How To Plot The Haplotype Block For A List Of Snps

Question

[J.F.Jiang]

Hello, everyone,

Here, I have a list of 1000 SNPs. I want to find how many of them fall into the same haplotype block （LD block） and the information of the enriched chrosome.

But I still have no idea how to perform the task, is there any website for this analysis that allow me to upload a list of SNP number?

Please give me some suggestion at your convenience! Thank you!

Answer 1

[Darren J. Fitzpatrick]

Haploview should be fit for your purposes.

[J.F.Jiang]

yes, I know the haploview software. But since I only have the snp number rather than the genotypes raw data, and it seems that the hapmap website do not have the entry for genotypes extraction using a list of SNPs as upload.

[J.F.Jiang]

So, it is a little difficult for me to do this problem.

[Darren J. Fitzpatrick]

You could upload your list of rs identifiers to Biomart and parse the output for the relevant information.

[J.F.Jiang]

YES， thank you very much. For biomart, which terms should be included for output and since some specific file types should be considiered as the input for Haploview, then how to make the output file of Biomart satisfied with the require?