Detail view for rs2038028

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 11979556 chr1 11919499 A G 0.82 0.52 0.63 0.54 No No none
Closest annotated gene
Source Distance Direction ID/Link Common name Description
GENCODE 3' 91 ENSG00000116685.11 KIAA2013 KIAA2013 [Source:HGNC Symbol;Acc:28513]
RefSeq 3' 87 NM_138346 KIAA2013 KIAA2013 [Source:HGNC Symbol;Acc:28513]
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
E002	ESC	ESC.WA7	ES-WA7 Cells
E003	ESC	ESC.H1	H1 Cells
E004	ES-deriv	ESDR.H1.BMP4.MESO	H1 BMP4 Derived Mesendoderm Cultured Cells
E005	ES-deriv	ESDR.H1.BMP4.TROP	H1 BMP4 Derived Trophoblast Cultured Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E006	ES-deriv	ESDR.H1.MSC	H1 Derived Mesenchymal Stem Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E007	ES-deriv	ESDR.H1.NEUR.PROG	H1 Derived Neuronal Progenitor Cultured Cells					H3K27ac_Enh	H3K9ac_Pro
E008	ESC	ESC.H9	H9 Cells					H3K27ac_Enh
E009	ES-deriv	ESDR.H9.NEUR.PROG	H9 Derived Neuronal Progenitor Cultured Cells
E010	ES-deriv	ESDR.H9.NEUR	H9 Derived Neuron Cultured Cells
E011	ES-deriv	ESDR.CD184.ENDO	hESC Derived CD184+ Endoderm Cultured Cells
E012	ES-deriv	ESDR.CD56.ECTO	hESC Derived CD56+ Ectoderm Cultured Cells					H3K27ac_Enh
E013	ES-deriv	ESDR.CD56.MESO	hESC Derived CD56+ Mesoderm Cultured Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E014	ESC	ESC.HUES48	HUES48 Cells
E015	ESC	ESC.HUES6	HUES6 Cells
E016	ESC	ESC.HUES64	HUES64 Cells
E017	IMR90	LNG.IMR90	IMR90 fetal lung fibroblasts Cell Line	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E018	iPSC	IPSC.15b	iPS-15b Cells						H3K9ac_Pro
E019	iPSC	IPSC.18	iPS-18 Cells						H3K9ac_Pro
E020	iPSC	IPSC.20B	iPS-20b Cells
E021	iPSC	IPSC.DF.6.9	iPS DF 6.9 Cells
E022	iPSC	IPSC.DF.19.11	iPS DF 19.11 Cells					H3K27ac_Enh
E023	Mesench	FAT.MSC.DR.ADIP	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	7_Enh	10_TxEnh5	H3K4me1_Enh
E024	ESC	ESC.4STAR	ES-UCSF4 Cells
E025	Mesench	FAT.ADIP.DR.MSC	Adipose Derived Mesenchymal Stem Cell Cultured Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh
E026	Mesench	STRM.MRW.MSC	Bone Marrow Derived Cultured Mesenchymal Stem Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E027	Epithelial	BRST.MYO	Breast Myoepithelial Primary Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh			H3K9ac_Pro
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
E030	HSC & B-cell	BLD.CD15.PC	Primary neutrophils from peripheral blood
E031	HSC & B-cell	BLD.CD19.CPC	Primary B cells from cord blood
E032	HSC & B-cell	BLD.CD19.PPC	Primary B cells from peripheral blood
E033	Blood & T-cell	BLD.CD3.CPC	Primary T cells from cord blood
E034	Blood & T-cell	BLD.CD3.PPC	Primary T cells from peripheral blood			H3K4me1_Enh
E035	HSC & B-cell	BLD.CD34.PC	Primary hematopoietic stem cells
E036	HSC & B-cell	BLD.CD34.CC	Primary hematopoietic stem cells short term culture
E037	Blood & T-cell	BLD.CD4.MPC	Primary T helper memory cells from peripheral blood 2			H3K4me1_Enh
E038	Blood & T-cell	BLD.CD4.NPC	Primary T helper naive cells from peripheral blood			H3K4me1_Enh
E039	Blood & T-cell	BLD.CD4.CD25M.CD45RA.NPC	Primary T helper naive cells from peripheral blood			H3K4me1_Enh
E040	Blood & T-cell	BLD.CD4.CD25M.CD45RO.MPC	Primary T helper memory cells from peripheral blood 1
E041	Blood & T-cell	BLD.CD4.CD25M.IL17M.PL.TPC	Primary T helper cells PMA-I stimulated			H3K4me1_Enh
E042	Blood & T-cell	BLD.CD4.CD25M.IL17P.PL.TPC	Primary T helper 17 cells PMA-I stimulated
E043	Blood & T-cell	BLD.CD4.CD25M.TPC	Primary T helper cells from peripheral blood			H3K4me1_Enh
