Not exactly this way, but you could build a hash of hashes of hashes where you could access your data this way:

my %hash;
# ... populate the hash and then possibly something like this:
my $value = $hash{chr1}{1092482}{REF};
[download]

But your question is too vague, I can't really offer actual code not knowing what you really want to store in your data structure.

Edit: Not only was choroba (++) faster than me to type an answer, but he did make some hypotheses on the data you need to offer a complete solution.