Figure 4.

Future challenges for the functional evaluation of enhancer variants. The challenges described in the conclusion section are depicted in this hypothetical enhancer locus. Chromatin immunoprecipitation combined with massively parallel DNA sequencing (ChIP-seq) tracks from ENCODE [77] and linkage disequilibrium (LD) plots from HapMap [78,79] are displayed via the UCSC genome browser. Number 1 highlights the challenge of utilizing the proper cell type to assess enhancer activity. Enhancers at this locus are only active in one of the three cell lines depicted. Challenge number 2 is the discrepancy between predicted and validated enhancer function. Shown is a putative enhancer defined by chromatin state that requires experimental validation of its enhancer activity. Challenge number 3 illustrates the large number of single nucleotide polymorphisms (SNPs) in LD that lie in putative enhancer elements, any of which could be functional. Number 4 is the challenge of determining the gene impacted by the enhancer variant. Here, the target of the enhancers at this locus could be IL22RA2, IFNGR1, or a gene distal to this locus. Number 5 is the complexity of enhancer gene regulation. Here, multiple enhancers each with several associated variants are distributed across the locus. One or a combination of several of the enhancer variants could influence target gene expression. chr, chromosome; GWAS, genome-wide association study; kb, kilobases.