hello. Somebody could please help me to understand how to read 23andMe raw datas?? I don't mean Genetic Genie results.
as example this is my result for the snp A1298C:
MTHFR 11854476
rs1801131 G or T GG
MTHFR The name of the gene
11854476 The position on the chromosome
rs1801131 Reference sequence number of the snp
G or T The usual two alternatives for this snp
GG Your genotype
Reference Links: dbSNP Orientation: Minus
Entrez Gene dbSNP Genotype: CC
dbSNP Lookup
Google Scholar (SNP)
what as example would it be that "dbSNP Genotype: CC" it would be this the risk allele??
Thanks
Clicking on any of these links will take you to information about the snp or the gene.
Note how for this snp it says Orientation: minus.
Your DNA has 2 strands with complentary alleles on each side. So if you have an A on one side it will have a T on the other. If you have a G on one side it will have a C on the other. These strands are called forward or positive and reverse or minus. It has something to do with the direction in which they are read.
Anyway, 23andme use the forward strand for genotyping. Others sometimes use forward and sometimes reverse. So you are GG for this snp on the forward strand which means you will be CC on the reverse strand. You have to keep that in mind when looking at the research. The reference link is telling you that for this snp dbSNP are reporting for the reverse strand.
It is not telling you anything about risk, simply what your genotype is for that snp according to dbSNP.
For this snp A1298C means that at position 1298 (of the gene) instead of an A there is a C. This is reported on the reverse strand. Because 23andme look at the positive strand their two alternatives are G and T instead.