Often when presenting statistics from a candidate gene study, or a region of interest from a genome-wide association study, it is useful to see various SNP-wise values in the context of linkage disequilibrium patterns. To aid the interpretation of regional association results, we developed a tool called LD-Plus that presents a familiar Haplo-view style correlation plot that is annotated with haplotypes, haplotype blocks, and haplotype frequencies, along with continuous and categorical SNP statistics. An example plot is shown below (click for the larger version).
This plot design displays p-values from association or other types of statistics in the context of quality control measures such as genotyping efficiency, HWE p-values, and minor allele frequency. It also displays association signals relative to LD structure, so the user can clearly see if multiple SNPs in the same LD block show evidence for association. The haplotypes and their relative frequencies are shown along the top of the figure, and gray shading carries the haplotype structure up through the other statistics in the figure. Categorical stats, such as inclusion on genotyping platforms, whether a SNP was imputed or typed, or the consequence of the SNP (coding/non-coding) can be displayed also.
LD-Plus is available via a web interface, and is an evolving project. To give it a try, visit https://chgr.mc.vanderbilt.edu/ldplus. Details on how to properly format input files is available under the "Documentation" link on the site. We'd love your feedback on the design, and what other features we might include in the design!