Hi!
I've read a lot of posts similar to this but I've not seen (or may have missed) a good solution of how to find all genes in a region when you have multiple (200+ regions).
For example, I have a list of regions like this
chr3:56953782-58953782
chr3:229305477-231305477
chr13:48536705-50536705
chr10:62754024-64754024
chr6:31633697-33633697
chr6:31608932-33608932
chr6:31587588-33587588
UCSC's interface is great, but it gives me a list of all results in one file without indication of which rows belong
#hg19.knownCanonical.chrom hg19.knownCanonical.chromStart hg19.knownCanonical.chromEnd hg19.kgXref.spDisplayID hg19.kgXref.geneSymbol
chr3 56761445 57113336 Q9NR81-2 ARHGEF3
chr3 56974067 56994880 ARHGEF3-AS1
chr3 57094468 57109460 SPT12_HUMAN SPATA12
chr3 57124009 57199403 I17RD_HUMAN IL17RD
chr3 57231943 57234280 HESX1_HUMAN HESX1
chr3 57261764 57307498 DP13A_HUMAN APPL1
chr3 57310555 57326132 C9JX97_HUMAN ASB14
chr3 57327726 57530071 DYH12_HUMAN DNAH12
chr3 57541980 57547768 PDE12_HUMAN PDE12
Ensambl's biomart is great too, but similar problem.
Is there a way I can get something along the lines of:
region Genes
chr3:56953782-58953782 GENE1
chr3:56953782-58953782 GENE2
chr3:56953782-58953782 GENE3
chr3:229305477-231305477 GENE4
chr3:229305477-231305477 GENE5
Thank you!