The UCSC Genome Browser (14) and ENSEMBL Genome Browser (15,16) both allow genomic regions to be annotated with the results of cutting-edge genomic data, including chromatin state segmentations, ENCODE data, 1000 Genomes variants, evolutionary constraint, LD calculations and NHGRI catalog variants. However, the output of these browsers can be overwhelming, especially when one is interested only in a limited subset of loci (such as the variants linked to a GWAS hit.) To this end, HaploReg combines the focus on haplotype blocks provided by tools such as SNAP and SNPinfo with the breadth of genomic annotation provided by the full-featured genome browsers.
