Detail view for rs489644

Link to dbSNP entry

Link to Ensembl Variation entry
Sequence facts
chr pos (hg19) chr pos (hg38) Reference Alternate 1000 Genomes Phase 1 Frequencies Sequence constraint dbSNP functional annotation
AFR AMR ASN EUR by GERP by SiPhy
chr1 23425939 chr1 23099446 A C 0.79 0.63 0.8 0.83 No No intronic
Closest annotated gene
Source Distance Direction ID/Link Common name Description
GENCODE NA Within gene ENSG00000169641.9 LUZP1 leucine zipper protein 1 [Source:HGNC Symbol;Acc:14985]
RefSeq NA Within gene NM_001142546 LUZP1 leucine zipper protein 1 [Source:HGNC Symbol;Acc:14985]
Regulatory chromatin states from DNAse and histone ChIP-Seq (Roadmap Epigenomics Consortium, 2015)

(Black = missing data)

Epigenome ID (EID)	Group	Mnemonic	Description	Chromatin states (Core 15-state model)	Chromatin states (25-state model using 12 imputed marks)	H3K4me1	H3K4me3	H3K27ac	H3K9ac	DNase
E001	ESC	ESC.I3	ES-I3 Cells		17_EnhW2	H3K4me1_Enh
E002	ESC	ESC.WA7	ES-WA7 Cells		17_EnhW2
E003	ESC	ESC.H1	H1 Cells
E004	ES-deriv	ESDR.H1.BMP4.MESO	H1 BMP4 Derived Mesendoderm Cultured Cells		17_EnhW2	H3K4me1_Enh		H3K27ac_Enh
E005	ES-deriv	ESDR.H1.BMP4.TROP	H1 BMP4 Derived Trophoblast Cultured Cells
E006	ES-deriv	ESDR.H1.MSC	H1 Derived Mesenchymal Stem Cells		17_EnhW2
E007	ES-deriv	ESDR.H1.NEUR.PROG	H1 Derived Neuronal Progenitor Cultured Cells
E008	ESC	ESC.H9	H9 Cells		17_EnhW2
E009	ES-deriv	ESDR.H9.NEUR.PROG	H9 Derived Neuronal Progenitor Cultured Cells		17_EnhW2
E010	ES-deriv	ESDR.H9.NEUR	H9 Derived Neuron Cultured Cells	7_Enh		H3K4me1_Enh
E011	ES-deriv	ESDR.CD184.ENDO	hESC Derived CD184+ Endoderm Cultured Cells			H3K4me1_Enh
E012	ES-deriv	ESDR.CD56.ECTO	hESC Derived CD56+ Ectoderm Cultured Cells		17_EnhW2	H3K4me1_Enh		H3K27ac_Enh
E013	ES-deriv	ESDR.CD56.MESO	hESC Derived CD56+ Mesoderm Cultured Cells	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E014	ESC	ESC.HUES48	HUES48 Cells	7_Enh	12_TxEnhW	H3K4me1_Enh		H3K27ac_Enh
E015	ESC	ESC.HUES6	HUES6 Cells	7_Enh	17_EnhW2	H3K4me1_Enh
E016	ESC	ESC.HUES64	HUES64 Cells	7_Enh		H3K4me1_Enh		H3K27ac_Enh
E017	IMR90	LNG.IMR90	IMR90 fetal lung fibroblasts Cell Line	7_Enh	17_EnhW2	H3K4me1_Enh			H3K9ac_Pro
E018	iPSC	IPSC.15b	iPS-15b Cells	7_Enh	17_EnhW2	H3K4me1_Enh
E019	iPSC	IPSC.18	iPS-18 Cells			H3K4me1_Enh
E020	iPSC	IPSC.20B	iPS-20b Cells			H3K4me1_Enh
E021	iPSC	IPSC.DF.6.9	iPS DF 6.9 Cells			H3K4me1_Enh
E022	iPSC	IPSC.DF.19.11	iPS DF 19.11 Cells
E023	Mesench	FAT.MSC.DR.ADIP	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	7_Enh	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro		H3K9ac_Pro
E024	ESC	ESC.4STAR	ES-UCSF4 Cells			H3K4me1_Enh
E025	Mesench	FAT.ADIP.DR.MSC	Adipose Derived Mesenchymal Stem Cell Cultured Cells	7_Enh	9_TxReg	H3K4me1_Enh	H3K4me3_Pro		H3K9ac_Pro
E026	Mesench	STRM.MRW.MSC	Bone Marrow Derived Cultured Mesenchymal Stem Cells	7_Enh	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E027	Epithelial	BRST.MYO	Breast Myoepithelial Primary Cells	7_Enh	10_TxEnh5	H3K4me1_Enh
