HaploReg v2

HaploReg v2

Broad Institute Homepage MIT

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.

Build Query

Use one of the three methods below to enter a set of variants. If an r² threshold is specified (see the Set Options tab), results for each variant will be shown in a separate table along with other variants in LD. If r² is set to NA, only queried variants will be shown, together in one table.

Query (comma-delimited list of rsIDs OR a single region as chrN:start-end):
or, upload a text file (one refSNP ID per line):
or, select a GWAS:

Set Options

LD threshold, r² (select NA to only show query variants):
1000G Phase 1 population for LD calculation: AFR AMR ASN EUR
Source for epigenomes: ENCODE Roadmap
Mammalian conservation algorithm: GERP SiPhy-omega both
Show position relative to: GENCODE genes RefSeq genes both
Condense lists in table longer than:
Condense indel oligos longer than:
Background set for enhancer enrichment analysis:
Output mode: HTML Text


For usage examples, click here (opens in a pop-up window.)

For details on data sources and methods, see the full documentation (opens in a new window.)

The HaploReg database and web interface were produced by Luke Ward and Manolis Kellis at the Computational Biology Group at MIT. HaploReg is hosted by the Broad Institute.

To cite HaploReg, please refer to our publication in Nucleic Acids Research: HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. (PMID:22064851).

The database underlying HaploReg v2 is available to download in VCF format: haploreg_v2.vcf.gz (7.4 GB).

Contact: lukeward@mit.edu.