Previously mentioned LocusZoom has undergone some major updates over the last few months. Many of the bugs mentioned in my previous post are now fixed, and now there's a good bit of documentation available. There are also a few new features, including the ability to add an extra column to your results file to change the plotting symbol to reflect your own custom annotation (i.e. whether the SNP was imputed or genotyped, or the SNP's function).
This software is seriously useful for plotting regional association results with the level of detail and annotation that you can't achieve using regular manhattan plots. Go give it a try, now. Also keep an eye out for a downloadable version that should be available in the next week or so.
LocusZoom: Create Regional Plots of GWAS Results
And as a suggestion to the developers: how about a radio button on the web app that would allow you to accept files in PLINK's .assoc/.qassoc format so PLINK users wouldn't have go through the awkward text-wrangling to get their results files in an acceptable format (instructions specific for LocusZoom), also making "P" and "SNP" the default column names for these values?