If we have list of cnvs and their start stops and another list of genes and their start and stops..How can we map CNV region i.e its start and stop to a gene and find if there is an overlap(whether gene falls outside this region or within this region) in an automated way?
It may depend on what you mean by automated, but this is a fairly simple programming task. It would make a good exercise for someone trying to learn a scripting language and they could probably figure it out in an afternoon. There are many methods for doing this in R (see this recent question). For someone who doesn't want to learn any programming, you could do this with Galaxy. It can also be done fairly easily in excel.
Use betools intersectBed : http://code.google.com/p/bedtools/wiki/Usage#intersectBed