[ensembl-dev] incorporation of dbSNP 132 into ensembl

[Andrea Edwards]

Dear all


I was hoping you might be able to help me with something to do with the 
incorporation of dbSNP 132 into ensembl

I was looking at rs43469576 a few weeks ago  in dbSNP and I am 99% 
positive it said on the webpage in big red letters that this snp mapped 
to 3 genome locations. I checked what ensembl does about this and i have 
code showing how ensembl too maps it to 3 genome locations

    * chr7(65859978), chr7(91674598), chr6(86134792)

Now when i look at dbSNP it says this variation isn't mapped to any 
assembly. If i search dbsnp for one of those genome locations (e.g. 
chr7(65859978)) rs43469576 is no longer in the results

Now i appreciate that I am a fallible human being and could have got 
confused but it looks to me as if dbSNP has changed and now doesn't seem 
to show snps as mapping to multiple locations. I looked on their build 
release notes and schema revisions etc but there is no mention of this. 
So perhaps i am mistaken. It often happens :)

But regardless of whether i am mistaken or not there still exists a 
difference between the info in ensembl and dbsnp and I would like to 
know what to expect from ensembl in the january release. Will i still 
see a variation like rs43469576 mapped to multiple genome locations or 
will it be mapped to no assembly.

Which then leads to the next question, what will you get for a variation 
feature start/end/chromosome if it isn't mapped. As i said at present 
ensembl seems to map the rs entries in dbSNP that are unmapped so I've 
not come across it.

thanks a lot

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