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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.

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    $\begingroup$ You don't explain how you get the dataset, but my guess is that you are looking at the diploid genotype. Hence two nucleotides for each location (diploid genome). $\endgroup$
    – benn
    Commented Sep 21, 2018 at 12:35
  • $\begingroup$ If you got the genotyping data from an array experiment, one of them is a major allele and the other is a minor allele. Its rare to see multi-neuclotide polymorphisms at least in human populations whereas your data contains them at every locus. I'd venture to guess its from multiple strains of mice or other non-human organism. $\endgroup$
    – Vivek
    Commented Sep 21, 2018 at 12:56
  • $\begingroup$ Welcome to the site. Could you please edit the question to include the format of the file or how did you obtain it? It could also be that one nucleotide is the actual nucleotide and the other is the reference (?). Knowing more about the file would help us understand better what it means $\endgroup$
    – llrs
    Commented Sep 21, 2018 at 14:25
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    $\begingroup$ I just add some info about the source of the dataset. Hope it could shed some light on the matter $\endgroup$
    – PP mistery
    Commented Sep 21, 2018 at 17:37

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Humans are diploid. This means they have two copies of each locus (with the exception of sex chromosomes in males). Your two alleles for each individual represent the two copies of this variant locus.

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