To use the Signal Explorer tool, provide the following inputs into the data configuration panel (figure 1), as explained in sections 1-3:
- A region of the genome or locus.
- A genetic reference population for the estimation of linkage disequilibrium (LD) and minor allele frequency (MAF).
Figure 1: The Signal Explorer data configuration panel.
1. Region
Specify the region of interest using one of the following options:
- Window around variant – Enter an ID for the variant, comprising the chromosome number, position of the variant, reference allele, and the alternative allele (CPRA).
Alternatively, enter an rs ID number from the dbSNP database, e.g rs7903146. If more than one variant is associated with the rs ID, a pop up window will prompt you to select one of the matching options.
Window size: By default the region is 1Mb in size - 500kb upstream and downstream of the position centre. This can be changed by updating the ‘Window size (kb)’ field. - Gene – Enter a gene name. E.g. SLC2A9.
- Range – Enter the chromosome number, followed by a start position and end position, to view the selected range. E.g. 4, 9993256 and 9997256.
2. Release
Check or amend your release settings:
Release – Check the data pre-selected from the Browse Datasets tool, or select the required release using the release selection options.
Ensembl – View the reference used by the dataset.
3. Datasets
Search for a dataset using the Datasets search field. Search by typing in a dataset name, phenotype or source and select the required datasets.
Alternatively, search for signals available in the region using the view signals in region button.
Previous: What is Signal Explorer?