Visualizing Of Genes In Haploview [Ld Blocks]

Question

[Alizaid12]

Hello everyone,

This might sound like a very naive question, regarding Haploview. I performed a GWAS in PLINK and got results from association testing for high ranked SNPs. --I viewed these in results Haploview, with the intention of making LD blocks [so I could assess of SNPs in linkage disequilibrium are also residing near genes of interests[ --as an alternate approach, I used dbSNP and manually assessed the the location of genes nearby by SNPs of interest.

I think the results of dbSNPs are quite relevant and visually confirmable. However, I was very surprised that Haploview gave completely different sets of results to those from visual curation of dbSNP [with no representation of genes of interest or even the highlighting of high-ranked SNPs! that I can see in dbSNP]!

I have tried various times but I am unsuccessful to understand the cause of this problem. Any helpful guidance will be highly appreciated

Answer 1

[Larry_Parnell]

The population greatly influences this comparison. If your population is geographically or genetically distinct, or admixed, the LD blocks or haplo-blocks will be quite different than those in one of the HapMap reference populations.

The other situation is one where the SNP location has little to do with the nearest or nearby genes. A SNP could reside, for example, in an enhancer that acts at a considerable distance to partially control transcription of a gene some tens of kb away.

Answer 2

[Occam]

forget haploview. locuszoom is a far superior tool that generates a graph reporting ld, gene location, annotation and genotyped SNP p-values in a single, elegant regional plot. and it is so easy a child could use it.

https://statgen.sph.umich.edu/locuszoom/genform.php?type=yourdata

[Alizaid12]

Thanks for the answers;-]. I am now looking at Locuszoom. I also found the answer by Larry Parnel to be quite relevant