One of the oldest entrants in the integration, visualization and analysis of data from various sources (genotype, phenotype etc.,) is Mix-omics. http://mixomics.org/
The project started in 2009 and has been a continuously developed framework for multiple data sources. The graphic shows the multivariate methods available today for users. There is also sample data sets available to get started quickly.
The best way to get started with this is to look at one of the case studies – PCA analysis with Liver toxicity data is a particularly good one…
You can learn more about this tool in this webinar