These associations could be direct (i.e., the identified variant is the causal variant) but are more likely to be associated indirectly in that the identified variant is correlated with some other genomic variant. For indirect association, the causal variant could be some other SNP, a set of interacting SNPs, a haplotype, an insertion/deletion polymorphism, a CNV, or a more complex type of genetic variant. It is also wise to leave open the possibility of a causal genetic mechanism that is currently unknown. The genetic effects are highly likely to be subtle and probabilistic (and even conditionally dependent on external influences) rather than deterministic as with classical Mendelian disorders.
