frequencies across different populations worldwide is also included, along with relevant biomedical information.

For graphical representations of allele frequencies, data is sourced from external databases such as EnsemblEntrez, UniProtKB, OMIM, and dbSNP. The extracted data is structured in JSON format.

Additionally, a ClinVar Data Table is provided, which includes identifiers assigned to the queried variant by ClinGen, UniProtKB, OMIM, and dbSNP. This table details aspects such as the cDNA change (alteration at the complementary DNA level), the variant's position in the hg38 version of the human genome, the associated trait name (Trait Name), the trait reference (Trait Reference), and the protein change (Protein Change) caused by the variant.