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	23005657	0.8	0.9	rs674136	T	C	0.80	0.64	0.79	0.83						Myb			1 hit
1	23005967	0.8	0.9	rs587626	T	C	0.82	0.64	0.79	0.83				BLD,LNG	CEBPB	CEBPB,NRSF			1 hit
1	23007272	0.8	0.9	rs603856	T	C	0.65	0.61	0.79	0.83				PLCNT,CRVX		Nrf1			1 hit
1	23008292	0.8	0.9	rs598785	C	G	0.82	0.64	0.79	0.83			PLCNT		SRF	HMG-IY			1 hit
1	23008590	0.8	0.9	rs610346	C	T	0.81	0.64	0.79	0.83									1 hit
1	23009708	0.8	0.9	rs11290997	CT	C	0.80	0.64	0.80	0.83						4 altered motifs			1 hit
1	23010582	0.8	0.9	rs562933	A	G	0.82	0.64	0.80	0.83		CRVX, SKIN	7 tissues	SKIN,CRVX,BLD		MZF1::1-4			1 hit
1	23012491	0.8	0.9	rs522802	G	A	0.77	0.63	0.79	0.83						4 altered motifs		1 hit	2 hits	intronic
1	23015026	0.8	0.9	rs6675101	G	A	0.80	0.65	0.79	0.83			BLD			Mef2			1 hit	intronic
1	23015869	0.8	0.9	rs681648	A	G	0.79	0.64	0.80	0.83			BLD	BLD		Pou3f2,Sox			2 hits
1	23016763	0.8	0.9	rs6658132	C	G	0.78	0.64	0.79	0.83						4 altered motifs			1 hit
1	23033772	0.8	0.9	rs10799789	G	A	0.59	0.61	0.79	0.83				LNG		FXR,SF1,YY1			2 hits	intronic
1	23036551	0.8	0.9	rs671357	G	A	0.84	0.64	0.78	0.83			ESC, ESDR, BRN			AP-1,BCL,STAT			2 hits	intronic
1	23038691	0.8	0.9	rs686663	A	G	0.84	0.64	0.79	0.83		BLD	6 tissues	SKIN		GATA,TATA		1 hit	2 hits	intronic
1	23041969	0.8	0.9	rs10737471	A	G	0.58	0.61	0.79	0.83						Foxm1,HNF6,YY1			1 hit	intronic
1	23045115	0.85	0.93	rs587168	A	C	0.65	0.60	0.79	0.83			GI, HRT			TATA,ZBTB7A		1 hit	2 hits	intronic
1	23048458	0.85	0.93	rs649648	A	G	0.80	0.64	0.79	0.83						HNF1,Pou6f1,Sox			2 hits	intronic
1	23048615	0.85	0.93	rs10753552	C	T	0.59	0.61	0.79	0.83						SRF			1 hit	intronic
1	23052134	0.85	0.93	rs559431	T	C	0.79	0.64	0.79	0.83			ESC, IPSC					1 hit	2 hits	intronic
1	23053705	0.85	0.93	rs579785	A	G	0.84	0.64	0.79	0.83						GR,TEF			1 hit	intronic
1	23056236	0.87	0.94	rs763310	A	G	0.84	0.64	0.79	0.83						Spz1,TFIIA		1 hit	2 hits	intronic
1	23057211	0.87	0.94	rs11806664	G	A	0.57	0.61	0.79	0.83						7 altered motifs			1 hit	intronic
1	23058044	0.87	0.94	rs2869044	C	T	0.57	0.61	0.79	0.83			ESDR			10 altered motifs			1 hit	intronic
1	23058263	0.87	0.94	rs1984978	G	A	0.57	0.61	0.79	0.83			ESDR			GR,Zfp691			1 hit	intronic
1	23058343	0.87	0.94	rs2007023	T	C	0.65	0.61	0.79	0.83			ESDR						1 hit	intronic
1	23063806	0.95	0.98	rs10753553	T	A	0.59	0.60	0.79	0.83						Gfi1			1 hit	intronic
1	23064151	0.96	0.99	rs2294517	A	G	0.80	0.64	0.79	0.83						NRSF,SP1,Sin3Ak-20			1 hit	intronic
