my %myHash = ();
my %tempHash = ();
foreach (@lines){
   my($key1,$key2,$val1,$val2,$rest) = split(/\s+/,$_,5);
   my $combinedValue = sprintf("%2s,%2s",$val1,$val2);
   $key1 =~ /SNP(\d+)/;  my $indx = $1;
   if(exists $myHash{$key2}){
      %tempHash = %{$myHash{$key2}};
      $tempHash{$indx} = $combinedValue;
      $myHash{$key2} = {%tempHash};
   } else {
      $tempHash{$indx} = $combinedValue;
      $myHash{$key2} = {%tempHash};
   }
}

foreach my $key (sort keys %myHash){
   my %tempHash2 = %{$myHash{$key}};
   my $line2output = "$key ";
   foreach my $sortedKey (sort keys %tempHash2){
      $line2output .=
         sprintf(" %2s %2s",split(',',$tempHash2{$sortedKey}));
   }
   print "$line2output\n";
}