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 strain or strain comparison, dbSNP attributes, marker, marker range or associated gene.
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.

Search Menu SNP QF

Example 1. Finding coding SNPs between genes Slc10a5 and Car3 for strains 129X1/SvJ, C57BL/6J and DBA/2J
  1. Select the following strains from the Available Strains list:

    • 129X1/SvJ
    • C57BL/6J
    • DBA/2J

  2. Click the Add button to move strains to the Selected Strains list.

  3. Select Coding-NonSynonymous and Coding-Synonymous from the dbSNP Function Class pick list.

  4. Type Slc10a5 in the first Marker range text box, and Car3 in the second.

  5. Click Search.
SNP QF Screen Shot
  1. Click any link to MGI SNP Detail in the SNP ID column to view flanking sequence for a SNP.
SNP Search Results