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What do you mean by the most significant SNPs? Do you have a p-value threshold in mind?
I need to find which SNPs can be related to the disease. I do not have a specific threshold.
Actually, I take the data from PGC and they are GWAS summary statistics results , I need to use these data to find the relation between the p-values and another matric I have for the same genes thus I want to filter/ do a more advanced analysis of the GWAS summary statistics results to can get the genes related to the disease.
Or can I take just the SNPs with the lowest p-value for example( 10^-8) from the GWAS summary statistics results and consider them as they related to the disease.