while (<FILE2>) 
{
   my ($key2,$data) = split(/,/, $_, 2);

# use grep to do the "join":
   my @match_keys = grep { my ($sid,$eid) = split(/ /,$_);
                           $key2 >= $sid and $key2 <= $eid } keys %VAR1;

   foreach my $matched_range ( @match_keys ) {
      my @matched_data = @{$VAR1{$matched_range}};
      # do something with @matched_data
   }
}