awk 'NR==FNR {a[$1]; next} $1 in a{print}' inputfile1.txt inputfile2.gen.gz >output.txt

zcat inputfile2.gz | awk 'NR==FNR {a[$1]; next} $1 in a{print}' inputfile1.txt inputfile2.gen.gz >output.txt

zcat inputfile2.gz |
awk 'NR==FNR {a[$1]; next}
    $1 in a' inputfile1.txt - >output.txt