Is it possible to remove genetic variance using GCTA

I understand that using the SNPs to simply predict phenotypes using this approach will not give a good result. 

i.e. Genome-wide association studies establish that human

intelligence is highly heritable and polygenic(Davis, 2011)

I was wondering if I could (for each individual) remove the genetic variance from the trait using this approach.

I wonder if this could work out. 

Thanks!