how could genes' positions overlap on a locus?

[jie huang]

Hi, guys:

I have 3 quick questions. I would deeply appreciate if someone could shed lights.

1. For the chr3 locus COVID-19, which was said to be inherited from Neanderthanls (based on a Nature paper in 2020), here is the Locuszoom plot https://my.locuszoom.org/gwas/474223/region/?chrom=3&start=45609651&end=46109651. I am suddenly wondering, at the bottom of this plot, how could the gene "CCR9" is completely within the gene "LZTFL1"? Isn't each DNA sequence only belonging to a single gene?  If someone knocks out CCR9 for a biological experiment, then he has to knock out LZTFL1 as well?

2. For another GWAS on Alkaline Phosphatase (ALP) , here is the Manhattan plot based on the UK Biobank GWAS (PMID: 33462484) https://my.locuszoom.org/gwas/376885/.  ALP is encoded by the ALPL gene. Why a protein that is coded by a single gene could be affected by so many genomic loci across the genome?

3. For those very significant nonsynonymous variants in the coding region of ALPL, how could they affect the phenotypic level of ALP? Since they are coding nonsynonymous variants, they should change the structure of the ALP protein instead, correct? This question applies to other serum biomarkers such as C-reactive protein (CRP). How could nonsynonymous variants in the coding region of CRP affect the level of CRP rather the protein structure of it?

THANKS!

Jie