If I have specific SNP chromsome locations, what applications can I use to look up if this location is a "gene", "promoter of a gene", "enhancer of a gene", etc, and if it IS any of those, to tell me which gene it is associated with?
I know about GENCODE and ENSEMBL, but I'm look for a more seamless, automatic conversion of BED file information (input) and annotation of genomic "type" and gene association (if there is one) as the outputs.
I'm new to the field so name dropping and tool suggestions are appreciated! If there is an R package that does this, that would be AMAZING.
Thanks for your insights!