Hello everyone!
I made a GWAS analysis and found several SNPs that are located close to each other (less than 0.5 megabases). Then I want to find haploblocks in order to make haploblock-trait association. In case If I want to find haploblocks that are associated with the trait of interest should I use only significantly associated SNPs in order to find haploblocks (in Haploview) or the other nearly located SNPs should also be included in the analysis?
Hey,

No, for HaploView, use all of your SNPs that have passed quality control checks. HaploView will then determine haploblocks and haplotypes based on whatever measure / metric that you select. You can note the haploblocks in which your statistically significant SNPs lie.

As far as I am aware, HaploView provides functions that also then permit you to perform association tests based on the defined haploblocks / types.

Kevin