Phenotype Variations of Polymorphic Sites: Genotyping against Haplotyping

Since nucleotide modifications including Single Nucleotide Polymorphisms (SNPs) may influence gene phenotypes thus, their studies highlight the distinctive features in pathogenesis of diseases. The reports onprediction of sequence profiles and patterns as indicated in Prosite database(http://prosite.expasy.org), suggest that the function of elements and motifs is related to cumulative effect of the conserved signatures so that the polymorphic changes could affect inter- and intra molecular interactions (Kd value) leading to phenotype variations. Additionally, self-assembling proteins on several separate nucleotide elements shows that the phenotype variations may be depend on the function of other involved elements. Our knowledge of the involvement of numerous elements on the gene phenotype is Limited. 

Furthermore, in most genotype reports obtained from multi SNPs studies, the heterozygotedistribution of polymorphic sites on homologue chromosomes is not Identified,so that they they could not exactly show the phenotype variations. Theoretically, the number of their two-allele haplotypes can be estimated As n! (n indicates the number of polymorphic sites), when the linkage failure exists between the sites. Thus, the phenotype reports based on the genotypes without consideration of haplotypes are not exactly estimated.