Hello from Cambridge

[EthoStrain]

Hiyo, my name is Jesse Whitworth and I have been working for the past year on IGV over at the Broad Institute. Before that I was leading Haploview development for a couple years in Mark Daly's lab.
I have spent a good amount of time working with the 1000 genomes people over at the Broad and continue to have more questions than answers I hope that this community will be able to provide me with answers and be able to absorb my input.

Cheers!

[alizaid12]

Greetings from Tokyo, Mr. Whitworth. This will seem to be a very naive question, but I hope you can give some useful feedback. I recently used PLINK/ Haploview for assessing the top ranked SNPs obtained from a GWAS analysis. I intended to use Haploview to visualize the SNPs in LD blocks, that might be residing near genes of interest. I also manually checked by results from visual curation of dbSNP.

I was surprised to find that no matter how hard I try to visualize the data in Haploview, it does not seem to correspond to give the genes of interest, that I can see residing close to my SNPs, when using dbSNP.

I have downloaded various tutorials and also checked out on many forums. I haven't found any answer related to this matter. I wonder if you can elucidate. I would happily share this reply with other students [I am using Haploview view for my PhD research].

Thanks in advance

A.Z