Background
Associations of several Single Nucleotide Polymorphisms (SNPs) with common diseases like Coronary Artery Disease (CAD), Crohn’s Disease (CD), Hypertension (HT), Bipolar Disorder (BD), Type 1 Diabetes (T1D), Type 2 Diabetes (T2D) and Rheumatoid Arthritis (RA) were identified in a study conducted by the Wellcome Trust Case Control Consortium (WTCCC) (1). WTCCC study compared the effects of genetic variations in 14,000 cases and 3000 shared controls and identified 24 independent associations with the diseases mentioned above using the genotype information of approximately 500,000 directly genotyped SNPs and genotype information simulated at 2.8 million loci studied by the International Hapmap Project(2). We hypothesize that there are more chances of finding association of rare SNPs with diseases by refined analysis of non-synonymous SNPs (nsSNPs) in genome wide association studies. In the present study we analyzed the association of 12,660 nsSNPs using a case control study in the WTCCC population.