I don't know if the data structure would overwhelm your system resources. Regardless, you'll probably want to do something besides splat out the resulting data.

Save the ram and put your data into something mungable. SQLite is one option for a self hosted, easy to port around database. Perl has SQLite::DB, DBIx::SQLite::Simple, Class::DBI::SQLite, and many other modules to assist in storing, retrieving and manipulate your millions of records.

There are also many modules and libraries for working with genomic data. They're out of my area of competence and I'll leave commentary on them to someone who has experience with them. Consider undertaking your own CPAN search to find them.