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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. 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?

Thanks all

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  • $\begingroup$ Without knowing where exactly your data comes from / how its formatted this is hard to answer. Generally the SNP notation with two bases is used to denote both the 'canonical' and the 'variant' base at each of the SNP positions (this would mean that exm355 doesn't have any SNP at ID 2, since its 'T_T'). You should look up which base is variant/canonical in an description of your data/file format $\endgroup$ – Nicolai Sep 21 '18 at 12:39
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Each chromosome location which has been identified as being a SNP is a location at which more than one nucleotide occurs at appreciable frequencies in the general population. This means that there are two or more bases which can occur there, so a person's test must show which bases actually occur there in that person's genome. Since a person has both a paternal and a maternal chromosome of a chromosomal type (a pair of homologous chromosomes), the person has two instances of the SNP location and so two nucleotides to be detected and reported. Hence your dataset has two nucleotides for each SNP location for each patient.

Just from the reported base or the SNP name you can't tell which is more frequent in the population. If you need to know that, you must consult SNP frequency data from some other database. (The SNP names in your example, e.g. "exm355" are not familiar; usually SNPs have names like "rs1234567".)

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