I am relatively new to these concepts and looking for any feedback. My question is if using the GCTA tool to estimate phenotypic variance is an appropriate application to my study. We have 59 cases and 424 controls genotyped on the Illumina Equine 50K Bead Chip. My concern is our sample size and SNP density is less compared to previous threads and what is in the literature. Also there is relatedness between the samples, it is not a family design but is not composed of unrelated individuals either. This has been accounted for in the mixed model SNP analysis effectively. My disease of interest is a equine skeletal disease suspected to be regulated by complex traits given previous work. Any thoughts/experience on the issues presented would be greatly appreciated. Thank you.