E028	Epithelial	BRST.HMEC.35	Breast variant Human Mammary Epithelial Cells (vHMEC)	7_Enh	10_TxEnh5	H3K4me1_Enh
E029	HSC & B-cell	BLD.CD14.PC	Primary monocytes from peripheral blood		17_EnhW2	H3K4me1_Enh
E030	HSC & B-cell	BLD.CD15.PC	Primary neutrophils from peripheral blood		17_EnhW2
E031	HSC & B-cell	BLD.CD19.CPC	Primary B cells from cord blood		12_TxEnhW
E032	HSC & B-cell	BLD.CD19.PPC	Primary B cells from peripheral blood		17_EnhW2
E033	Blood & T-cell	BLD.CD3.CPC	Primary T cells from cord blood		17_EnhW2	H3K4me1_Enh
E034	Blood & T-cell	BLD.CD3.PPC	Primary T cells from peripheral blood	7_Enh		H3K4me1_Enh		H3K27ac_Enh
E035	HSC & B-cell	BLD.CD34.PC	Primary hematopoietic stem cells	7_Enh	17_EnhW2	H3K4me1_Enh
E036	HSC & B-cell	BLD.CD34.CC	Primary hematopoietic stem cells short term culture	7_Enh	17_EnhW2	H3K4me1_Enh
E037	Blood & T-cell	BLD.CD4.MPC	Primary T helper memory cells from peripheral blood 2	7_Enh	15_EnhAF	H3K4me1_Enh		H3K27ac_Enh
E038	Blood & T-cell	BLD.CD4.NPC	Primary T helper naive cells from peripheral blood	7_Enh	14_EnhA2	H3K4me1_Enh
E039	Blood & T-cell	BLD.CD4.CD25M.CD45RA.NPC	Primary T helper naive cells from peripheral blood	7_Enh	17_EnhW2	H3K4me1_Enh
E040	Blood & T-cell	BLD.CD4.CD25M.CD45RO.MPC	Primary T helper memory cells from peripheral blood 1	7_Enh	17_EnhW2	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E041	Blood & T-cell	BLD.CD4.CD25M.IL17M.PL.TPC	Primary T helper cells PMA-I stimulated	7_Enh	15_EnhAF	H3K4me1_Enh		H3K27ac_Enh
E042	Blood & T-cell	BLD.CD4.CD25M.IL17P.PL.TPC	Primary T helper 17 cells PMA-I stimulated	7_Enh	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E043	Blood & T-cell	BLD.CD4.CD25M.TPC	Primary T helper cells from peripheral blood	7_Enh	17_EnhW2	H3K4me1_Enh		H3K27ac_Enh
E044	Blood & T-cell	BLD.CD4.CD25.CD127M.TREGPC	Primary T regulatory cells from peripheral blood		17_EnhW2	H3K4me1_Enh		H3K27ac_Enh
E045	Blood & T-cell	BLD.CD4.CD25I.CD127.TMEMPC	Primary T cells effector/memory enriched from peripheral blood	7_Enh	17_EnhW2	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E046	HSC & B-cell	BLD.CD56.PC	Primary Natural Killer cells from peripheral blood	7_Enh		H3K4me1_Enh		H3K27ac_Enh
E047	Blood & T-cell	BLD.CD8.NPC	Primary T CD8+ naive cells from peripheral blood	7_Enh	17_EnhW2	H3K4me1_Enh
E048	Blood & T-cell	BLD.CD8.MPC	Primary T CD8+ memory cells from peripheral blood	7_Enh	17_EnhW2	H3K4me1_Enh
E049	Mesench	STRM.CHON.MRW.DR.MSC	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	7_Enh	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E050	HSC & B-cell	BLD.MOB.CD34.PC.F	Primary hematopoietic stem cells G-CSF-mobilized Female	7_Enh	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E051	HSC & B-cell	BLD.MOB.CD34.PC.M	Primary hematopoietic stem cells G-CSF-mobilized Male	7_Enh	14_EnhA2	H3K4me1_Enh	H3K4me3_Pro
E052	Myosat	MUS.SAT	Muscle Satellite Cultured Cells	7_Enh	9_TxReg	H3K4me1_Enh	H3K4me3_Pro		H3K9ac_Pro
E053	Neurosph	BRN.CRTX.DR.NRSPHR	Cortex derived primary cultured neurospheres	7_Enh		H3K4me1_Enh
