7482. SLC6A20 (rs11385942)


GWAS論文にはHLAもone of themとして出てきます。

There were no SNP or allele associations signals at the HLA complex meeting neither genome-wide nor suggestive association significance threshold of P=1×10-5 (Supplementary Table 6). 


本命は 別の遺伝子を探すことになります。(HLAは見せかけの人種差を説明するには簡単に使いやすいから、良くゲノムって何?って時には例としては使うけど)






One notable candidate is SLC6A20, which encodes the
Sodium/Imino-acid (proline) Transporter 1 (SIT1) that functionally interacts with angiotensin converting enzyme 2 (ACE), the SARS-CoV-2 cell surface receptor.19,20 SIT1 expression in the lungs is mainly present in pneumocytes 21, where SIT1 should be scrutinized for involvement in SARS-CoV-2 viral entry. However, the relevant locus also contains a cluster of genes encoding
chemokine receptors, including the CC-motif chemokine receptor 9 (CCR9) and the C-X-C motifchemokine receptor 6 (CXCR6), the latter have been shown to regulate the partitioning of lungresident memory CD8 T-cells throughout the sustained immune response to airway pathogens,including influenza viruses.22


Aのinsertionが、その後にどうなるのかが、よくわからん。splicing variantでも作られるんだろうか?

allele frequencyが6%程度でだとhomozygoteはほとんどいないだろうに。

However, it should be noted that the leadSNP at the ABO locus in our study (rs657152) has been associated with elevated interleukin-6 (IL-6) levels in childhood obesity in previous GWAS27


Furthermore, genetic variation at the ABO locus has previously been associated with a number of procoagulant markers such as von Willebrand factor and Factor VIII, and the potential relationship between our genetic findings and the significant coagulopathy that is observed in severe Covid-19 warrants further attention.



ヨーロッパとEast Asiaでmajor allele Cとminor allele Aが逆転してますね。そして、African とSouth Asianはアジア系ではない。

Odd Ratio 1.3は差は小さいけど、こっちの方が本命かな?

Not Reported in ClinVar だから、これまでに何らかの病気との相関は報告されてないので機能未知のintron SNP・・・・ GWASはここで行き止まりになることが多いんだよね・・・