text: user3388: 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.
  
  user1332: 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.
  
original_text: 3388: <p>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 AT<strong>T</strong>G and there's a variation AT<strong>A</strong>G then the SNP is <strong>A</strong>. 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:</p>
  
  <pre><code>ID  exm355 exm615
  1     T_T   A_C
  2     T_T   C_C
  3     A_T   C_C
  </code></pre>
  
  <p>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?</p>
  
  <p>The source says that the case and control subjects were genotyped by the <a href="http://www.agrf.org.au" rel="nofollow noreferrer">Australian Genome Research Facility</a> using the Illumina HumanExome BeadChip-12v1_A, which exonic content consists of <span class="math-container">$&gt;$</span> 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.</p>
   1332: <p>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.</p>
  