E054	Neurosph	BRN.GANGEM.DR.NRSPHR	Ganglion Eminence derived primary cultured neurospheres	7_Enh	17_EnhW2	H3K4me1_Enh	H3K4me3_Pro
E055	Epithelial	SKIN.PEN.FRSK.FIB.01	Foreskin Fibroblast Primary Cells skin01	7_Enh	17_EnhW2	H3K4me1_Enh		H3K27ac_Enh
E056	Epithelial	SKIN.PEN.FRSK.FIB.02	Foreskin Fibroblast Primary Cells skin02	7_Enh	17_EnhW2	H3K4me1_Enh		H3K27ac_Enh
E057	Epithelial	SKIN.PEN.FRSK.KER.02	Foreskin Keratinocyte Primary Cells skin02	7_Enh	12_TxEnhW	H3K4me1_Enh
E058	Epithelial	SKIN.PEN.FRSK.KER.03	Foreskin Keratinocyte Primary Cells skin03	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E059	Epithelial	SKIN.PEN.FRSK.MEL.01	Foreskin Melanocyte Primary Cells skin01	7_Enh		H3K4me1_Enh
E061	Epithelial	SKIN.PEN.FRSK.MEL.03	Foreskin Melanocyte Primary Cells skin03			H3K4me1_Enh
E062	Blood & T-cell	BLD.PER.MONUC.PC	Primary mononuclear cells from peripheral blood		17_EnhW2	H3K4me1_Enh			H3K9ac_Pro
E063	Adipose	FAT.ADIP.NUC	Adipose Nuclei	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E065	Heart	VAS.AOR	Aorta		17_EnhW2
E066	Other	LIV.ADLT	Liver		17_EnhW2	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E067	Brain	BRN.ANG.GYR	Brain Angular Gyrus	7_Enh	18_EnhAc	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E068	Brain	BRN.ANT.CAUD	Brain Anterior Caudate	7_Enh		H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E069	Brain	BRN.CING.GYR	Brain Cingulate Gyrus	7_Enh	17_EnhW2	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E070	Brain	BRN.GRM.MTRX	Brain Germinal Matrix		17_EnhW2
E071	Brain	BRN.HIPP.MID	Brain Hippocampus Middle	7_Enh		H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E072	Brain	BRN.INF.TMP	Brain Inferior Temporal Lobe		17_EnhW2	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E073	Brain	BRN.DL.PRFRNTL.CRTX	Brain_Dorsolateral_Prefrontal_Cortex	7_Enh	17_EnhW2	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E074	Brain	BRN.SUB.NIG	Brain Substantia Nigra			H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E075	Digestive	GI.CLN.MUC	Colonic Mucosa		17_EnhW2	H3K4me1_Enh
E076	Sm. Muscle	GI.CLN.SM.MUS	Colon Smooth Muscle	7_Enh	18_EnhAc	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E077	Digestive	GI.DUO.MUC	Duodenum Mucosa			H3K4me1_Enh			H3K9ac_Pro
E078	Sm. Muscle	GI.DUO.SM.MUS	Duodenum Smooth Muscle		17_EnhW2	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E079	Digestive	GI.ESO	Esophagus
E080	Other	ADRL.GLND.FET	Fetal Adrenal Gland	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E081	Brain	BRN.FET.M	Fetal Brain Male		17_EnhW2	H3K4me1_Enh
E082	Brain	BRN.FET.F	Fetal Brain Female		17_EnhW2
E083	Heart	HRT.FET	Fetal Heart	7_Enh	17_EnhW2	H3K4me1_Enh
E084	Digestive	GI.L.INT.FET	Fetal Intestine Large			H3K4me1_Enh
E085	Digestive	GI.S.INT.FET	Fetal Intestine Small			H3K4me1_Enh
E086	Other	KID.FET	Fetal Kidney	7_Enh	17_EnhW2
E087	Other	PANC.ISLT	Pancreatic Islets			H3K4me1_Enh
E088	Other	LNG.FET	Fetal Lung		17_EnhW2	H3K4me1_Enh			H3K9ac_Pro
E089	Muscle	MUS.TRNK.FET	Fetal Muscle Trunk		17_EnhW2			H3K27ac_Enh
E090	Muscle	MUS.LEG.FET	Fetal Muscle Leg
