The problem is that a Perl hash key can only have one value, but you assigned the Rs key to 3 values. Here is one way to get what you want:

use warnings;
use strict;
use XML::Twig;

my $xml = <<XML;
<foo>
    <Rs rsId="3894" snpClass="snp" snpType="notwithdrawn" molType="gen
+omic" genotype="true" bitField="050028000005130500030100" taxId="9606
+"/>
</foo>
XML

my $twig = XML::Twig->new
(
twig_handlers => 
    {
        'Rs' => \&rs,
    }
);
$twig->parse($xml);

sub rs 
    {
        my ($twig, $elt) = @_;
        print $elt->att('rsId'), "\n";
        print $elt->att('snpType'), "\n";
        print $elt->att('snpClass'), "\n";
    }         

__END__

3894
notwithdrawn
snp
[download]