23andMe and Risk Alleles Question

[leela]

I am wondering how you find out which are the risk alleles, or mutations that potentially cause disease.
For instance I found out which genes to look for for Ehlers Danlos--in my raw data there are gobs of
homozygous results, but I don't know how to tell which versions are the normal or the risk alleles.

Mutations in the following can cause Ehlers–Danlos syndrome:

• Fibrous proteins: COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, and TNXB
• Enzymes: ADAMTS2, PLOD1, B4GALT7

Can someone help? On a steep learning curve with the genetic stuff.
I currently have no less that 15 ribs out of place (super painful), so I'm thinking EDS right about now and would like to know more.

 

[adreno]

You can look up the genes you are interested in on SNPedia:

http://snpedia.com/index.php/SNPedia

 

[Sea]

An added bonus I discovered was SNPtips. It's a Firefox add on that automatically shows what your SNPs are on any page that you are looking at SNPs on. So instead of going back and forward to SNPedia and 23andme for example, any SNPs on the SNPedia page that you have results for from 23andme will be highlighted. When you hover over them your alleles for that SNP are shown.

 

[adreno]

An added bonus I discovered was SNPtips. It's a Firefox add on that automatically shows what your SNPs are on any page that you are looking at SNPs on.

I am somewhat worried about the privacy issues of giving them access to your 23andme information.

 

[leela]

Thanks. I have used SNPedia, but I have not seen that they mention which allele is a risk allele.
like, in some cases GG is bad, but in another disease it's AA? Or is the risk allele always the same across diseases?
In fact for COL1A1 for example, SNPedia has an entry but the only data listed is how it is mentioned by the different
sequencing outfits.

 

[adreno]

COL1A1 is a gene. It contains 82 SNPs. You have to look up individual SNPs to find the risk allele.

 

[merylg]

OpenSNP gives a Genotype Frequency (taken from their user group) eg rs9286043 a snp for ADAMTS2 for which I'm CC

http://opensnp.org/snps/rs9286043 Only 20% of their users are CC