1	23065282	0.95	0.98	rs2235549	G	T	0.59	0.61	0.78	0.83						5 altered motifs			2 hits	intronic
1	23069462	0.92	0.99	rs656053	A	C	0.84	0.64	0.79	0.82			VAS		GATA2	CEBPB			1 hit	intronic
		0.96	0.99	rs78316344	C	T	0.59	0.61	0.79	0.83			VAS							intronic
1	23073439	0.99	1	rs967605	C	T	0.80	0.64	0.79	0.83			MUS			Myc,p53			2 hits	intronic
1	23074479	0.97	1	rs1329282	T	C	0.63	0.62	0.79	0.83			MUS			4 altered motifs			1 hit	intronic
1	23075526	0.87	0.99	rs2869038	G	A	0.58	0.59	0.78	0.82						4 altered motifs			1 hit	intronic
1	23078178	0.87	0.99	rs4655145	A	G	0.65	0.81	0.86	0.85									1 hit	intronic
1	23079301	0.87	0.99	rs2072945	A	C	0.59	0.80	0.86	0.85			ESDR, LNG, BRST			8 altered motifs			1 hit	intronic
1	23080604	0.85	0.99	rs579098	A	G	0.75	0.82	0.86	0.85						TCF12			1 hit	intronic
1	23081219	0.99	1	rs2072943	G	C	0.59	0.60	0.79	0.83			IPSC						1 hit	intronic
1	23083646	1	1	rs201520274	TG	T	0.83	0.64	0.79	0.83			FAT			17 altered motifs			1 hit	3'-UTR
1	23084228	1	1	rs505938	A	T	0.83	0.64	0.79	0.83			7 tissues	BRN	POL2	Hsf			1 hit	3'-UTR
1	23084249	1	1	rs506004	A	C	0.83	0.64	0.79	0.83			7 tissues	BRN	POL2	AIRE,HNF4,Rad21			1 hit	3'-UTR
1	23086534	0.99	1	rs605775	T	C	0.83	0.64	0.79	0.83			MUS, LNG			Foxp1,GLI			2 hits	3'-UTR
1	23086965	0.99	1	rs580878	T	G	0.80	0.63	0.79	0.83			HRT	LNG	POL2,ZNF263	5 altered motifs			1 hit	3'-UTR
1	23087214	0.96	0.99	rs592611	T	C	0.65	0.61	0.79	0.84						Hoxa7,Ik-2,Smad			2 hits	3'-UTR
1	23088609	0.99	1	rs683893	T	C	0.80	0.63	0.79	0.83						PU.1,SRF,STAT			1 hit	3'-UTR
1	23089829	0.95	0.99	rs6667643	C	T	0.79	0.63	0.79	0.84						4 altered motifs			1 hit	intronic
1	23091660	1	1	rs10799790	C	T	0.83	0.64	0.79	0.83						T3R		2 hits	2 hits	missense
1	23092768	1	1	rs477717	G	A	0.65	0.61	0.79	0.83			FAT, HRT			p300		1 hit	2 hits	synonymous
1	23092881	1	1	rs3765407	G	T	0.59	0.60	0.79	0.83			FAT, HRT			4 altered motifs		1 hit	2 hits	missense
1	23092890	1	1	rs477830	C	T	0.65	0.61	0.79	0.83			FAT, HRT			5 altered motifs			2 hits	missense
1	23093362	1	1	rs1983965	T	C	0.83	0.64	0.79	0.83						RREB-1		1 hit	3 hits	synonymous
1	23096199	1	1	rs614612	T	C	0.80	0.63	0.79	0.83			4 tissues	BRN		CEBPB,HNF1,Hmbox1		1 hit	1 hit	intronic
1	23096881	1	1	rs10799791	G	A	0.59	0.60	0.79	0.83						9 altered motifs			1 hit	intronic
1	23099446	1	1	rs489644	A	C	0.79	0.63	0.80	0.83			18 tissues			7 altered motifs			1 hit	intronic