Why lack of SNPs within a window of 3.06 million bp (58887738 - 61949597) in chromosome 6?

Question

[jiumeng66]

I am doing GWAS, and I found that there are no SNPs within a window of 3.06 million bp (58887738 - 61949597, for example, in HapMap3) in chromosome 6, in almost all dataset, including 1000 genome and Hapmap3 (as shown in the attached figure), and of course in my own datasets. Could someone tell me why?

Here is the figure

[greeshmathulasi1]

Hi jiumeng66, Would you please mind to let me know how did you plot this ?

Answer 1

[h.mon]

Did you check the position of the centromere? Can you plot its position along the SNPs?

[jiumeng66]

Yes, I have checked just now. This is the region of centromere. Thank you very much.

Answer 2

[jiumeng66]

I have checked the chr7. There are also no SNPs in the region of centromere. It looks that the centromere regions of all chromosomes have no SNPs. It's an interesting phenomenon for me.

[h.mon]

It is not so surprising once you know human centromeres are comprised of repetitive DNA (alphoid sequences).

[d-cameron]

The hg19 reference genome has placeholder N bases for all centromeres. There is plenty of variation there but your sequencing technology and tools are unable to detect them.