#!/usr/bin/perl
use warnings; 
use strict;
use Data::Dumper;

my $file1 = <<END;
chr7	151046672
chr7	151047369
chr3	127680920
chr3	127680920
END

my $file2 = <<END;
chr1	66953622	66953654
chr1	67200451	67200472
chr1	67200475	67200478
chr1	67058869	67058880
chr1	67058881	67058885
chr7	151046672	127680920
chr7	151047369	127680920
chr3	127680920	151046672
chr3	127680920	151047369
END

open my $infile1, '<', \$file1 or die "unable to open first file $!";
open my $infile2, '<', \$file2 or die "unable to open 2nd file $!";

### create memory structure of file 2:
### so that we only have to read file2 once!
#

my %file2_hash;

while (my $line = <$infile2>)
{
   next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof)
   
   my ($chr, $value1,$value2) = split /\s+/, $line; # use better "names" I have
                                            # no idea of what a chr col means
   push @{$file2_hash{$value1}},$chr; 
   push @{$file2_hash{$value2}},$chr; 
}
close $infile2;  # file handle closure is optional, but I'd do it.

###  process each line in file1:
###  If a line "matches" with any line in file2, then "E", else "M"
###  I don't know that these numbers mean, come up with better comment.

while (my $line = <$infile1>)
{
   chomp $line;  #so that output with E or M can be on same line
   next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof)
   
   my ($chr, $val1) = split /\s+/,$line;
   
   if ( grep{$chr}@{$file2_hash{$val1}} )         
   {
      print "$line\tE\n";  # match exists with file 2
   }
   else
   {
      print "$line\tM\n";  # match does NOT exist with file 2
   }
}


__END__
Prints the following:
chr7	151046672	E
chr7	151047369	E
chr3	127680920	E
chr3	127680920	E