So the SNP query you want is something like:
http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.snp.ensembl_gene_id|hsapiens_gene_ensembl.default.snp.external_id|hsapiens_gene_ensembl.default.snp.synonymous_status|hsapiens_gene_ensembl.default.snp.snp_chromosome_strand|hsapiens_gene_ensembl.default.snp.chromosome_location&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id
<http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.snp.ensembl_gene_id|hsapiens_gene_ensembl.default.snp.external_id|hsapiens_gene_ensembl.default.snp.synonymous_status|hsapiens_gene_ensembl.default.snp.snp_chromosome_strand|hsapiens_gene_ensembl.default.snp.chromosome_location&FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id>."ENSG00000212912,ENSG00000000003,ENSG00000000005,ENSG00000000419,ENSG00000000457,ENSG00000000460,ENSG00000000938,ENSG00000000971,ENSG00000001036,ENSG00000001084,ENSG00000001167"|hsapiens_gene_ensembl.default.filters.snptype_filters."UPSTREAM"&VISIBLEPANEL=resultspanel
But instead of pasting in the gene IDs you want this to be the result of
another BioMart query, correct? Is the gene query one using the same
ensembl genes dataset - if so you can just set the appropriate filters
along with upstream snps only? If its a novel dataset of yours then you
just need to set up dataset linking between human ensembl genes and your
dataset on ensembl gene IDs.
Thanks for the very helpful reply - I was forgetting upstream as a
consequence in this dataset, which doesn't help... Your suggestions
comes extremely close to fitting the bill and I could definitely use it
as a solution for the user (in the variation mart, rather than the main
mart).
However, lets suppose that the users wanted an upstream window 10kb or
other arbitrary figure (which is actually the original number I was
given), not the 5kb that the consequence represents. Beyond changing how
the consequence is created (or some other way of doing some
precalculation to populate the mart), could I do that?
Cheers,
Dan.
--
Dan Staines, PhD Ensembl Genomes Technical Coordinator
EMBL-EBI Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
