A method of identifying a marker for a trait or phenotype comprising preparing a sequence polymorphism cluster network of a genomic region of interest, wherein preparing said SPC network comprises the steps of: a. obtaining in vitro the nucleic acid sequence of said genomic region of interest from a plurality of subjects; b. identifying using a computer a plurality of polymorphisms in said nucleic acid sequences; c. identifying using a computer the diploid genotypes of said polymorphisms in said nucleic acid sequences; d. computing in a computer the pairwise diploid genotypes in said nucleic acid sequences for each combination of two polymorphisms of said polymorphisms by combining for each of said nucleic acid sequences the genotype of the first polymorphism with the genotype of the second polymorphism; e. assigning in said computer a polymorphism as belonging to an SPC network if the pairwise diploid genotypes for each combination of the polymorphism with each of the polymorphisms of the SPC network comply with one or more of the following rules: (i) two polymorphisms are defined as belonging to one SPC in the network when they exhibit only the homozygous major, homozygous minor and heterozygous pairwise diploid genotypes; (ii) two polymorphisms are defined as having a dependent relationship with each other in the network when they exhibit only the homozygous major, mixed, mixed, heterozygous, mixed and homozygous minor pairwise diploid genotypes, or they exhibit only the homozygous major, mixed, mixed, heterozygous, mixed BH), and homozygous minor pairwise diploid genotypes; (iii) two polymorphisms are defined as having an independent, relationship with each other in the network when they exhibit only the homozygous major, mixed, mixed, mixed, mixed and heterozygous pairwise diploid genotypes; f. compiling in said computer an SPC network by repeating step (e) until the largest possible number of polymorphisms from the genomic region of interest have been assigned to said SPC network; and assessing said assigned polymorphisms of step (f) to identify an association between a trait or phenotype and at least one said polymorphism, wherein identification of said association identifies said polymorphism as a marker for said trait or phenotype. a. obtaining in vitro the nucleic acid sequence of said genomic region of interest from a plurality of subjects; b. identifying using a computer a plurality of polymorphisms in said nucleic acid sequences; c. identifying using a computer the diploid genotypes of said polymorphisms in said nucleic acid sequences; d. computing in a computer the pairwise diploid genotypes in said nucleic acid sequences for each combination of two polymorphisms of said polymorphisms by combining for each of said nucleic acid sequences the genotype of the first polymorphism with the genotype of the second polymorphism; e. assigning in said computer a polymorphism as belonging to an SPC network if the pairwise diploid genotypes for each combination of the polymorphism with each of the polymorphisms of the SPC network comply with one or more of the following rules: (i) two polymorphisms are defined as belonging to one SPC in the network when they exhibit only the homozygous major, homozygous minor and heterozygous pairwise diploid genotypes; (ii) two polymorphisms are defined as having a dependent relationship with each other in the network when they exhibit only the homozygous major, mixed, mixed, heterozygous, mixed and homozygous minor pairwise diploid genotypes, or they exhibit only the homozygous major, mixed, mixed, heterozygous, mixed BH), and homozygous minor pairwise diploid genotypes; (iii) two polymorphisms are defined as having an independent, relationship with each other in the network when they exhibit only the homozygous major, mixed, mixed, mixed, mixed and heterozygous pairwise diploid genotypes; (i) two polymorphisms are defined as belonging to one SPC in the network when they exhibit only the homozygous major, homozygous minor and heterozygous pairwise diploid genotypes; (ii) two polymorphisms are defined as having a dependent relationship with each other in the network when they exhibit only the homozygous major, mixed, mixed, heterozygous, mixed and homozygous minor pairwise diploid genotypes, or they exhibit only the homozygous major, mixed, mixed, heterozygous, mixed BH), and homozygous minor pairwise diploid genotypes; (iii) two polymorphisms are defined as having an independent, relationship with each other in the network when they exhibit only the homozygous major, mixed, mixed, mixed, mixed and heterozygous pairwise diploid genotypes; f. compiling in said computer an SPC network by repeating step (e) until the largest possible number of polymorphisms from the genomic region of interest have been assigned to said SPC network; and assessing said assigned polymorphisms of step (f) to identify an association between a trait or phenotype and at least one said polymorphism, wherein identification of said association identifies said polymorphism as a marker for said trait or phenotype.