How to include global MAF in GWAS analysis?

Question

[LNA]

Hi, I wonder if there is a possibility to use the global MAF for additional filtering of SNPs.

I have a distribution of a quantitative trait for a few thousand people and SNP data for some individuals with extreme values. I was thinking that the effect allele should be highly enriched in the group with extreme values and the distribution of the trait tells me that it should occur rather seldom usually, which should be reflected in the global MAF.

Is there a possibility to use that kind of information for my GWAS study? (Or is there a reason not to use it?)

Thanks in advance! LNA