Where can I find the info about the start/end position of sets of SNP's that are inherited in a block (haplotype block)?

Question

[a4xrbj1]

Hi,

while I could find references to the 1000 Genomes data and the vcf files there (I've looked at the smallest one possible, chr 22 in ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf) I was unable to identify the start/end position of those haplotypes in a block.

Hope my explanation makes sense to all of you. If I do understand it right what I read then there are several definitions which influence the haplotype block and it's start/end and length. Those are LD-based, recombination-based, information-complexity-based and diversity-based. I'm interested in diversity-based haplotype blocks.

Thank you in advance!

Answer 1

[pfs]

For diversity based haploblock see Alfred's database. Ethnic breakdown of haplotypes will be available for at least the haploblocks discussed in this paper (https://www.sciencedirect.com/science/article/pii/S1872497317300613?via%3Dihub#upi0010). Another source would be to use STRs. See link for a place to start searching for STR ethnic frequencies (http://strbase.nist.gov/fbicore.htm)

[a4xrbj1]

Thanks pfs. Found the link to Alfred's db in the paper you linked above. Just for easier reference if something else is searching for the same, the URL is The ALlele FREquency Database