Single nucleotide polymorphisms (SNPs) are more common than other types of polymorphisms and occur at a frequency of approximately 1 in 1000 base pairs throughout the genome (promoter region, coding sequences, and intronic sequences) (Brookes, 1999). Single nucleotide polymorphisms (SNPs) on chromosome 9p21 are associated with coronary artery disease, …, diabetes, ischemic stroke, aortic aneurysm, type II diabetes, glioma, and malignant melanoma, breast carcinoma, ovarian carcinoma, pancreatic carcinoma, melanoma, and acute lymphoblastic leukemia ( Cunnington et al.,). SNPs close to particular gene acts as a marker for that gene.

Indeed, 500 kb region on human chromosome 5q31 that is implicated as containing a genetic risk factor for Crohn disease. For example Hierarchical linkage disequilibrium mapping of a susceptibility gene for Crohn ’s disease to the cytokine cluster on chromosome 5 (Rioux, J. D et al., 2001).The HLA-DQB1 and HLA-DRB1 loci, which are located in the middle of these 14-Mb, are known to be the primary factors for type 1 diabetes. Therefore, genotype alone is not sufficient to predict or of susceptibility to disease (Martin et al. 1997) nor is phenotype variation alone necessarily linked to DNA sequence variation (Lander and Schork 1994; Weeks and Lathrop 1995).

that is what i am asking for eg if i have 100 patients' sample and i get SNP in 60 cases and rest 40 are anot having that SNP.In that case can i say that this SNP can be considered as a marker for this disease?

Dear Brijesh Dabhi,

SNPs never become markers. SNPs can be considered as a risk factors but not markers. Bio-marker means that it would increase/decrease with the progression of disease. But SNPs won't increase or decrease. SNPs would be there from the birth to death. But it can be considered as a risk factor. In your case, those having particular SNPs have more chances to develop disease under certain particular conditions. Also it is not necessary that all persons would develop the disease.