Get dbSNP ids for a gene name
Hi all,
I have a list of genes and I would like a list of rs# for that gene. I can see that one can view such a list at the following URL:
http://www.ncbi.nlm.nih.gov/snp?cmd=search&term=LPL
But my question is how could I do this programatically and get a list of rs#.
Thanks
3 answers
Programatically, you can use BioMart. Here's an example using the R/Bioconductor biomaRt package.
library(biomaRt)
mart.genes <- useMart("ensembl", "hsapiens_gene_ensembl")
getRsids <- function(gene = "LPL", mart = mart.genes) {
results <- getBM(attributes = c("external_id", "external_gene_id"),
filters = "hgnc_symbol", values = gene, mart = mart)
return(results)
}
# default gene = LPL
lpl <- getRsids()
head(lpl)
external_id external_gene_id
1 rs368991480 LPL
2 rs200280296 LPL
3 rs186940970 LPL
4 rs151133350 LPL
5 rs180845880 LPL
6 rs3043732 LPL
# or specify gene e.g. p53
p53 <- getRsids(gene = "TP53")
It seems this is what you want ( ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/gene_report/ ).
It also seems that Bioconductor maintains an annotation package for some of the dbSNP releases, eg http://www.bioconductor.org/packages/release/data/annotation/html/SNPlocs.Hsapiens.dbSNP.20120608.html
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