There are many things you can do with the association, here's a non-exhaustive list: - do the SNPs cause changes in a gene of interest? are the changes synonym

There are many things you can do with the association, here's a non-exhaustive list: - do the SNPs cause changes in a gene of interest? are the changes synonymous (cause base change, but the protein amino acid is identical since several codons code for the same amino acid, but this can cause problems in mRNA folding)? Are the changes non-synonymous (cause base change, and a different amino acid)? How strong are the non-synonymous changes? It could be that you get a shorter protein because a SNP introduced an early STOP codon, or changes a hydrophile to a hydrophobe amino acid, etc. From there you can check whether this change influences the phenotype by introducing this changed protein into another individual to see whether the phenotype is reproduced, this rarely works in more complex species as you don't have a single gene -> single phenotype cause - you can use the ratio of synonymous/non-synonymous SNPs to approximate selection: genes under positive selection show more non-synonymous changes, these are usually genes involved in resistance who have to keep up with fungal/viral invaders, or venom genes, etc., genes under negative selection show more synonymous changes, these are usually housekeeping genes or other single copy genes that are important - are the SNPs closely upstream or downstream from a gene of interest? It's still a bit hard to find binding sites for transcription factors (esp. outside of model species), so the SNP could be in a binding site where the whole transcription apparatus binds - do we see different transcription level for this gene in other individuals without the SNP? - after DNA folding, is the SNP close to an interesting gene? Only with new HiC data can we test this, SNPs that were >10,000 base pairs away are after folding right next to the gene - is the SNP in Linkage Disequilibrium with something interesting? In other words, is the SNP inherited together with something interesting? This could point towards selection