Reviewer name and names of any other individual's who aided in reviewer	Wentian Li
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Additional Comments	Many aspects of Fig.1 are not explained.
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Any Additional Overall Comments to the Author	Plots with allele frequency as x axis and effect size (e.g. odds ratio) as y axis is a very common display of the contribution from both common and rare alleles to genetic association. A schematic form of this plot is practically on almost everybody's presentation slides when introduce this topic (to see an example, see, e.g. Science (23 Nov 2012), vol 338(6110), pp.1016-1017 ). Considering how many people have already been familiar with this type of plot, I feel that very little new is added in this paper: maybe only a new name ("trumpet"), and/or the power lines. The other methods contributions (log-x, one variant per LD, avoiding gene-level statistics) are rather straightforward. People without experience with "shiny" (R package) can still use ggplot2 or plot in R to get the same result. Generally speaking, I think the paper is weak, though OK as a program/package announcement. Major comments: * I think the trumpet shape (increase of "effect size" for rare variant) is probably a direct consequence of using odds-ratio as a measure of effect size. If the allele frequency in normal population is p0, that in disease population is p1, [p1/(1-p1)]/[p0/(1-p0)] ~ p1/p0 tends to be large for small p0's, simply because the denominator is small. On the other hand, if population attributable risk (p0*(RR-1)/(1+p0*(RR-1))) is used as the y-axis, I am uncertain what the shape of the plot would be. * A risk allele has these pieces of information: 1. allele frequency, 2. effect size (e.g. odds ratio), 3. type-I error/p-value, 4. type-II error/power. The plot in this paper show #1 vs #2 and #4 being added as extra. In another publication with a proposal to plot genetic association results (Comp Biol. and Chem. (2014), 48:77-83 doi: 10.1016/j.compbiolchem.2013.02.003), #2 is against #3 with #1 being an added extra. I'm sure using other combinations could lead to other types of plots. The authors should discussion/compare these possibilities. Minor comments: In Fig.1, the size of the dots, the brown vs cyan color, the discontinuity of scatter dots around 0.01, are not explained.
Recommendation	Major Revisions