I am getting some of my SNPs significant for a phenotypic trait but they are not in LD with their nearby SNPs. My question is that these SNPs which are significant but not in LD with their left and right SNPs are important for my further association work or not? What should I do?
See papers by Lai, Ordovas, et al on the APOA5 gene in humans. A key SNP in this gene is not in LD with its nearby SNPs and shows some very pertinent associations to triglyceride levels. Furthermore, the associations are modified by dietary factors, such that the risk allele does not show as risk until an aspect of the diet passes a certain threshold. In this case, I must respectfully disagree with swbarnes2.
It is also possible that your SNP is tagging a CNV (copy number variant), which other SNPs do not, and it is that CNV that is the causal variant. That was originally thought to be the situation for the lead GWAS signal at IRGM and Crohn disease risk, but that SNP turned out to alter a miR binding site within the 5'-UTR. Nonetheless, that your SNP tags something else is a possibility to consider.
Lastly, what is in LD in one population may not be so in another.