I am not sure what you are trying to do. @{$file2_hash{$val}} is an array assigned to a hash key of $val. The array contains at least one string like "Chr12" and could potentially contain multiple ChrX strings. Whether there is just one or more than one Chr string depends upon the data.

The grep{} looks at all of the Chr strings and if one is found that matches $chr, then you get a "true" in the if statement.

It is easy to change the tests on the Chr strings. Looking for a range of hash keys (values) is a whole different story.

We are back to the same problem where your description of what you want is not clear.