HaploReg v4.2

HaploReg v4.2

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 chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Update 2015.11.05: Version 4.1 GWAS and eQTL have been updated; a simpler pruning strategy is applied when combining GWAS; and links out to other NHGRI/EBI GWAS hits and GRASP QTL hits are provided.

Update 2015.09.15: Version 4.0 now includes many recent eQTL results including the GTEx pilot, four different options for defining enhancers using Roadmap Epigenomics data, and a complete set of source files for download and local analysis. Older versions available: v3, v2, v1.

Update 2023.04.29: Version 4.2 released. Parts of the site may still not work correctly - please email haploreg (at) mit.edu for support.

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:
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:
Output mode: HTML Text


For details on data sources and methods along with usage examples, see the full documentation (opens in a pop-up window.)

The HaploReg database and web interface were produced by Luke Ward in the Kellis Lab 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 underlying data are available in the following directory.

Contact: haploreg@mit.edu