E091	Other	PLCNT.FET	Placenta			H3K4me1_Enh		H3K27ac_Enh
E092	Digestive	GI.STMC.FET	Fetal Stomach			H3K4me1_Enh
E093	Thymus	THYM.FET	Fetal Thymus		17_EnhW2
E094	Digestive	GI.STMC.GAST	Gastric
E095	Heart	HRT.VENT.L	Left Ventricle			H3K4me1_Enh		H3K27ac_Enh
E096	Other	LNG	Lung
E097	Other	OVRY	Ovary		17_EnhW2
E098	Other	PANC	Pancreas
E099	Other	PLCNT.AMN	Placenta Amnion			H3K4me1_Enh
E100	Muscle	MUS.PSOAS	Psoas Muscle
E101	Digestive	GI.RECT.MUC.29	Rectal Mucosa Donor 29		19_DNase	H3K4me1_Enh			H3K9ac_Pro
E102	Digestive	GI.RECT.MUC.31	Rectal Mucosa Donor 31		12_TxEnhW	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E103	Sm. Muscle	GI.RECT.SM.MUS	Rectal Smooth Muscle		18_EnhAc	H3K4me1_Enh	H3K4me3_Pro
E104	Heart	HRT.ATR.R	Right Atrium	7_Enh	17_EnhW2
E105	Heart	HRT.VNT.R	Right Ventricle
E106	Digestive	GI.CLN.SIG	Sigmoid Colon			H3K4me1_Enh
E107	Muscle	MUS.SKLT.M	Skeletal Muscle Male	7_Enh		H3K4me1_Enh			H3K9ac_Pro
E108	Muscle	MUS.SKLT.F	Skeletal Muscle Female	7_Enh	18_EnhAc	H3K4me1_Enh
E109	Digestive	GI.S.INT	Small Intestine	7_Enh		H3K4me1_Enh
E110	Digestive	GI.STMC.MUC	Stomach Mucosa		17_EnhW2	H3K4me1_Enh			H3K9ac_Pro
E111	Sm. Muscle	GI.STMC.MUS	Stomach Smooth Muscle			H3K4me1_Enh		H3K27ac_Enh
E112	Thymus	THYM	Thymus		17_EnhW2
E113	Other	SPLN	Spleen					H3K27ac_Enh
E114	ENCODE2012	LNG.A549.ETOH002.CNCR	A549 EtOH 0.02pct Lung Carcinoma Cell Line	7_Enh	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E115	ENCODE2012	BLD.DND41.CNCR	Dnd41 TCell Leukemia Cell Line		17_EnhW2
E116	ENCODE2012	BLD.GM12878	GM12878 Lymphoblastoid Cells		17_EnhW2
E117	ENCODE2012	CRVX.HELAS3.CNCR	HeLa-S3 Cervical Carcinoma Cell Line	7_Enh	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro
E118	ENCODE2012	LIV.HEPG2.CNCR	HepG2 Hepatocellular Carcinoma Cell Line			H3K4me1_Enh
E119	ENCODE2012	BRST.HMEC	HMEC Mammary Epithelial Primary Cells	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E120	ENCODE2012	MUS.HSMM	HSMM Skeletal Muscle Myoblasts Cells	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E121	ENCODE2012	MUS.HSMMT	HSMM cell derived Skeletal Muscle Myotubes Cells	7_Enh	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E122	ENCODE2012	VAS.HUVEC	HUVEC Umbilical Vein Endothelial Primary Cells	7_Enh	9_TxReg	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E123	ENCODE2012	BLD.K562.CNCR	K562 Leukemia Cells		17_EnhW2	H3K4me1_Enh
E124	ENCODE2012	BLD.CD14.MONO	Monocytes-CD14+ RO01746 Primary Cells			H3K4me1_Enh
E125	ENCODE2012	BRN.NHA	NH-A Astrocytes Primary Cells	7_Enh	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E126	ENCODE2012	SKIN.NHDFAD	NHDF-Ad Adult Dermal Fibroblast Primary Cells	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E127	ENCODE2012	SKIN.NHEK	NHEK-Epidermal Keratinocyte Primary Cells	7_Enh	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E128	ENCODE2012	LNG.NHLF	NHLF Lung Fibroblast Primary Cells	7_Enh	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E129	ENCODE2012	BONE.OSTEO	Osteoblast Primary Cells	7_Enh	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh

