How to get list of GeneIDs using SNP ID list?

Question

[goksoy66]

Is there any way to get the list of gene IDs by giving SNP IDs, via a web (REST) service? I need services like following:

http://www.kegg.jp/kegg/docs/keggapi.html

I have a SNP list (like rs1312321, rs4524523), and I need to find the mapping gene list of these SNPs. Then I will search for KEGG pathways having these gene IDs.

SNP List --> Gene List --> Pathway List

Answer 1

[Emily]

You can use the Ensembl VEP.

[goksoy66]

Thanks for answer.

Now I can get gene ids, but they are in type of Ensembl Gene ID. So I need to convert them to KEGG Gene ID.

KEGG REST API allows conversion from ncbi-gi, ncbi-geneid and uniprot. So these types are also ok for me. I can convert them using following rest url.

http://rest.kegg.jp/conv/genes/ncbi-geneid:3113320

Do you know a way to convert from ENSG to other ids?

[Emily]

You can get Uniprot IDs as VEP output. Just open up the Identifiers and frequency data menu and select Uniprot.

[goksoy66]

I couldn't find any web service. Here we can query via graphical user interface, only.

[Emily]

Really? The link I sent you has a big blue button that says Launch VEP.

[goksoy66]

Really? Did you understand what I mean? I want to convert IDs programmatically. So I need a rest service like this.

http://rest.kegg.jp/conv/genes/ncbi-geneid:3113320

If we click to that big blue button, we only get a GUI.

[Emily]

Yes, you said you wanted a GUI, so I pointed you to a GUI. If you want a REST service then click on the big white button that says REST.

[EagleEye]

You can try this one:

http://idconverter.bioinfo.cnio.es/

And if you want to try in my way, you just have to tweak these files:

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

Answer 2

[EagleEye]

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/

variant_summary.txt.gz file has all clinical variants mapped to Genes (Column4: GeneID, Column5: GeneSymbol and Column7: rsID)

Answer 3

[Maxime Lamontagne]

SNPnexus