GenomeRunner
Annotation and enrichment of Next-Gen sequencing data
...It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser.
Input - any genome-wide data data in .bed format (tab-delimited text file with chrom, chromStart, chromEnd).
Annotation analysis output - detailed annotation of each genomic region in input data. Used to prioritize individual genomic regions by the total number of epigenomic features they co-localize with.
Enrichment analysis output - p-values of statistically significant co-localizations of input genome-wide data with genome annotation features selected for the analysis. ...