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 in Slc10a5 for strains 129X1/SvJ, C57BL/6J and DBA/2J
  1. Select the following strains from the Available Strains list by highlighting them and clicking the Add key (box) to move them into the Selected Strains window. Select multiple entries at the same time by holding down ⌘ (Mac) or CTRL (PC). Adjust the display order of strains using the arrows to the right.

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

  2. Optional: Choose one strain (in this example, C57BL/6J) as the reference strain by clicking the lower Add button next to the Reference Strain window. This will allow you to display alleles as S (same) or D (different).

  3. Choose to return SNPs which are the same between selected strains, different, or both using the drop down menu.

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

  5. Type Slc10a5 in the text box in the Associated Gene(s) row. Alternatively, you could search by position (GRCm38/mm10 coordinates), or by a marker range (use official gene symbols, rsID numbers are not supported).

  6. Select additional output options and specify whether output should be displayed on the web (as here), or downloaded.

  7. 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