Hello Jie, For the 1000 Genomes Project SNPs, if there is an associated dbSNP rs# ID, then the table snp130CodingDbSnp may be useful -- it contains dbSNP's annotations the of functional effects of SNPs.
1000 Genomes Project SNPs from the December 2008 release are included in snp130, but not necessarily the more recent ones. Be aware that there is a lot of overlap between SNPs found by 1000 Genomes and SNPs already in dbSNP. For newer SNPs not yet in dbSNP, we do not currently have an alternative method using the UCSC Browser. There is however an interesting tool in Galaxy that you may find worth experimenting with, under Evolution -> Mutate Codons. The input data could be sent from the UCSC Table browser, the analysis performed at Galaxy, then a custom track sent back into the Browser or simply downloaded directly. http://main.g2.bx.psu.edu/ Back in the UCSC Browser, all dbSNP information can be viewed in the browser (graphically or using the Table browser) as-is, for individual or batch queries, using the dbSNP (130) track. Not all have functional annotation, but it may also be worth examining. To access the data in file format, either ftp the table(s) from the Downloads server or use the Table browser and download (file named and compressed). http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser As an example, an ftp for the data from the Human Mar. 2006 (hg18) assembly, would be to this browsable location: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ Specifically, after login onto the Downloads server via anonymous ftp, cd into the goldenPath/hg18/database/ location Thank you! Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jie Huang (NIH/NHLBI) [F]" <[email protected]> wrote: > From: "Jie Huang (NIH/NHLBI) [F]" <[email protected]> > To: [email protected] > Sent: Monday, January 11, 2010 1:27:13 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] identify nonsynonymous SNPs using UCSC browser > > Hi, I have a list of SNPs. Dose UCSC genome browser/table have a > feature to automatically identify which SNPs are nonsynonymous? For > many SNPs on the 1000 genome project, they only have CHR and POS. can > the UCSC browser query tool work with those type of SNPs? > > Thank you & best regards, > Jie > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
