I've created a webapp for quickly and easily generating graphs and analysis.
Drag & drop small files (BED, expression CSV and VCF files) onto the page to upload, and it will generate some graphs and analysis. This can be further customised and downloaded in different image formats.
A quick overview (with screenshots) can be found here:
A SVD (similar to PCA) plot.
A diagram of chromosome regions, generated from a .bed file.
Source available under creative commons attribution licence, paper to be released one day...