How to get SNP information.

[Venkat Addala]

Hello,

I have list of 700 genes, i want entire SNP information i.e (start, end, observed, moltype, valid, avhet, function, exceptions, allele, allele frequency) from USCS table. Please Help.

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Thanks & Regards

Venkat Addala

Computational Biologist

[Pauline Fujita]

Hello Venkat,

The best option for that number of gene regions would be to use the Table Browser and the define regions function. To do this go to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and select:

group: Variation and Repeats

track: All SNPs (137)

table: snp137

region: click the "define regions" button

In the region definition menu, you can paste or upload a file containing the coordinates of your gene regions of interest. These coordinates will need to conform to the syntax used in the browser - which is described just below the box where you can enter them.

Note also that our coordinates always have a zero-based start and a one-based end - you can read more about that in this FAQ:

http://genome.ucsc.edu/FAQ/FAQtracks#tracks1

If you do not already know the coordinates of your regions of interest, you could also generate a list of coordinates based on a list of genes using the Table Browser. To do this select:

group: Genes and Gene Prediction Tracks
track: your preferred gene prediction track (i.e. UCSC Genes)
table: knownGene

region: genome

identifiers: click "paste list" and enter your list of gene names - note that they will have to be of the form described by the examples

output format: BED

then after clicking 'get output' you will need to specify which genic regions you want to include (i.e. intron/exons etc). You can then use this BED output in the "define regions" step above.

If you have further questions please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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