Like our other 2 SNPs, rs2229741 and rs4986938 are not amino acid changing variants, being intronic and part of the 3′ UTR of their genes respectively, and it is possible that the weakness of the associations we have identified also indicate linkage to functional polymorphisms nearby.
This implies that Alu-D-type might associate with higher ACE serum activity because of the tight linkage with functional polymorphisms, which belong to stalk domain of ACE.
Other variants, even if not functional, can be associated with phenotype because of linkage to closely situated functional polymorphisms.
In reality, given the single locus dominant nature of the carbonaria polymorphism, we expect a 100% match between offspring phenotype and genotype for a marker locus tightly linked to the functional polymorphism, and a marginally weaker association if linkage is weaker (e.g. cis-regulatory element).
Genotypes were determined with respect to a functional polymorphism of the serotonin transporter gene promoter region (5HTTLPR).
The regions surrounding each polymorphism are well conserved with little recombination, therefore, it likely that, if the associations are real, the observed associations are due to linkage disequilibrium with another functional polymorphism in the region.
Alternatively, the rs2297630 SNP might be a functionally neutral marker that is in linkage disequilibrium with a functional polymorphism located elsewhere at the SDF1 locus.
Thus, the significance of the association may be brought up by still unknown mechanisms or by linkage disequilibrium (LD) with functional polymorphisms.
Third, the SNPs assayed in the association analyses could be too distant from (or not in linkage disequilibrium with) the functional polymorphism in the gene.
Sst I polymorphism is located in 3′-untranslated 3′-untranslatedpoC3 gene, and it is possible that this polymoregion is in linkage disequilibrium with ofher functhenApoC3lymorphism in the nearby regene, such andT-455C polymorphitm.
However, the TNF-238 polymorphism may be in linkage disequilibrium with a functional polymorphism that impacts TNF production, either within the TNF gene or another gene within the MHC.
