Genome wide association studies (GWA) tests the entire genome for the genes, which are contributing to variation in traits. But, they do not prove that allelic variation causes variation in the trait.
All the alleles in the population are scanned at the same time by association studies. It shows the influence of SNPs (single nucleotide polymorphisms) in the gene on the variation of trait. In many genes, the SNPs are in strong linkage disequilibrium.
Such SNPs are transmitted to the offspring as a haplotype block. So, any gene in the block can be the actual cause for the variation of the trait.
In molecular analysis, the function of each gene in the haplotype block is analyzed. Also through this analysis, we can know if the two alternate alleles produce mRNA or functional proteins, and also the cellular function of each gene. Hence, molecular analysis will be establishing if the gene function and variation in function associated with SNP could be the cause of variation of trait of concern.
We can make use of recombinants. Here the linkage disequilibrium is disrupted by hotspots. The SNP s on both the sides of the hotspot is in equilibrium with each other. The SNPs which are not separated like this form a unit called haplotype block of correlated SNPs. If the SNP genotypes are correlated then the values of trait also will be correlated. We will be able to find out if the correlation between the SNP and the trait persisted.