Why does dbSNP and ENSEMBL list rs4420638 as an A/G SNP, but this page used to say T/C? This has since been corrected. But my initial misinterpretation led to the passage below, which is still of some value.
great question. planned as a topic for an upcoming blog post. Short answer, they are equivalent.
DNA pairs up into the double helix (twisted ladder) shape. When you have an A in one position, it will be paired with a T on the other side. A pairs with T. C pairs with G. If you read the DNA from one side, and you would see the A. From the other side you would see the T.
So rs1234(A;G) would be read as rs1234(T;C) if read from the opposite strand. The decision about which side to read from is rather arbitrary, and different sources sometimes pick different answers.
Since we have 2 different copies of dna (1 from mom, 1 from dad), and each copy of your dna has 2 sides to its ladder, it can be quite confusing, but if you can just remember this set of rules you should do fine.
- In SNPedia, we choose the strand shown in the dbSNP entry for that rs#
rs1234(A;G) can also be written as rs1234(T;C), or rs1234(C;T) or rs1234(G;A) rs1234(A;C) can also be written as rs1234(T;G), or rs1234(G;T) or rs1234(C;A) rs1234(A;A) can also be written as rs1234(T;T) rs1234(A;T) can also be written as rs1234(T;A)
further questions or explanations are welcome, as it will help to address a question *everyone* has in the beginning, and to provide material for the next blog post.
I understand that SNP alleles can be written as: regular, complement, reverse, reverse complement. However, I think that there is a mistake in SNPedia for this specific SNP: dbSNP lists it as A/G. SNPedia lists it as T/G, not T/C (which would be complementary). I have seen this type of thing for other SNP's listed here, so I'm not sure if it's a mistake or not.
- blush*. Right you are. corrected. many thanks. If you find any others, your comments or corrections are very much appreciated.
Cariaso 17:04, 4 August 2007 (CDT)