Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-09-23T06:46:06.273Z
Answers.LastActivityDate: 2018-09-23T06:46:06.273Z
Answers.UserDisplayName: Emily_Ensembl
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-21T12:35:08.843Z
Comments.Text: 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).
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-21T12:56:29.263Z
Comments.Text: 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.
Comments.UserDisplayName: Vivek
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-21T14:25:05.983Z
Comments.Text: 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
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-09-21T17:37:49.987Z
Comments.Text: I just add some info about the source of the dataset. Hope it could shed some light on the matter
Comments.UserDisplayName: PP mistery
Tags: <snp>
Title: Understanding SNP coding for association analysis
ThreadText: # Understanding SNP coding for association analysis
  
  (Asked by: username_0 on 2018-09-21)
  
  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**T**G and there's a variation AT**A**G 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](http://www.agrf.org.au) 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.
  
  **Tags:** snp
  
  > **Comments:**
  > **username_1**: 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).  
  > **username_2**: 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.  
  > **username_3**: 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  
  > **username_0**: I just add some info about the source of the dataset. Hope it could shed some light on the matter  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2018-09-23. Score: 3 | Accepted answer
  
  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.
  
  
  ---
  
  