How to get gene name for SNPs RS ids

Question

[valerie]

Hi!

I want to obtain a table of correspondence of all the existing SNP RS ids to the genes they are located in (if they are located in genes). I've tried to use for that biomart, but the download is extremely slow, even though the other files are downloaded quickly. I also found a table in UCSC table browser, but there I can get RefSeq names only, and as the file is large, the translation again takes a lot of time. Is there a simle way to get this kind of table?

Thanks!

[Pierre Lindenbaum]

use mysql , see How To Map A Snp To A Gene Around +/- 60Kb ? (note; the mysql query has changed : mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 )

Answer 1

[GenoMax]

Use EntrezDirect:

$ esearch -db snp -query "rs555895" | esummary | xtract -pattern GENE_E -element NAME
PTEN
PTEN

If you need additional information.

$ esearch -db snp -query "rs555895" | esummary | xtract -pattern DocumentSummary -element SNP_ID,NAME,CHRPOS,DOCSUM
555895  PTEN    10:87961150     HGVS=NC_000010.11:g.87961150T>G,NC_000010.10:g.89720907T>G,NG_007466.2:g.102712T>G,NW_013171807.1:g.176939T>G|SEQ=[T/G]|GENE=PTEN:5728

Answer 2

[Emily]

Run them through the Ensembl VEP. You'll get the genes plus a bunch of other information about how the variants affect the genes.

Answer 3

[Kevin Blighe]

Yet another answer, via biomaRt, in R: A: How to retrieve Gene name from SNP ID using biomaRt

Kevin