Question about chromosome 12
John Boyle
Brian Lee
Dear Jack,
Thank you for using the UCSC Genome Browser and your question about investigating a SNP given "chr12:612,2713G>A".
You are correct to think that this likely indicates a variation of a G to A. If you go to our website, http://genome.ucsc.edu/, and select under "Genomes" on the blue bar menu "Human GRCh37/hg19" and then in the box where it says "enter position, gene symbol, HGVS or search terms" paste your coordinates only chr12:612,2713 you will end up in the region of the gene VWF and see a G at the very top of the screen indicating the base at this location is a G in this version of the human assembly.
The Browser has many tools to help researchers investigate their data. One of the biggest tools is the ability to load custom tracks to annotate regions of the genome. There are a variety of custom track types, one of which is called the Personal Genome SNP format (pgSnp): http://genome.ucsc.edu/FAQ/FAQformat.html#format10
You can take the information you have shared, "chr12:612,2713G>A" and convert it into this pgSnp format and load it into the browser. To do this you have to subtract one (-1) to the coordinate as we use a 0-based in our data system (the first base in a chromosome is numbered 0). The other columns in the pgSnp format allow you to define what is happening, for example you share that either a G/A is possible, so this goes in column 4, and the other columns reflect the ability to share possible frequency information (if it was known). Then to become a custom track, you can also add a track line, where you share this data is going to be of "type=pgSnp" and give it a name and description:
track type=pgSnp name=SNP description="chr12:612,2713G>A"
chr12 6122712 6122713 G/A 2 0,0 0,0
With this text that describes your "chr12:612,2713G>A" inquiry, you can go the "My Data" menu in the top blue bar and then select Custom Tracks. In the top right corner be sure that "assembly GRCh37/hg19" is displayed. In the big box you can paste the above text. Then click the "go" button on the following screen or click "Genome Browser' from the top blue bar and navigate back to the chr12:612,2713 location.
With this custom track loaded, you can use another tool called the "Variant Annotation Integrator" by clicking the "Tools" menu and then selected it as the third option. This tool will allow you to find out what impact this SNP will have on genes. Under "Select Variants" you should see what was put in the description="chr12:612,2713G>A" displayed for your pgSnp track. Scroll down the "output format" section and change it to the " (HTML)" option then click the "Get results" and then click the "I understand and agree" message about how this is for research only. You will see there is a "Consequence" column where for one gene the change from a G to an A has an impact on one of the genes. Note that you can scroll back up tot he top of the previous page and change the "Select Genes' option from "UCSC Genes..." to "RefSeq Genes" or other options and get the impacted results of this change on other gene sets.
To help with illustrating this process, here is a session link where the above custom track has been loaded: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.pgSnpExample
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Brian Lee
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CANO0VSqFo5KrFC031oeEw%3DqHc-NbQ1YmOzpaKJUD0f3HAHtokg%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.