[ensembl-dev] BIOMART segment(SNP) query

[Matthias Macé]

Dear all,
First thank you for any suggestion.
We are trying to get genes overlapping with segments comprised between
two SNPs.
Input = rsID from start snp, rsID for end snp (as shown below).
Expected output : gene IDs

Example:

query:            rs_ID_1---------------------------rs_ID_2
<-----------gene_1------------->
                                        <-------gene_2--------->
                                                       
<-----------gene_3------------->

It would return : gene_1, gene_2, gene_3


We would like to perform this in a unique query (e.g. not with a first
query SNP >> coordinates followed by a second coordinates >>> genes).

We tried this using Biomart (db=Homo sapiens Variation (dbSNP
132;ENSEMBL); Filters: REGION/Marker-end-start; Attributes: any ID)
without success (it returns a null output). In a general way, nothing
happens when using this filter.

So here comes our questions:
- how to use this filter ?
- do you have any suggestion for doing this ?


Best regards,
MM


-- 
"Only two things are infinite, the universe and human stupidity, and I'm
not sure about the former." -Albert Einstein

Dr Matthias Macé, DVM, PhD
*INSERM U1043*

C.H.U. Purpan - BP 3028

31024 TOULOUSE CEDEX 3

tel: (33) 562 74 45 09

mobile: (33) 608 881481

http://www.u563.toulouse.inserm.fr/

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