Get gene names from rs SNP ids for mmusculus_gene_ensembl

Question

[julian.d.stamp]

I have mouse data with an old mapping from rs SNP IDs to base pair position and chromosome. I would like to query Ensembl to get the genes and then the gene annotations for the rs SNP IDs in my data. When I go to the Ensembl website (http://useast.ensembl.org/Mus_musculus/Info/Index) with GRCm39, I can enter the rs ID and get information on that SNP. I would like to do this in code because I have about 250 SNPs that I want to look at.

I found this old post, that does what I want for homo sapiens: Get gene names from rs SNP ids

This code still works for homo sapiens. However, when changing it to the mouse genome GRCm39 (mmusculus_gene_ensembl), there does not seem to be a single filter by which I could query the database using the rs IDs.

Here is my code:

ensembl <- useEnsembl(biomart = "genes", dataset = "mmusculus_gene_ensembl")
filters <- listFilters(ensembl)
attributes = listAttributes(ensembl)

for (f in filters[,1]) {
  print(f)
  searchFilterOptions(mart = ensembl, filter = f, pattern = "rs")
}

None of the filters shows any results for any rs query. Does anyone understand what I am doing wrong?

Answer 1

[LChart]

If your snp IDs are truly from the mouse dbSNP (i.e., differences between mouse strains), you can paste the list into the batch query field on the jackson lab website:

http://www.informatics.jax.org/batch

and you can download the result as a text file

[julian.d.stamp]

This does give me information for a large chunk of the IDs I have! Thank you!