Criteria for Overlapping SNPs

Question

[alexandramirandaaa]

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!!!

[finswimmer]

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

[alexandramirandaaa]

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.

Answer 1

[WouterDeCoster]

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.

[alexandramirandaaa]

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!!!

[WouterDeCoster]

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.