E044	Blood & T-cell	BLD.CD4.CD25.CD127M.TREGPC	Primary T regulatory cells from peripheral blood			H3K4me1_Enh
E045	Blood & T-cell	BLD.CD4.CD25I.CD127.TMEMPC	Primary T cells effector/memory enriched from peripheral blood			H3K4me1_Enh
E046	HSC & B-cell	BLD.CD56.PC	Primary Natural Killer cells from peripheral blood			H3K4me1_Enh
E047	Blood & T-cell	BLD.CD8.NPC	Primary T CD8+ naive cells from peripheral blood			H3K4me1_Enh
E048	Blood & T-cell	BLD.CD8.MPC	Primary T CD8+ memory cells from peripheral blood			H3K4me1_Enh
E049	Mesench	STRM.CHON.MRW.DR.MSC	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	6_EnhG	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
E051	HSC & B-cell	BLD.MOB.CD34.PC.M	Primary hematopoietic stem cells G-CSF-mobilized Male
E052	Myosat	MUS.SAT	Muscle Satellite Cultured Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh
E053	Neurosph	BRN.CRTX.DR.NRSPHR	Cortex derived primary cultured neurospheres		11_TxEnh3	H3K4me1_Enh
E054	Neurosph	BRN.GANGEM.DR.NRSPHR	Ganglion Eminence derived primary cultured neurospheres		11_TxEnh3
E055	Epithelial	SKIN.PEN.FRSK.FIB.01	Foreskin Fibroblast Primary Cells skin01	6_EnhG	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E056	Epithelial	SKIN.PEN.FRSK.FIB.02	Foreskin Fibroblast Primary Cells skin02	6_EnhG	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E057	Epithelial	SKIN.PEN.FRSK.KER.02	Foreskin Keratinocyte Primary Cells skin02	6_EnhG	10_TxEnh5	H3K4me1_Enh
E058	Epithelial	SKIN.PEN.FRSK.KER.03	Foreskin Keratinocyte Primary Cells skin03	6_EnhG	10_TxEnh5	H3K4me1_Enh
E059	Epithelial	SKIN.PEN.FRSK.MEL.01	Foreskin Melanocyte Primary Cells skin01		11_TxEnh3	H3K4me1_Enh		H3K27ac_Enh
E061	Epithelial	SKIN.PEN.FRSK.MEL.03	Foreskin Melanocyte Primary Cells skin03		11_TxEnh3	H3K4me1_Enh		H3K27ac_Enh
E062	Blood & T-cell	BLD.PER.MONUC.PC	Primary mononuclear cells from peripheral blood				H3K4me3_Pro		H3K9ac_Pro
E063	Adipose	FAT.ADIP.NUC	Adipose Nuclei	6_EnhG	9_TxReg	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E065	Heart	VAS.AOR	Aorta	7_Enh	11_TxEnh3	H3K4me1_Enh		H3K27ac_Enh
E066	Other	LIV.ADLT	Liver		11_TxEnh3
E067	Brain	BRN.ANG.GYR	Brain Angular Gyrus	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E068	Brain	BRN.ANT.CAUD	Brain Anterior Caudate	6_EnhG	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E069	Brain	BRN.CING.GYR	Brain Cingulate Gyrus	6_EnhG	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E070	Brain	BRN.GRM.MTRX	Brain Germinal Matrix		11_TxEnh3	H3K4me1_Enh
E071	Brain	BRN.HIPP.MID	Brain Hippocampus Middle	6_EnhG	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E072	Brain	BRN.INF.TMP	Brain Inferior Temporal Lobe	6_EnhG	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E073	Brain	BRN.DL.PRFRNTL.CRTX	Brain_Dorsolateral_Prefrontal_Cortex	6_EnhG	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E074	Brain	BRN.SUB.NIG	Brain Substantia Nigra	6_EnhG	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E075	Digestive	GI.CLN.MUC	Colonic Mucosa		11_TxEnh3	H3K4me1_Enh
E076	Sm. Muscle	GI.CLN.SM.MUS	Colon Smooth Muscle	6_EnhG	9_TxReg	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E077	Digestive	GI.DUO.MUC	Duodenum Mucosa	6_EnhG	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro		H3K9ac_Pro
E078	Sm. Muscle	GI.DUO.SM.MUS	Duodenum Smooth Muscle	6_EnhG	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E079	Digestive	GI.ESO	Esophagus	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E080	Other	ADRL.GLND.FET	Fetal Adrenal Gland
E081	Brain	BRN.FET.M	Fetal Brain Male
E082	Brain	BRN.FET.F	Fetal Brain Female		11_TxEnh3	H3K4me1_Enh
