Question: More Than One Rs Number For Snp
2
gravatar for Bdv
9.8 years ago by
Bdv310
Bdv310 wrote:

Hi

Why sometimes the same SNP has 2 completely different rs numbers?

snp identifiers • 6.0k views
ADD COMMENTlink modified 9.8 years ago by User 35170 • written 9.8 years ago by Bdv310
1

could you please provide an example?

ADD REPLYlink written 9.8 years ago by Doctoroots790
1

This question has already been addressed here.

ADD REPLYlink modified 17 months ago by Ram32k • written 9.8 years ago by Jorge Amigo12k

Jorge, I think that is the opposite question, how one SNP can map to multiple locations, and not why multiple SNPs can map to a single location.

ADD REPLYlink written 9.8 years ago by Chris Evelo10k

thanks Chris, you're completely right. sorry bdv, I've surely read your question too fast. I'm removing my previous comment not to mislead anyone reading this post.

ADD REPLYlink written 9.8 years ago by Jorge Amigo12k

Thank you for the answers. An example of such a situation is rs35742686,rs4986774 which I believe to be the same... – bdv 0 secs ago

ADD REPLYlink written 9.8 years ago by Bdv310
4
gravatar for Chris Evelo
9.8 years ago by
Chris Evelo10k
Maastricht, The Netherlands
Chris Evelo10k wrote:

Sometimes the dbSNP team originally thought that it really were two different SNPs and thus assigned two different rs numbers which were merged in later builds.

Also see the answer to this question: [?]"How do I query dbSNP so that it will return a flat or xml file containing the new RefSNP (rs) ID number into which a previously valid rs recently merged?"[?] in the SNP FAQ archive book on the NCBI bookshelf. It gives links and information on where you can find [?]the archive[?] of merged rs numbers and how to deal with those.

ADD COMMENTlink written 9.8 years ago by Chris Evelo10k

those different rs numbers pointing to the same biological SNP should then be merged on forthcoming dbSNP builds. each dbSNP build tries to solve issues previously arose, but of course we aren't completely free of finding some after all.

ADD REPLYlink written 9.8 years ago by Jorge Amigo12k
1
gravatar for Larry_Parnell
9.8 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

The answer from Chris is correct. One reason for duplicate rs numbers arises from the fact that SNP discovery work started before the genome was "complete." SNPs were mapped to the Golden Path - and that simple statement does not begin to divulge how hard that work was. Nonetheless, as genome contigs merged into segments representing chromosome arms, so did SNP rs accessions merge into a single entry.

Back in the days of single-gene or single-cDNA sequencing, it would not be uncommon to see that two different groups each submit to GenBank their sequence data for the same gene. Each would be assigned an accession number but each represented the same gene.

ADD COMMENTlink written 9.8 years ago by Larry_Parnell16k

Thank you for the answers. An example of such a situation is rs35742686, rs4986774 which I believe to be the same...

ADD REPLYlink modified 15 months ago by Ram32k • written 9.8 years ago by Bdv310
1
gravatar for Pi
9.8 years ago by
Pi520
Pi520 wrote:

Checkout the flanking sequence of these 2 snps. They are not the same hence the 2 different rs entries

ADD COMMENTlink written 9.8 years ago by Pi520
0
gravatar for Swbarnes2
9.8 years ago by
Swbarnes21.5k
Swbarnes21.5k wrote:

Sometimes I've seen SNP that could be described ambiguously split into two entries.

For instance, one SNP will be described as AGTCC[C-], and a second SNP is described as AGT[C-]CC, and positioned two bases away from the first one.

Yes, proper form dictates that the former is preferred, but if the latter was described properly in reference to a transcript that runs the other way, it's an easy mistake to understand.

ADD COMMENTlink written 9.8 years ago by Swbarnes21.5k
0
gravatar for User 3517
9.4 years ago by
User 35170
User 35170 wrote:

This can be quite common in dbSNP and in version 129 there was a huge surge of such entries (probably due to automated assignment of rs No.?)

Our tool (http://pfs.nus.edu.sg) can help to clarify this problem. Just search the rs No. and all the other rs No. pointing to the same position would be listed as "Alias" in the search result. (e.g: search for rs2032582 will give you 2 entries.)

You can also use http://pfs.nus.edu.sg/handytools.aspx if your know the gene context of your SNP. Just specify the gene context and all rs No. referring to this context would be given.

ADD COMMENTlink written 9.4 years ago by User 35170
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