Question: Dbsnp Records That Map To Multiple Genome Locations
gravatar for Andrea_Bio
8.3 years ago by
Andrea_Bio2.5k wrote:

Wise bioinformaticians

Please can you clarify something for me regarding dbSNP. I know dbSNP stores lots of different types of variations but lets just use SNPs for simplicity. How can a SNP map to multiple different genomic locations? I thought a SNP was defined by its flanking sequence so if a SNP maps to multiple genomic locations it means the the entire flanking sequence of the SNP is repeated in multiple genomic locations so 'they' don't know which location it maps to. Is that correct?

Am i also right in noticing that in the latest release of dbSNP, SNPs that used to be classed mapping to multiple genomic locations seemed to have been merged ito new rs ids and now classed as not mapping to a particular assembly. I don't know if this is a new trend or just a coincidence in the records i was looking at.


dbsnp • 2.1k views
ADD COMMENTlink written 8.3 years ago by Andrea_Bio2.5k

As someone who doesn't deal with this kind of data often, could you point to some examples please?

ADD REPLYlink written 8.3 years ago by Daniel Swan13k
gravatar for Neilfws
8.3 years ago by
Sydney, Australia
Neilfws48k wrote:

The first part of this question has been discussed here previously:

Second part: examples please, showing at least one SNP that was previously mapped to multiple locations and now is not.

ADD COMMENTlink written 8.3 years ago by Neilfws48k

if you did discover which of the 'identical' genomic regions it mapped to, how would you distinguish them. I presume you would have to increase the flanking sequence until it became unique for the location of your snp?

ADD REPLYlink written 8.3 years ago by Andrea_Bio2.5k

e.g rs43469576 used to map to these locations but not any more chr7(65859978), chr7(91674598), chr6(86134792)

ADD REPLYlink written 8.3 years ago by Andrea_Bio2.5k
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