# $_= ~ /ssId=\s*?(\S+)/
$_ =~ /ssId=\s*?(\S+)/

#if ($_= ~ /subSnpClass=\s*?(\S+)/)
if ($_ =~ /subSnpClass=\s*?(\S+)/)
[download]

I got this result

RS_SNPs    subSnpClass3931
    snp
76536062
    snp
[download]

#!perl
use strict;
use warnings;

my $Gene    = 'ds_chY.xml';
my $outfile = 'ID.txt';

open my $out,'>',$outfile or die "Could not open file '$outfile' $!";
print $out "RS_SNPs\tsubSnpClass\n";

open my $in,'<',$Gene or die "Could not open file '$Gene' $!";
while (<$in>){
  
  if ( /ssId=\s*"([^"]+)/ ){
    print $out "$1\t";
  }
  
  if ( /subSnpClass=\s*"([^"]+)/ ){
    print $out "$1\n";
  }
  
}
[download]

Oh, thanks a lot, it works now, but when I tried to print observed data such C/T, it does not work. and very thanks for your help

Consider using XML::Twig for parsing XML

#!perl
use strict;
use warnings;
use XML::Twig;

my $twig = new XML::Twig(  twig_handlers =>{ 'Ss' => \&Ss } );
$twig->parsefile('ds_chY.xml');

sub Ss {
  my ($t,$e) = @_;
  my $obs = $e->first_child('Sequence')->first_child('Observed');
  print $e->att('ssId')."\t".$e->att('subSnpClass')."\t";
  print $obs->text."\n";
}
[download]

UPDATE : added Observed

poj