Introns and junk-DNA for phenotype

[Mr.Zurich92]

When you look at the GWAS you can see that many SNP which influece a trait, phenotype or disease risk are in the introns or outside a gene! That's weird, because at the end the mRNA is important for Protein creating! Intron don't get trancribed!?? Do you get that?

[CharonY]

Regions characterized as non-coding can still harbor unidentified sRNA or, more commonly have a regulatory role (e.g. as transcription factor binding sites). In fact, many (most) cases SNPs exert their effects due to regulatory changes rather than actual mutations in protein-coding regions themselves.

[Mr.Zurich92]

Regions characterized as non-coding can still harbor unidentified sRNA or, more commonly have a regulatory role (e.g. as transcription factor binding sites). In fact, many (most) cases SNPs exert their effects due to regulatory changes rather than actual mutations in protein-coding regions themselves.

So this means the major cause why people do have different disease risk or traits is because:

 

1. Different amount of mRNA?

2. How active certain genes are during pregnancy and life?

3.How well proteins and enzymes can bind with such regulatory sequences?

 

 

Let's say it's clear people have different faces. So variance in face shape of people has rather to do how active genes are and not with the protein structure itself?

Edited September 9, 2014 by Mr.Zurich92

[chadn737]

GWAS does not find causative SNPs, it finds associated SNPs. If a non-causative SNP is in tight linkage with a causative one, it will show up as significant in a GWAS study. Typically, in GWAS, one uses common SNPs, not rare SNPs. It is often suspected that rare SNPs are causative, rather than common SNPs. The point of GWAS is to identify regions and hopefully even genes that are associated with a trait, not necessarily the SNP itself.

Edited September 9, 2014 by chadn737

[CharonY]

That is a crucial point (which I conveniently and to my shame overlooked). But on the other aspects, yes development of complex traits are also regulated by quantitative balances of the various players (including transcriptome, proteome and metabolome). The balance of many of these constituents is what results in certain cellular and tissue phenotypes and not only the types of proteins present (though that is an important point, too, of course).

[Mr.Zurich92]

Good to know!