Question: Criteria for Overlapping SNPs
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gravatar for alexandramirandaaa
27 days ago by
alexandramirandaaa0 wrote:

Hello. Need help again. What needs to be considered for one to say that it is an overlapping SNPs? I mean, should the Chromosome Number, Position, Marker Name, Major and Minor Allele, etc. be the same? Or as long as the Chromosome Number and Marker Name are the same, it is already an overlapping SNPs?

And is Major Allele is the same as Non-Effect Allele and Minor Allele is the same as Effect Allele?

Thank you so much!!!

snp • 110 views
ADD COMMENTlink modified 27 days ago by WouterDeCoster35k • written 27 days ago by alexandramirandaaa0
1

Could you give some more information about the context in which you are using these terms?

ADD REPLYlink written 27 days ago by finswimmer7.9k

I have the data of SNPs of Alzheimer's Disease and what's included is Chromosome, Position, Marker Name, Effect Allele, Non-Effect Allele. I found this data from IGAP.

And I also have the data of SNPs of Testosterone/Estradiol which includes Chromosome, Position, Marker Name, Major Allele, Minor Allele.

I wonder if Major Allele is the same as the Non-Effect Allele, and Minor Allele is the Effect Allele? Or two different things.

ADD REPLYlink written 27 days ago by alexandramirandaaa0
0
gravatar for WouterDeCoster
27 days ago by
Belgium
WouterDeCoster35k wrote:

A SNP is uniquely defined by:

  • chromosome
  • position on chromosome
  • alternative allele

And is Major Allele is the same as Non-Effect Allele and Minor Allele is the same as Effect Allele?

Not necessarily. Also, I'd say "(Non)-Effect Allele" is inaccurate terminology and should be avoided.

ADD COMMENTlink modified 27 days ago • written 27 days ago by WouterDeCoster35k

So as to interpret your answer. When two SNPs doesn't have the same Chromosome Position even if the involved allele are the same, they still don't overlap? Okay, got it.

Thank you so much!!!

ADD REPLYlink written 27 days ago by alexandramirandaaa0

When two SNPs doesn't have the same Chromosome Position even if the involved allele are the same, they still don't overlap?

This sentence suggests that you do not really understand some fundamentals of genetics.

ADD REPLYlink written 27 days ago by WouterDeCoster35k
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