Significant Snps With Maf Within A Range Of 10% From A Gwas For Plant Quantitative Traits?

Question

[kumar.vinod81]

My GWA study resulted in some significant SNPs which have MAF <10% (2-10%). Should I include them in my further functional validation study or I should left them? As, I am reading from the literature that such type of rare variants have little more chances of higher significance. Also my plant is highly inbreed while I am getting higher level of heterozygocity, should I remove them from the study or include them. As a very low level of heterozygocity is known in rice. What should I do? Thanks