Newbie, SNP to gene analysis question

Question

[ena4487]

Hi,

I am learning how to identify candidate genes for schizophrenia given a SNP on the UCSC genome broswer. Can anyone familiar with this process let me know if I'm on the right track? If not what can I do differently.

The SNP is rs11682175. I think the candidate gene is either RTN4 or VRK2 because their promoter show enhancer activity in the brain but I don't know which is the better candidate? Or maybe there is a way better candidate that I'm missing!

The links

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr2%3A55273072-55282547&hgsid=448748255_AW41GPHAXg1WnZtw1LLCLTCxQVb0

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr2%3A58090363-58189363&hgsid=448748255_AW41GPHAXg1WnZtw1LLCLTCxQVb0

Thanks in advance!

Answer 1

[cpad0112]

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=11682175

[ena4487]

Thanks for the link. I don't see anything about any likely genes in the link....

[cpad0112]

• Could you see "HGVS Names" in the top right corner of the page (dbSNP link)? If you look at it, it clearly says that this SNP (rs11682175) is non-coding. If you do not understand HGVS names, scroll further down below. There will be graphics view displaying the snp. Zoom out and you would see that it falls in an uncharacterized loc.
• Next to "HGVS Names", there are two buttons: "links" and "linkout". Click on links option and a menu appears with "UC Santa Cruz" as 4th option. Click on it. It would be open another page with 4 links. Click on the links (any one). It would take you to UCSC browser. Zoom out by 1.5x, 3x, 10x. You wo.uld not find any human mRNA track at that position