MGI 6.18 Find Coding SNPs

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How do I find all known coding SNPs in a specific genomic location for one or more strains?

Overview

You can use the Mouse SNP Query Form to search for mouse single nucleotide polymorphisms represented in dbSNP. Use this form to search for SNPs by associated gene, strain or strain comparison or genome coordinates.

Accessing the Mouse SNP Query Form

On most MGI pages, you can access the Mouse SNP Query Form from the Search menu as shown in the image at right.

For this tutorial, open the Mouse SNP Query Form in a new window. Scroll down this page for further instructions.

Example 1. Finding coding SNPs in Slc10a5 for strains 129X1/SvJ, C57BL/6J and DBA/2J

Type Slc10a5 in the text box in the Associated Genes section.
Select the following strains from the list in Strains and Strain Comparisons section by first clicking the Clear All option and then checking the box next to the desired strains.
- 129X1/SvJ
- DBA/2J
Optional: Choose one strain (in this example, C57BL/6J) as the reference strain by selecting it from the Reference Strain for Comparison drop-down list.
Choose to return SNPs which are the same between selected strains, different, or both by selecting it.
Click Search.

Click any link to MGI SNP Detail in the SNP ID column to view flanking sequence for a SNP.

Filter SNPs result by selecting from dbSNP Function Class. Click Filter.