Talk:Rs4420638

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)