This site is very cool.
Let's make it even more cool by adding a whole-genome view that seamlessly lets you zoom into single chromosomes and down to regions.

There are a couple of LD displays that would be useful.

• the usual haploview-style LD display (with coloured squares at 45 degrees.)
• It would be really useful to be able to choose a SNP and paint the surrounding SNPs by LD with the chosen SNP. (Probably with heatmap colours -> white = highest LD, red = low LD)

Implement pages along the lines of the Pf Popgen pages allowing to view data about study sites and to browse allele frequency data, etc., linked to the genome browser.

Currently y-axes are fixed to scale 0-8.
It would be great if the scale was a) scaleable, maybe by using the scrollwheel, and b) draggable.

In this context I think each variable should have a scale and range associated with it.
E.g. P-values are on -log10 scale and go from 0 to infinity. BFs are on log10 scale and can take any value. Allele frequencies (not currently shown, but they could be range from 0 to 1.) I think that sort of info would be useful to get the zoom / drag right.

I think a crucially useful feature will be to be able to get a link to any particular view that can be sent to colleagues. E.g. a button like Google maps' link button would be very useful.

Currently locations are displayed as numbers without annotation. I think this could be improved a bit

• Just adding 'Mb' after the number would help a lot.
• On browsers like UCSC genome browser the locations switch to kb and then base-pair resolution as you zoom in, I think that's pretty nice.

I would like to see genes displayed a little differently - something like this:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=334663339&hgt_doJsCommand=&hgt.out1=1.5x&dirty=false&position=chr4%3A144796468-144826716

or this:

http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000197465;r=4:144800476-144939263

i.e. lines for introns, boxes for exons, and somewhere or other arrows indicating the direction of transcription.

Currently we have several tabs with plots and tables.
Work out how to present this information so as to be most useful.
And then implement it!

The filterbank approach is working very smoothly and it's very cool.

I would like a few tweaks, however.

1. at each zoom level, I'd like some SNPs picked out and plotted (probably just those with the smallest P-values). Then what's leftover should be filterbank'd and plotted as a filterbank.
2. So, as you zoom in we'll get more SNPs and less filterbanking.
3. Also, while having the max value and the quantiles is cool, I think it's too visually noisy at the moment. So I would suggest to just show the maximum value and maybe also the median as a faint or dotted line.

It would be very cool if the display of location on a chromosome at the top can be modified to look like a real chromosome. Ok, not like a real chromosome, but like the usual display of a chromosome with the centromere depicted.

Also I think we could move or probably get rid of (?) the box showing the Zoom level - it takes up space and doesn't seem that informative to the user. The space could be used to make the chromosome display bigger.

When clicking on a SNP, a display box should appear that gives access to

• details of allele frequency in cases and controls in each pop (or maybe on a map). Something like the ones on this page: http://wattle.well.ox.ac.uk/wtccc2/external/ms/
• a bar plot showing posterior probability of each model for which there's a Bayes factor.
• a forest plot showing effect size / standard error / and probably allele frequency in each population.

Imputed snps and directly genotyped SNPs should be shown (probably with different shapes, e.g. plusses for imputed, small circles for typed.)