Hits from selected eQTL studies

Study ID Paper Title PMID Tissue Correlated gene p-value
GTEx2015_v6 The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans 25954001 Testis LACTBL1 2.90889677754652e-11

Regulatory motifs altered

Position Weight Matrix ID
(Library from Kheradpour and Kellis, 2013) Strand Ref Alt Match on:
Ref: TGTATTTTAAAGAGATAAACTTCATGATAAATAAAGCATATCTCAATAAAGCTGTTAAA
Alt: TGTATTTTAAAGAGATAAACTTCATGATACATAAAGCATATCTCAATAAAGCTGTTAAA
Egr-1_disc4 - -18.6 -6.6
RACTACAWBTCCCRGMRKGCMYCGC
Foxf2 - 11.4 -0.5
BNANSRTAAACAWD
Foxp1 - -14.1 -26
AWAMWMRMMAAYAYAAATAA
Mef2_known1 + 10.2 -1.4
VKSDYTAWAWAWAVCYMM
Mef2_known3 + 12.9 1.2
YTWAAWATARCH
Pou3f2_1 + 11.8 8.1
NNCATBSDWAATRMRY
Pou6f1_1 - 13.6 1.6
ATWAWTTATGY
TATA_known3 + 11.3 5.2
KATAAATW

Closest annotated gene
Source	Distance	Direction	ID/Link	Common name	Description
GENCODE	NA	Within gene	ENSG00000169641.9	LUZP1	leucine zipper protein 1 [Source:HGNC Symbol;Acc:14985]
RefSeq	NA	Within gene	NM_001142546	LUZP1	leucine zipper protein 1 [Source:HGNC Symbol;Acc:14985]

Study ID	Paper Title	PMID	Tissue	Correlated gene	p-value
GTEx2015_v6	The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans	25954001	Testis	LACTBL1	2.90889677754652e-11

Position Weight Matrix ID (Library from Kheradpour and Kellis, 2013)	Strand	Ref	Alt	Match on: Ref: TGTATTTTAAAGAGATAAACTTCATGATAAATAAAGCATATCTCAATAAAGCTGTTAAA Alt: TGTATTTTAAAGAGATAAACTTCATGATACATAAAGCATATCTCAATAAAGCTGTTAAA
Egr-1_disc4	-	-18.6	-6.6	RACTACAWBTCCCRGMRKGCMYCGC
Foxf2	-	11.4	-0.5	BNANSRTAAACAWD
Foxp1	-	-14.1	-26	AWAMWMRMMAAYAYAAATAA
Mef2_known1	+	10.2	-1.4	VKSDYTAWAWAWAVCYMM
Mef2_known3	+	12.9	1.2	YTWAAWATARCH
Pou3f2_1	+	11.8	8.1	NNCATBSDWAATRMRY
Pou6f1_1	-	13.6	1.6	ATWAWTTATGY
TATA_known3	+	11.3	5.2	KATAAATW