Snp In A Haplotype Chromosome Block

Question

[brentp]

Simply put, my question is: I have a SNP from a GWAS that if I find records associated with it in UCSC snp135, I get 2 records, one on chr17 and one on chr17ctg5hap1, what should I do?

Since it's in that region (which I assume to be a region with strong LD), there are also a bunch of other significant SNPs near-by. Is this interesting or does it present an opportunity for further analysis?

For example, I was thinking maybe certain haplotypes are more likely to be disease-prone? Worth looking into? How?

[Zev.Kronenberg]

That is cool that you found a disease SNP in a haplotype. Is this haplotype under selection? Check outr http://haplotter.uchicago.edu/. Do you have some sort of population stratification issue in your GWAS? PCA / ADMIXTURE around your snp / haplotype might be fun to look at. http://cran.r-project.org/web/packages/rehh/index.html might be fun to use to make a bifrucation plot.

[brentp]

it's not a stratification issue. just that region is a hap block. thanks for these ideas. both of them look promising. I had not seen bifurcation plots like that before.

Answer 1

[deanna.church]

It looks like chr17ctg5hap1 is the H2 haplotype at the MAPT region: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/region.cgi?name=MAPT&asm=GRCh37.p10

The chromosome contains the H1 haplotype. Because this is an inversion polymorphism, there is recombination suppression in this region. The H2 locus is the predisposing locus for the 17q21 deletion syndrome as it has the segmental duplication configuration to allow for NAHR, while the H1 haplotype does not have this configuration.