Diagnostic value of SNP's and Genes - find SNPs on genes with high allele differential

Question

[Human]

Hello fellow humans,

I am currently starting to get into population genomics and I am doing an FST analysis to distinguish to populations with different ecotypes. For this I need to find SNP's with high diagnostic value. So, the SNP's should ideally lay on genes with a high allele frequency differentiation. I have already a candidate list of SNP's and Genes (based on high peaks within the Manhattan plot)

Now I am wondering, how I can use IGV and the files from the analysis (rc-file with allele counts, pwc-file with FST’s and a sync file) to get the information I need. Means to find SNPs that distinguish the populations consistently.