How to get rs number for the variants list?

Question

[Andy]

Hi, I have a list of variants with varints id like 1_98929_A_G_b37 and repsonding GENE id like ENSG00000237094.7. Is there any R package or on-line tools that can convert these kind of hg 19 SNp id and ensenble id into rs id and ordianry gene names? Any ideas is appreciated

[GenoMax]

BioMart from Ensembl is generally the way to retrieve this type for information. You may need to use hg19 archive if you specifically wanted to do that. If you are comfortable with a programmatic solution then there is Variation API from Ensembl.

Answer 1

[dyollluap]

If you've got the list of variants in VCF format, I'd recommend using the VEP tool http://www.ensembl.org/info/docs/tools/vep/index.html

It enables further annotation with gene name symbols and dbgap accessions etc.

Answer 2

[loic.mangnier.1]

I have just came upon this post because of similar question. If you have eQTLs data from GTEx, you are better to use the annotation file from the corresponding version in GTEx Portal.

For example, if you are using the v7 release, the liftover file between rsid and GTEx constructed id could be found in the file GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_635Ind_PASS_AB02_GQ20_HETX_MISS15_PLINKQC.lookup_table.txt.gz

Here a little sample from the file:

chr variant_pos variant_id  ref alt num_alt_per_site    rs_id_dbSNP147_GRCh37p13
1   10478   1_10478_C_G_b37 C   G   1   rs528916756
1   10480   1_10480_C_A_b37 C   A   1   .
1   10482   1_10482_G_C_b37 G   C   1   .
1   10489   1_10489_C_T_b37 C   T   1   .
1   10497   1_10497_C_T_b37 C   T   1   .
1   10523   1_10523_TCCG_T_b37  TCCG    T   1   .
1   10563   1_10563_C_A_b37 C   A   1   .
1   10565   1_10565_C_T_b37 C   T   1   .
1   10579   1_10579_C_A_b37 C   A   1   rs538322974

Hope this help.

Answer 3

[sk792]

Hi everyone, I have prepared a video on YouTube using Kaviar to show you how to map from Chromosome and Base Pair Information to rsID #s for Single Nucleotide Polymorphisms (SNPs):

For example, how do you go from converting from Genetic Variant at chr1, 715265 to the SNP ID: rs12184267

Please note that a key website used here is: http://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.pl Kaviar's limit is only 100,000 genetic variant Ids in 1 query search at a time.

I hope this helps! Please let me know if you have any questions at all. I hope to help with more videos, so please subscribe to my channel (https://www.youtube.com/channel/UCNhVAcIdarXzTCWZ27N1EmQ) for more updates :)

Best wishes, Saniya Khullar