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!
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written
by
valerie
3 answers
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
Run them through the Ensembl VEP. You'll get the genes plus a bunch of other information about how the variants affect the genes.
Yet another answer, via biomaRt, in R: A: How to retrieve Gene name from SNP ID using biomaRt
Kevin
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