How to estimate the phenotypic variation explained by top SNPs from a GWAS study?
Answer from @maximilian-press, converted from comment:
At a guess, the GEMMA linear mixed model is controlling for population structure and other SNPs, which your R example is not (it only fits 1 SNP?), but it's hard to be sure with this information. It would be helpful to see data samples. There is probably more context and usage information available in those resources beyond just the equations. It is especially difficult to evaluate with no terms defined as in your last example (defining the terms in the earlier ones is a good start).