E083	Heart	HRT.FET	Fetal Heart		11_TxEnh3	H3K4me1_Enh			H3K9ac_Pro
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		11_TxEnh3
E087	Other	PANC.ISLT	Pancreatic Islets		11_TxEnh3				H3K9ac_Pro
E088	Other	LNG.FET	Fetal Lung		11_TxEnh3
E089	Muscle	MUS.TRNK.FET	Fetal Muscle Trunk	6_EnhG	10_TxEnh5	H3K4me1_Enh
E090	Muscle	MUS.LEG.FET	Fetal Muscle Leg	6_EnhG	10_TxEnh5	H3K4me1_Enh
E091	Other	PLCNT.FET	Placenta
E092	Digestive	GI.STMC.FET	Fetal Stomach			H3K4me1_Enh
E093	Thymus	THYM.FET	Fetal Thymus			H3K4me1_Enh
E094	Digestive	GI.STMC.GAST	Gastric		10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E095	Heart	HRT.VENT.L	Left Ventricle	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E096	Other	LNG	Lung		10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh
E097	Other	OVRY	Ovary		11_TxEnh3
E098	Other	PANC	Pancreas			H3K4me1_Enh
E099	Other	PLCNT.AMN	Placenta Amnion			H3K4me1_Enh		H3K27ac_Enh
E100	Muscle	MUS.PSOAS	Psoas Muscle	7_Enh	11_TxEnh3	H3K4me1_Enh		H3K27ac_Enh
E101	Digestive	GI.RECT.MUC.29	Rectal Mucosa Donor 29		11_TxEnh3	H3K4me1_Enh			H3K9ac_Pro
E102	Digestive	GI.RECT.MUC.31	Rectal Mucosa Donor 31	6_EnhG	10_TxEnh5	H3K4me1_Enh
E103	Sm. Muscle	GI.RECT.SM.MUS	Rectal Smooth Muscle	6_EnhG	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E104	Heart	HRT.ATR.R	Right Atrium	7_Enh	11_TxEnh3	H3K4me1_Enh		H3K27ac_Enh
E105	Heart	HRT.VNT.R	Right Ventricle	6_EnhG	9_TxReg	H3K4me1_Enh		H3K27ac_Enh
E106	Digestive	GI.CLN.SIG	Sigmoid Colon		11_TxEnh3	H3K4me1_Enh		H3K27ac_Enh
E107	Muscle	MUS.SKLT.M	Skeletal Muscle Male	3_TxFlnk	9_TxReg	H3K4me1_Enh	H3K4me3_Pro		H3K9ac_Pro
E108	Muscle	MUS.SKLT.F	Skeletal Muscle Female	2_TssAFlnk	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E109	Digestive	GI.S.INT	Small Intestine			H3K4me1_Enh		H3K27ac_Enh
E110	Digestive	GI.STMC.MUC	Stomach Mucosa			H3K4me1_Enh			H3K9ac_Pro
E111	Sm. Muscle	GI.STMC.MUS	Stomach Smooth Muscle	3_TxFlnk	9_TxReg	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E112	Thymus	THYM	Thymus
E113	Other	SPLN	Spleen		10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh
E114	ENCODE2012	LNG.A549.ETOH002.CNCR	A549 EtOH 0.02pct Lung Carcinoma Cell Line	6_EnhG	10_TxEnh5	H3K4me1_Enh	H3K4me3_Pro	H3K27ac_Enh	H3K9ac_Pro
E115	ENCODE2012	BLD.DND41.CNCR	Dnd41 TCell Leukemia Cell Line			H3K4me1_Enh	H3K4me3_Pro		H3K9ac_Pro
E116	ENCODE2012	BLD.GM12878	GM12878 Lymphoblastoid Cells				H3K4me3_Pro
E117	ENCODE2012	CRVX.HELAS3.CNCR	HeLa-S3 Cervical Carcinoma Cell Line		11_TxEnh3		H3K4me3_Pro
E118	ENCODE2012	LIV.HEPG2.CNCR	HepG2 Hepatocellular Carcinoma Cell Line			H3K4me1_Enh
E119	ENCODE2012	BRST.HMEC	HMEC Mammary Epithelial Primary Cells	6_EnhG	11_TxEnh3	H3K4me1_Enh
E120	ENCODE2012	MUS.HSMM	HSMM Skeletal Muscle Myoblasts Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh
E121	ENCODE2012	MUS.HSMMT	HSMM cell derived Skeletal Muscle Myotubes Cells	7_Enh	9_TxReg	H3K4me1_Enh		H3K27ac_Enh	H3K9ac_Pro
E122	ENCODE2012	VAS.HUVEC	HUVEC Umbilical Vein Endothelial Primary Cells		11_TxEnh3
E123	ENCODE2012	BLD.K562.CNCR	K562 Leukemia Cells
E124	ENCODE2012	BLD.CD14.MONO	Monocytes-CD14+ RO01746 Primary Cells					H3K27ac_Enh
E125	ENCODE2012	BRN.NHA	NH-A Astrocytes Primary Cells	7_Enh	10_TxEnh5	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
E127	ENCODE2012	SKIN.NHEK	NHEK-Epidermal Keratinocyte Primary Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh
E128	ENCODE2012	LNG.NHLF	NHLF Lung Fibroblast Primary Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh
E129	ENCODE2012	BONE.OSTEO	Osteoblast Primary Cells	6_EnhG	10_TxEnh5	H3K4me1_Enh		H3K27ac_Enh

