while(<INlist>){
    chomp;
    $scGeneids{$_} = "";
}

...

while (<IN>){
    chomp;
    my @columns=split /\t/;
    my $gene_id=$columns[0];
    my $SNP_pos=$columns[2];
    if ( exists $scGeneids{$gene_id} ){
        $scGeneids{$gene_id} .= "$gene_id\t$SNP_pos\n";  # collect by ID
    }
}

for my $key (sort keys %scGeneids) {
    print OUT $scGeneids{$key};
}