This is my attempt,

use strict;
use List::Util qw(min max);
my %hash=();
while(<DATA>)
{
my @fields=split /\s+/;
my $i=0;
push @{${$hash{$fields[0]}{$fields[3]}}->[$i++]},$_ for @fields[1,2,4]
+;
}

foreach my $hkey1 (keys %hash)
{
foreach my $hkey2 (keys %{$hash{$hkey1}})
        {
        print join "\t",$hkey1,$hkey2,min(@{${$hash{$hkey1}{$hkey2}}->
+[0]}),max(@{${$hash{$hkey1}{$hkey2}}->[1]}),max(@{${$hash{$hkey1}{$hk
+ey2}}->[2]}),"\n";;
        }
}
__END__
chrX    2680092    2744539    XG    1
chrX    2680090    2744529    XG    2
chrX    2680080    2744519    XG    3
chrX    2680070    2744509    XG    4
chrX    2680070    2744509    DT    1
chrX    2680090    2744519    DT    2
[download]

~suhail