HaploReg v2 |
HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state, their sequence conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.
Update 2014.10.13: Version 3 is now avabilable in beta.
Update 2013.02.14: Version 2 now includes an expanded library of SNPs (based on dbSNP 137), motif instances (based on PWMs discovered from ENCODE experiments), enhancer annotations (adding 90 cell types from the Roadmap Epigenome Mapping Consortium), and eQTLs (from the GTex eQTL browser). In addition, LD calculations are provided based on the 1000 Genomes Phase 1 individuals, and r² and D' measurements are available down to an r² threshold of 0.2. Display improvements include improved cell metadata, gene metadata, and PWM display on the detail pages and the option for text output. Version 1 is available here.