Question about gwas

[Youpu-Chen]

Hi there, thanks for this great tool!

About the demonstration of gwaslab, I have one little question about gwas analysis.
Certain gwas results may represent sproadic signals across whole genome, like this:

But, some may show an enrichment of signals in certain genomic region:

I wonder which factors can be the determinant, e.g., population stratification, LD, or minor allele count...
I'll really appreciate it if you could give me a hint.

[Cloufield]

Hi,
Thanks for the question. I think your question is mainly related to genetic architecture, and I recommend reading this review.

Timpson, N. J., Greenwood, C. M., Soranzo, N., Lawson, D. J., & Richards, J. B. (2018). Genetic architecture: the shape of the genetic contribution to human traits and disease. Nature Reviews Genetics, 19(2), 110-124.

Besides the biological reasons, other technical factors may also affect the "appearance" of the Manhattan Plot.
For example, QC, genomic inflation, statistical power, variants coverage, and so forth.