I am doing GWAS SNP association studies on diseases by using a software called plink (http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml).

With association results I get p-values for all the SNPs that was analyzed. Now, I use a QQ-plot of those p-values to show if a very low p-value differs from the expected distribution of p-values (a uniform distribution). If a p-value deviates from the expected distribution one “may” call that p-value for statistic significant.

As you can see in the QQ-plot, at the top tail end, the last 4 points are somewhat hard to interpret. Two of the last points in the grey suggests that those p-values are in the expected distribution of p-values, whilst the other two are not.

Now, how to interpret this, the last two points have *lower* p-values but are not “significant” according to the QQ-plot, whilst the other two points with *higher* p-values are “significant”? How can this be true?