Reference and mutant allele of a SNP rsID

Question

[DanielC]

Dear All,

Can someone please tell me how to get the reference and the mutant allele of a rsID; like for this rsID "rs80357307" what is the reference allele and the mutant allele?

Thanks much!

Answer 1

[Ben_Ensembl]

Hi Deepak,

This is something that you can do with the Ensembl REST API with the following POST request: http://rest.ensembl.org/documentation/info/variation_id

Best wishes

Ben Ensembl Helpdesk

[DanielC]

Thanks much! But, am a little lost since there is a lot of information in the link. If you could please guide me to what information I should be looking in the link, I would really appreciate. I do see "rsnumber ID" like this:

/variation/human/rs56116432?content-type=application/json

"name": "rs56116432",
  "MAF": 0.00259585,
  "ambiguity": "Y",
  "var_class": "SNP",
  "synonyms": [
    "NM_020469.2:c.689G>A",
    "NP_065202.2:p.Gly230Asp"

Is this the info I should be focussing on? And is "G" the reference allele and "A" the mutant allele?

Thanks.

[Ben_Ensembl]

Hi Deepak,

I think you'd be most interested in the "allele_string" listed as C/T for this variant, for example: http://rest.ensembl.org/variation/human/rs56116432?content-type=application/json

This is the reference allele / alternate allele. i.e C is the reference allele, T is the alternate allele.

Best wishes

Ben Ensembl Helpdesk

Answer 2

[pfs]

You could download the entire data set locally and either query it using a script or load it into a database and query it using a SQL statement. ftp://ftp.ncbi.nih.gov/snp/

Answer 3

[Max Ivon]

You may go directly to dbSNP and check it there https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=80357307 Here "RefSNP Alleles" lists all observed alleles associated with this rsId (keep in mind strand - reverse or forward) Ancestral Allele is listed below as well as contig allele (reference) which is provided in the integrated maps

Also I suppose that it would be more appropriate to not spread same or similar questions among several topics and stick to the original one. Im talking about p/275854/ p/275875/ p/274222/ and p/274026/. If you didnt get the answer you wanted you may just update topic with the new message, no need to create another one. So it would be easier to answer when everybody can see the history of topic

[DanielC]

thanks! but, I want to get this information locally, as I have to do this for 1000s of rsIDS. Can you tell me how can I get this information locally using any tool or linux command or script?

[Max Ivon]

For this goal you may download VCF files from dbSNP ftp server and surf them for each rsID you need. For example here ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/ will be files you need for hg38 genome build. Nevertheless it may require sufficient computational resources and there may be issues with merged rsID's. Therefore i suppose that use of web API would be better solution: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=80357307&retmode=xml This is equivalent to the https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=80357307 So any information can be grasped by script for the sufficient number of mutations.