to continue on: (untested)
open( my $FH1 , '<', $file1 ) or die "Couldn't open file \"$file1\": $!";
open( my $FH2 , '<', $file2 ) or die "Couldn't open file \"$file2\": $!";

my %ids;
while <my $id = <$FH2>)
{
   chomp $id;  #remove line ending
   $ids{$id} = 1;
}

my $line = <$FH1>; #throw away first header line
while ($line = <$FH1>)
{
    #get 'rs2342349' from: "chr1  11223   11224  rs2342349\n"
    
    my ($id) = (split /\s+/,$line)[3]; #whitespace chars also includes tabs
    print $line if exists $ids{$id};
}