The SNP Consortium Database

Discovery Questions


Let’s take a look at some SNP data that is compiled on a database at Cold Spring Harbor Laboratories on Long Island, NY. Go to the SNP Consortium (TSC) web home page <http://snp.cshl.org/> and follow these directions.

1) You have to use a browser that works with the Java applet that is supported only by IE on the Macintosh platform. Click on the SNP for chromosome 1 called “ TSC0019265”. Find the highlighted SNP and use the key to figure out what bases have been found at this locus. In the key is a link called “mapping primer” which leads you to the PCR primers used to amplify this SNP in case you wanted to survey a population at this locus.

5) In the Details box, you can see the frequency of the two bases. Below this is a link that says “View Traces”. Click on this and you can see the chromatograms for the three alleles that have been sequenced for this SNP.

6) While on this page, you can go to the top and compare the “tree view’ and “graphic view”. They allow you to see the same information in different layouts.

7) While on the TSC0019265 page, scroll to the top of the page and click on the link located to the right of “dbSNP Acc#”. This will take you to the NCBI page with information about this particular SNP. You can see similar information about the SNP, but now there are new links in the left column. Under the heading of “search”, click on the link that says “population”. This lists all the different human populations that were used to search for SNPs. You can scroll down and see some obvious populations while other names are more cryptic.

8) Scroll down to the population submitted by DEBNECK and is called “MDECODE-3”. When you click on this link, you will see the description of this population. Based on what you learned in chapter 3 about the evolution of humans, would you predict there will be a lot or few SNPs in this population?

9) Click on the link that says “View SNP used on this population” and see if your prediction was correct or not. Compare this list with any other population you choose to see which list is longer.

10) Return to the MDECODE-3 list of SNPs. Click on SNP “ae1163” and see if this is an uncommon SNP or a more common one. Apolipoprotein E is a gene that has been associated with early onset Alzheimer’s disease. This is a coding SNP and therefore of special interest. You can click on the other 3 MDECODE populations to see their descriptions as well.

11) Compare the proportions for SNP ae1163 with another SNP in the same gene (any that start with “ae” on this page). Does ae1163 exhibit more or less frequent diversity than other SNP points in this gene? Do you think this is due to chance or selection pressures?

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