find SNP in UCSC map

[Min Zhang]

Dear Tech support,

Can you show me how to:

1.      Find SNP in UCSC genome browser map view and show the region (exon) and location (number)

2.      Coordinate SNP found in HapMap with UCSC database? They have different ID. I use the SNP found in HapMap and input the region number to Illumina DesignStudio (UCSC database), but it gives me the different genes.

 

Thank you very much.

 

Min Zhang M.D.

Project Scientist III

NeoGenomics Laboratories

5 Jenner, Ste 100

Irvine, CA 92618

Phone: +1 949 206 1695 Ext 2622

mobile: +1 949 246 1110

Email: mzh...@neogenomics.com

 

---

This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secured or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version.
NeoGenomics Laboratories, Suite 5, 12701 Commonwealth Dr, Fort Myers, FL 33913, http://www.neogenomics.com

[Luvina Guruvadoo]

Hello Min,

Thank you for your question. For part one, type in the rs ID in the search box and click 'go' to view this SNP in the browser display. If you click on the item within the display, this will open a page containing all the details for your SNP. If you have a batch of rs IDs, you can use the Table Browser to retrieve this information. See this previously answered MLQ for details: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/2FDJlTTOkEo/OogoLP4eGKcJ. Note in this example, the query is performed on the hg19 assembly using dbSNP build 137. Depending on your research interests, you may also find our Variant Annotation Integrator useful: http://genome.ucsc.edu/cgi-bin/hgVai

For part 2 of your question, are you referring to rs IDs? If not, could you provide us with an example ID? If you are using rs IDs, please make sure you are using the same genome assembly version in the Genome Browser as in the Illumina tool. The rs IDs can be used as input for the position, which will work for most HapMap SNPs. If you don't find a SNP in the Genome Browser, it's possible this particular SNP was merged into a new rs ID. If this is the case, you can search for it and see if there's a note about being merged into a new rs ID on the following page: http://www.ncbi.nlm.nih.gov/SNP/

I hope this is helpful. 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.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group

--