The rs number is an accession number used by researchers and databases to refer to specific SNPs. It stands for Reference SNP cluster ID.

When researchers identify a SNP, they send the report, which includes the sequence immediately surrounding the SNP, to the dbSNP database. If overlapping reports are sent in, they are merged into the same, non-redundant Reference SNP cluster, which is assigned a unique rsid.

More information is available in following link http://www.ncbi.nlm.nih.gov/sites/books/NBK44406/

The rs number is an accession number used by researchers and databases to refer to specific SNPs. It stands for Reference SNP cluster ID.

When researchers identify a SNP, they send the report, which includes the sequence immediately surrounding the SNP, to the dbSNP database. If overlapping reports are sent in, they are merged into the same, non-redundant Reference SNP cluster, which is assigned a unique rsid.

More information is available in following link http://www.ncbi.nlm.nih.gov/sites/books/NBK44406/

Whether you are studying a new SNP or which is already studied. If it is a old one, the SNP might have some position information. Try to look for papers with that information and there is a possibility that you may find.

Hi, if you know the name of the gene and the location of the SNP (like intron, exon, utr..) you can use the UCSC browser.

If you have the primer sequences used to amplify the region of interest reported in a paper, paste it into in-silico PCR of UCSC genome browser. this will return the pcr amplicon region. click further into this region and add color codes or font sizes. this can be added to highlight the exons or introns, SNPs can also be highlighted in this region, clicking on each SNP will open a page giving its rs number, ancestral allele, frequency etc. Look for the sequences flanking the SNP. Then cross validate this rs id in dbSNP in NCBI. 

Hope this helps.

Hello 

You can try ENSEBL http://www.ensembl.org/index.html

I tried it once, it helped.

Hello Ghannimah Alghuwainem,

You can try Variant Name Mapper option of HuGENavigator

http://www.hugenavigator.net/HuGENavigator/startPageMapper.do

Good luck.

If you have the chromosomal position of the variant go to http://www.ncbi.nlm.nih.gov/snp/advanced.  You usually can get by with typing in the chromosome number:base position (i.e. 11:24619741) in the "builder" field.  Sometimes it's easier to add your specific organism if you don not want to see multiple snps.  I hope this helps.

Hi--if one by one is too painful, you could make a list of positions (one per line) and grep -f in unix/linux versus a downloaded version of dbsnp.  This is definitely the better way to do it if you have many variants.

Thank you for this question and answers.

I have similar problem. 

However, I still don't know how do I extract the information from this paper to search for the rs number.

Can anyone help me?

Many thanks.

The biomaRt package is really powerful, which is an API of Ensembl. It also can access all database in Ensembl.

For example, if you want know the rs id of snp at 20:4916731 in cow. The code is showed below:

snpmart = useEnsembl(biomart="snp", dataset="btaurus_snp")

getBM(attributes=c('refsnp_id','allele','chrom_start','chrom_strand'), filters = c('chr_name',"start","end"), values =list(20,4916731,4916731),mart = snpmart)

If you have a large number of snps to convert, just write a simple loop to get it.

Hello

You can try https://www.ncbi.nlm.nih.gov/snp/?term= 

Kaviar (http://db.systemsbiology.net/kaviar/) can give you the RS information using the coordinates

Just go to https://www.snpedia.com/ and find anything about dbSNP_rs

ClinVar is good tool for rs search