I am working on the Plink Tutorial dataset: case/control dataset with two subpopulations http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtm
I applied a logistic regression with a covariate for nationality of the individual. In total there are more than 60.000 SNPs which show a significant influence of the covariate. In particular, the most crucial SNP rs2222162 shows a p-value < 10^-4 and the additive coefficient is 10^-5
My question is : How to continue ? Now I know that there is a population structure, how do I draw further conclusions using my logistic regression model ?
Thanks for your comments.