5.6 years ago by
You can use the Ensembl Variant Effect Predictor to see which genes are affected by your SNPs.
This is available as an online tool and as a Perl script. It will predict the consequences of each variant in the genes affected, giving you SO terms (see the link below). Variants within 5kb of a gene will be listed as upstream or downstream gene variants. You can also choose to get SIFT and PolyPhen scores for amino acid changes. And you can check if your variants have already been annotated in our database.
If you really want to use a 10kb flank, there is a plugin that you can use with the VEP script that will allow you to change the flanks. You'll find it here:
perl variant_effect_predictor.pl -i input.txt -plugin UpDownDistance,10000
to set the distance to 10kb. Up/down distances can also be set separately:
perl variant_effect_predictor.pl -i input.txt -plugin UpDownDistance,10000,20000
sets up to 10kb and down to 20kb.