#usr/bin/perl -w
use strict;
use Data::Dump qw(pp);
 
open (my $fileReg, '<', 'chromfile1.txt') or die "unable to open chromfile1.txt $!\n";
open (my $fileBase, '<', 'chromfile2.txt') or die "unable to open chromfile2.txt $!\n";

my %region;

while (<$fileBase>)
{
   chomp;
   my ($chr, $base) = (split)[0,1];
   push @{$region{$chr}}, [$base, $_];
}
close $fileBase;

my %seen;
while (my $regionline = <$fileReg>)
{
   chomp ($regionline);
   my ($base,$start,$end)= (split(/\s+/,$regionline))[0,1,2];
   
   next if $seen{"$base-$start-$end"}++;
   next if !defined $region{$base};
   
   foreach my $ptr (@{$region{$base}})
   {
      print "$regionline $ptr->[1]\n" if ($ptr->[0]>= $start and $ptr->[0]<=$end);
   }
}

__END__
prints:
chr1    100 159 0    chr1    104 104 0   0   +
chr1    100 159 0    chr1    145 145 0   0   +
chr1    200 260 0    chr1    205 205 0   0   +
chr1    500 750 0    chr1    600 600 0   0   +
chr3    450 700 0    chr3    500 500 0   0   +
chr4    100 300 0    chr4    150 150 0   0   +
chr4    100 300 0    chr4    175 175 0   0   +
chr7    350 600 0    chr7    400 400 0   0   +
chr7    350 600 0    chr7    550 550 0   0   +
chr9    100 125 0    chr9    100 100 0   0   +
chr11   679 687 0    chr11   680 680 0   0   +
chr11   679 687 0    chr11   681 681 0   0   +
chr22   100 200 0    chr22   105 105 0   0   +
chr22   100 200 0    chr22   110 110 0   0   +
chr22   300 400 0    chr22   350 350 0   0   +

file1:
chr1    100 159 0   
chr1    100 159 0   
chr1    200 260 0   
chr1    500 750 0   
chr3    450 700 0   
chr4    100 300 0   
chr4    100 300 0   
chr7    350 600 0   
chr7    350 600 0   
chr9    100 125 0   
chr11   679 687 0   
chr11   679 687 0   
chr22   100 200 0   
chr22   100 200 0   
chr22   300 400 0   

file2:
chr1    104 104 0   0   +
chr1    145 145 0   0   +
chr1    205 205 0   0   +
chr1    600 600 0   0   +
chr3    500 500 0   0   +
chr4    150 150 0   0   +
chr4    175 175 0   0   +
chr7    400 400 0   0   +
chr7    550 550 0   0   +
chr9    100 100 0   0   +
chr11   680 680 0   0   +
chr11   681 681 0   0   +
chr22   105 105 0   0   +
chr22   110 110 0   0   +
chr22   350 350 0   0   +