HaploReg v4.2

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

Documentation

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

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

chr	pos (hg38)	LD (r²)	LD (D')	variant	Ref	Alt	AFR freq	AMR freq	ASN freq	EUR freq	SiPhy cons	Promoter histone marks	Enhancer histone marks	DNAse	Proteins bound	Motifs changed	NHGRI/EBI GWAS hits	GRASP QTL hits	Selected eQTL hits	dbSNP func annot
1	11889913	0.81	0.94	rs2336377	G	A	0.81	0.52	0.62	0.56			LIV			6 altered motifs		2 hits	8 hits
1	11890334	0.81	0.94	rs4846072	T	C	0.82	0.52	0.62	0.56			LIV			5 altered motifs			3 hits
1	11907848	0.95	0.98	rs6662295	G	C	0.60	0.48	0.60	0.54		7 tissues	13 tissues	53 tissues	19 bound proteins	8 altered motifs			6 hits
1	11908216	1	1	rs6684539	A	C,G	0.66	0.49	0.59	0.54		19 tissues	ESDR, BLD	53 tissues	57 bound proteins				7 hits
1	11908349	0.97	0.98	rs12092734	T	C	0.66	0.50	0.60	0.54		23 tissues		53 tissues	51 bound proteins	Sox			3 hits
1	11911288	0.86	0.97	rs4845889	T	C	0.81	0.52	0.63	0.56			4 tissues			4 altered motifs			3 hits
1	11913785	0.95	0.97	rs6541010	A	G	0.80	0.50	0.60	0.54			7 tissues			GATA,Nrf-2,TCF11::MafG			3 hits
1	11915109	0.86	0.98	rs7525521	G	A	0.82	0.52	0.63	0.57			BLD, PLCNT, LIV		HNF4A,SP1				3 hits
1	11916162	0.92	0.96	rs12742241	C	T	0.78	0.50	0.59	0.54						EBF,Pax-5			3 hits
1	11916174	0.92	0.97	rs12741138	G	A	0.78	0.50	0.60	0.54						HP1-site-factor,Zbtb3			2 hits
1	11916688	0.93	0.97	rs7518827	A	G	0.82	0.52	0.63	0.55			ESDR, SKIN			EBF,Ets,Irf			3 hits
1	11919499	0.92	0.97	rs2038028	A	G	0.82	0.52	0.63	0.54		MUS	12 tissues			9 altered motifs		1 hit	6 hits
1	11919852	0.91	0.96	rs3209284	T	C	0.81	0.52	0.63	0.54			12 tissues			Smad3			6 hits	3'-UTR
1	11926564	0.92	0.97	rs6682554	T	C	0.64	0.50	0.59	0.54		23 tissues	6 tissues	53 tissues	15 bound proteins	Zic		3 hits	7 hits