I'm working on a project about detecting SNP association with a disease. As I understand, SNP is a single variation of the nucleotide that occurs for more than 1% of the population. So, if a gene is ATTG and there's a variation ATAG then the SNP is A. However, I couldn't connect this idea with the dataset in hand. The rows in my dataset represent each patient and the columns contain SNP information. For example:
ID exm355 exm615 1 T_T A_C 2 T_T C_C 3 A_T C_C
I have no idea why the SNP columns contain 2 nucleotides(T_T, A_T, A_C, C_C). As the definition of SNP, I thought it should show only the variant nucleotide or am I misunderstanding anything? How could I interpret T_T or C_C and how could I know which nucleotide is the variation from the common ones in the population?
The source says that the case and control subjects were genotyped by the Australian Genome Research Facility using the Illumina HumanExome BeadChip-12v1_A, which exonic content consists of $>$ 250 000 markers representing diverse populations and a range of common conditions. An individual was duplicated to test genotyping reliability and quality. The identity by descent (IBD) matrix between all pairs of individuals was estimated after linkage disequilibrium (LD) pruning and used for quality control and for the mixed linear models analyses.