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User Question 2: Genome Oriented SNP Visualization

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Sample User Question back to top

Mutations in Dopamine Receptor 5 (DRD5) gene have been observed in patients with various neurological disorders. How many ref SNPs records you can find for DRD5 and how many of them are present in its coding region? Show all ref SNPs in the context of a chromosome.

Flow Chart back to top

  1. Entez Gene - Search Entrez Gene database to find gene-centered information and use link to access dbSNP and Map Viewer
    Down Arrow
  2. Entez SNP - Find SNP information for a gene
    Down Arrow
  3. Map Viewer - Display all SNPs in the context of a chromosome


Step By Step Guide back to top

  1. Entez Gene
    • Enter "DRD5" in the search box
    • Click on "Limits"
    • Select "Gene Name" from the drop down list of "To limit your search to a specific field"
    • Go to "Limit by Taxonomy" and select "Homo sapiens"
    • Click "Go"
    • Click on "DRD5" from "Entrez Gene" search result to view gene information
    • Click on "Links" and select "SNP" to retrieve all SNPs records from dbSNP
    • Click on "Links" and select "GeneView in dbSNP" to find location of SNPs on the gene
    • Click on "Links" and select "Map Viewer" to display all SNPs in Map Viewer

  2. Map Viewer
    • Click on "Map and Options" (appears at left side bar)
    • A new pop up window will appear, Select "Variation" available under "Sequence Maps" in "Available Maps" section and click on "ADD" button to include it in "Maps Displayed (left to right)" box
    • Select "Variation" in "Maps Displayed (left to right)" box and Click on "Make Master/Move to Bottom" button
    • Click on "Apply" button


Genetic Variation Return to Slides (*.html or *.mht format -- slide 36)
Return to Exercises List		 Revised 07/24/2007