If you are worried about leaving out covariates you could regress out them first and analyse the residuals against the Snps.
In the experimental design , Covariates are independent variables , Experimenters can't manipulate , But it still affects the experimental results .
I want to know the effect of temperature on precipitation , But altitude 、 Longitude and latitude 、 Variables such as local humidity also affect precipitation . that , In my research , Temperature is the independent variable , Precipitation is a dependent variable , And altitude 、 Latitude and longitude and local humidity are covariates .

Analysis of Covariance (ANCOVA) easily explained

Analysis of Covariance (ANCOVA) with Two Groups

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