use warnings;
use strict;
open my $filehandle, "<", "filename.bed" or die "open: $!\n";
my @data;
while (<$filehandle>) {
 chomp; # remove the line ending character
 push @data, [ split /\t/ ]; # split the rest and append it to our data
};

print $data[0]->[0];
# access the first element of the array
# it's a reference, "->" dereferences it
# at last, access the first element of the dereferenced array