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VDR Taq has a minor allele (MAF) of "G":
http://www.ncbi.nlm.nih.gov...

Here are some studies that reference VDR Taq (rs731236):

"We observed that women with GG (rs731236), ... were characterized by a significant correlation between vitamin D vs testosterone concentration and FAI value. We found a significant correlation between testosterone level and FAI vs vitamin D concentration in men with heterozygote AG in the rs731236 polymorphism"
http://www.ncbi.nlm.nih.gov...

"The VDR polymorphism, TaqI (rs731236), was associated with a 26 % risk reduction (TT vs. CC, OR 0.74)"
http://www.ncbi.nlm.nih.gov...

All ... ..more

RefSNP alleles are the alleles submitted by genetic researchers for a particular SNP. for example CBS C699T has RefSNPs A/G. This means that the researcher found A on one chromosome strand and G on the other, at the gene location for CBS C699T.

RefSNP Alleles for a particular gene location in a genome build, are submitted to dbSNP by multiple genetic researchers. Each SNP will usually only have two RefSNP alleles. When different researchers submit conflicting information about RefSNP alleles, then it is possible for more than 2 alleles to be listed for one SNP, making it more difficult ... ..more

I found this excellent description in Amy Yasko's forum: ch3nutrigenomics.com. It was posted by one of the members on the site- raji: http://www.ch3nutrigenomics...
This is a private blog, but it is a very rich source of information about methylation, nutrigenomics and dietary supplementation

Here is a copy of the post:

"Common Terminology:

Methyl group: A methyl group is simply a single carbon atom bonded to 3 hydrogen atoms (CH3).

Methylation: Transfer of methyl groups from one chemical to another is called methylation. Essentially any chemical compound that has a methyl group as part of its chemical ... ..more

The most likely reason for these differences is the choice of minor allele used by the app to determine phenotype.

The criteria seems to be constantly changing, probably because this a relatively new and rapidly evolving field of science. To quote openbioinformatics.org:

"One obvious problem with this coding scheme is that one must know the "forward strand" with certainty, but this is usually not the case. Even for the well studied human genome, there are still many holes to be filled. It is possible that a sequence is assembled into the forward strand in 2004 human genome assembly, but ... ..more

At the bottom of your #Livewello gene variance report there is a legend table that describes what your results mean.

The variance report is essentially a table where each row represents a Single Nucleotide Polymorphism (SNP). The columns in the table are:

1) SNP or name of the gene variation.

2) rsID. This is a unique number assigned to each SNP, by dbSNP.

3) Minor Allele. An allele is the nucleotide that is present at a gene location. This can be one of 4 nucleotides - A, T, C and G. A pairs with T on the opposite DNA strand, and ... ..more

SNPs in this table we're previously part of the #Livewello standard report, but with version 2.0, they have been removed because they have ambiguous RefSNPs, which makes it difficult to accurately determine their minor allele.

MNPs: Some SNPs on dbSNP are listed with three RefSNP alleles instead of two. SNPs should only have two alleles (refSNP alleles). One on the plus strand and another on the minus strand.
After talking to a representative at NCBI about why some SNPs have 3 alleles, Livewello’s Founder was told that these types of SNPs are considered ambiguous because they can ... ..more

This is a statement from Dr. Iwegbue, Founder and Lead Developer of the Livewello Gene App:

I'd like to share with you the reason why 23andMe Variance Report results sometimes differ depending on the App used. Results are determined by the Minor Allele used:
All of LiveWello's Minor Allele information is retrieved directly from dbSNP. A link to dbSNP is added to every SNP in a Livewello Gene Variance Report. That way, a user and their Practitioner can verify minor allele information for themselves.

At Livewello, we only use the forward strand for interpreting all our SNPs. This ... ..more

Annonymous

What is a " strand " ?

  6 years, 7 months ago

#Strand refers to #DNA strand. There are 2 of these for every #gene location. Plus (or forward) strand and minus (or reverse) strand.

Both of these have complementary information i.e. they have the opposite #nucleotide of a pair of nucleotides: A, T, C, G, such that if one has ‘A’ the other will have ’T’, and if one has ‘C’, the other will have ‘G’. This is usually the way in which nucleotides pair up on a person’s chromosome. So, chipsets used by personal genomic data companies like #23andMe , will only read from one of these two #chromosome ... ..more

Annonymous

Why does 23andMe use the plus strand

  6 years, 7 months ago
Annonymous

What is a DNA "strand”?

  6 years, 7 months ago

Strand refers to DNA strand. There are 2 of these for every gene location. Plus (or forward) strand and minus (or reverse) strand. Both of these have complementary information i.e. they have the opposite nucleotide of a pair of nucleotides: A, T, C, G, such that if one has ‘A’ the other will have ’T’, and if one has ‘C’, the other will have ‘G’. This is usually the way in which nucleotides pair up on a person’s chromosome. So chipsets used by personal genomic data companies like 23andMe, will only read from one of these two chromosome ... ..more

This was copied from a Facebook post made by the Founder and Lead Developer of Livewello who is also an M.D. and has a son on the #Autism Spectrum

"I'd like to share with you the reason why 23andMe Gene results sometimes differ depending on the App used. This is because of the Minor Allele used:
All of LiveWello's Minor Allele information is retrieved directly from dbSNP. A link to dbSNP is added to every SNP in a Livewello Gene Variance Report. That way, a user and their Practitioner can verify minor allele information for themselves.

At ... ..more

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