We illustrate the epigenomic annotation of two non-coding GWAS SNPs associated with multiple sclerosis (MS)10 by clustering the H3K4me1 profile of SNP-harboring regions and RNA-seq signal of their closest genes across multiple primary tissues and cells (Fig. 1). Both SNPs lie within putative enhancer regions. While rs307896 marks an enhancer common across cell types, rs756699 is located in an enhancer specific to immune cells and is potentially targeting TCF7, a T cell specific gene, 3.8kb downstream (Fig. 1, Supplementary Fig. 5). Thus, reference epigenomes provide important clues into the functional relevance of these genetic variants in the context of the pathophysiology of MS, including inflammation11. Investigators can also use the Browser to identify co-variation of epigenomic, transcriptomic, and transcription factor binding profiles across cell types to predict relationships between regulatory sites and target genes (Supplementary Notes, Tutorial 1, Supplementary Fig. 6–8). Additionally, investigators can explore multiple complete reference epigenomes in different Browser panels in parallel using synchronized genomic coordinates or independent genomic coordinates. A variety of EpiGenome Browser functions, including gene set view, genome juxtaposition, chromatin interaction display, and statistical
