Just a general question about GWAS studies. Probably this has already been addressed but browsing through the literature I couldn't find any specific mention of this issue. I was wondering if GWAS studies take haplotype length into account as a potentially confounding variable? If you are using SNP data from a population and doing a GWAS to identify regions of the genome contributing to an extremely polygenic trait, aren't SNPS on long haplotypes more likely to show significant associations because, firstly, you are more likely to tag them with a SNP and, secondly, they are more likely to contain multiple causative alleles (especially if you assume a highly polygenic additive model with each variant contributing an equally small amount to a trait)?
Couldn't this result in an enrichment for GWAS hits on young haplotypes or regions that have recently experienced a selective sweep?
If anybody knows any papers that address this I would be grateful to hear about them, or if anyone can explain why this is not an issue. Perhaps this is not directly a bioinformatics question but I wonder if software for GWAS controls for this, or if it needs to.