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Locus Details Page

Learn about data showcased on the Cohort Browser's locus details page.

The Cohort Browser is accessible to all users of the UK Biobank Research Analysis Platform and the Our Future Health Trusted Research Environment.

For DNAnexus Platform users, an Apollo license is required to access the Cohort Browser. Contact DNAnexus Sales for more information.

Overview

When genomic information is ingested and made available in the Cohort Browser, variants can be annotated using NCBI's dbSNP and Ensembl's gnomAD. The specific versions of each are provided during the ingestion process and allows the ingestion process to create a set of tables optimized for cohort creation through the Cohort Browser.

Accessing the Locus Details Page

In the Cohort Browser, specific annotation data are already available for both cohort creation and for quick cohort interrogation. This can include gene names, consequences, or reference SNP IDs. To access more detailed information, in the variant section of the Cohort Browser, simply click the location in the allele table and the locus detail's page will open in a new tab.

An example using synthetic UKB data shows how clicking a locus launches a locus details page.

Locus Details Page Subsections

The page is split into 3 sections, all pre-calculated during ingestion of the dataset. The sections start with a summary of the locus, including the genotype frequencies for the datasets at the locus and then there's a detailed breakdown of annotations by allele.

Location Info

The Location Info shows a quick summary of the given locus in the dataset. It shows the chromosome and starting position, the frequency of both the reference allele and the no-calls, and the sum total of alleles available.

An example of a location detail pane.

Genotypes

Synthetic genotype distribution of a dataset

The genotypes section allows users to see a detailed breakdown of the genotypes in the dataset. Given order is not preserved, which means a C/A and A/C will count in the same bucket so only half of the crosstab is populated. These genotypes are for the dataset as a whole at the specific location, and are not specific to the selected cohort.

Alleles

Sample annotation information for the 13:32,332,383 C>A allele

Each allele in the dataset displays information collected from dbSNP and gnomAD during data ingestion. If an rsID or AffyID is available, it appears with a link to the corresponding NCBI dbSNP page. The allele type, dataset frequency, and gnomAD frequency are provided for quick reference. Additional details about each allele are organized by transcript, with columns that may vary depending on the annotation resources used.

For canonical transcripts, a blue indicator will appear next to the ID of the transcripts.

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