I will admit that I got a bit lost reading your code. I opened the file with the single points and made a hash table keyed on chromosome with values being the single point value and the text of the line. Then I went line by line thru the first file and for each chromosome range, and printed one line for each single point value that fit within the range. If a range line is seen more than once it is skipped.

Maybe this helps, maybe not. I am sure that I botched the terminology up somehow - you'll have to fix that in the program. But the number of levels of "while" is less in the approach below. Anyway for each range, you get one line of output for each of the single points that is within that range.

#usr/bin/perl -w
use strict;
use Data::Dump qw(pp);
 
open (my $fileReg, '<', 'chromfile1.txt') or die "unable to open chrom
+file1.txt $!\n";
open (my $fileBase, '<', 'chromfile2.txt') or die "unable to open chro
+mfile2.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   +
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