You're looking for lines that are common between two files. Ther are plenty of solutions on the net already. You could use comm command or if you want to use perl and both files fit in memory, you can read then into arrays and use List::Compare.

I would rather prefer to solve it in easy and quicker way,

grep -w -Ff File2.txt File1.txt > commonFile1File2.txt

Sorry if I understood your question wrong.

I wrote a script that suggests one approach:

Usage:

$ intersect.pl --fileA="A.txt" --fileB="B.txt" > answer.txt

This uses Perl's experimental "smartmatch" feature, which can give an annoying warning message that can be discarded by directing standard error to /dev/null. If you're not comfortable using experimental features, there is a List::Util library that offers limited set-style operations.

You could iterate through one hash, and for each gene ID (location) key in the hash, check if it is present in the other hash, and whether the values are the same, and print out the Location and Position when you find matching values. But you would have to make hashes of arrays, because hash keys in perl have to be unique values, so each gene ID could only be present once as a hash key. This may not be the most efficient way to go about this.