The Y-axis shows the negative logarithm of the p-value for each single nucleotide polymorphism (SNP) displayed as coordinates on the X-axis.

It is difficult to show small p-values on a plot in a way that is easy to understand. For example, how do you display 10^-20 and 10^-30 values when both are tiny? However, when you take a -log10 of those values, they become 20 and 30, which is much easier to plot. Also, the more significant p-values (smaller numbers) end up being larger after the -log10 transformation, and for most people it is more intuitive that larger means better (or stronger association, in this case).