GRASP QTL hits

Trait p-value PMID
Gene expression of RNU5E-1 in normal prepouch ileum 3.03245E-10 23474282

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 Esophagus_Mucosa MFN2 1.91938579162362e-07
GTEx2015_v6 The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans 25954001 Testis MFN2 1.01699137876476e-06
GTEx2015_v6 The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans 25954001 Whole_Blood KIAA2013 5.51363139883882e-07
Westra2013 Systematic identification of trans eQTLs as putative drivers of known disease associations 24013639 Whole_Blood KIAA2013|NPPA 4.294409136890139E-6
Westra2013 Systematic identification of trans eQTLs as putative drivers of known disease associations 24013639 Whole_Blood MFN2 9.321555981139448E-49
Westra2013 Systematic identification of trans eQTLs as putative drivers of known disease associations 24013639 Whole_Blood PLOD1 1.2613801622942733E-75

Regulatory motifs altered

Position Weight Matrix ID
(Library from Kheradpour and Kellis, 2013) Strand Ref Alt Match on:
Ref: ATACCAGAAAGGAATAGCATTGTGACAGCAGGGCCGGGTGGGTGTCCTGCTTCTGACAG
Alt: ATACCAGAAAGGAATAGCATTGTGACAGCGGGGCCGGGTGGGTGTCCTGCTTCTGACAG
AP-1_disc10 + 8.3 10.9
SSSVVGSVSS
BHLHE40_disc2 - 10.9 10.2
SNSSNSSNSNSNSNSNS
E2F_disc8 + 10.1 11.5
SSSSSBSCNGS
ELF1_disc3 + 10.7 10.8
SSNSNVSSSSSNS
Egr-1_disc1 - -5.2 6.7
GCGKGGGCGK
Egr-1_disc6 + 11.1 10.6
SSNGSSSSSGS
NRSF_disc9 + 11.7 11.3
GSNSDSSSNGSNSS
SRF_disc2 + 7.7 11.1
SNSVSSSVGSS
Tgif1_1 - 13.3 4.3
WHNTGACARST
Tgif1_2 - 12.5 13.6
DRBWWTGACAGSTVVBD
Znf143_known1 - 10.7 10
KCDWKGMABBMTGGRWVDKV

Closest annotated gene
Source	Distance	Direction	ID/Link	Common name	Description
GENCODE	3'	91	ENSG00000116685.11	KIAA2013	KIAA2013 [Source:HGNC Symbol;Acc:28513]
RefSeq	3'	87	NM_138346	KIAA2013	KIAA2013 [Source:HGNC Symbol;Acc:28513]

Trait	p-value	PMID
Gene expression of RNU5E-1 in normal prepouch ileum	3.03245E-10	23474282

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	Esophagus_Mucosa	MFN2	1.91938579162362e-07
GTEx2015_v6	The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans	25954001	Testis	MFN2	1.01699137876476e-06
GTEx2015_v6	The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans	25954001	Whole_Blood	KIAA2013	5.51363139883882e-07
Westra2013	Systematic identification of trans eQTLs as putative drivers of known disease associations	24013639	Whole_Blood	KIAA2013\|NPPA	4.294409136890139E-6
Westra2013	Systematic identification of trans eQTLs as putative drivers of known disease associations	24013639	Whole_Blood	MFN2	9.321555981139448E-49
Westra2013	Systematic identification of trans eQTLs as putative drivers of known disease associations	24013639	Whole_Blood	PLOD1	1.2613801622942733E-75

Position Weight Matrix ID (Library from Kheradpour and Kellis, 2013)	Strand	Ref	Alt	Match on: Ref: ATACCAGAAAGGAATAGCATTGTGACAGCAGGGCCGGGTGGGTGTCCTGCTTCTGACAG Alt: ATACCAGAAAGGAATAGCATTGTGACAGCGGGGCCGGGTGGGTGTCCTGCTTCTGACAG
AP-1_disc10	+	8.3	10.9	SSSVVGSVSS
BHLHE40_disc2	-	10.9	10.2	SNSSNSSNSNSNSNSNS
E2F_disc8	+	10.1	11.5	SSSSSBSCNGS
ELF1_disc3	+	10.7	10.8	SSNSNVSSSSSNS
Egr-1_disc1	-	-5.2	6.7	GCGKGGGCGK
Egr-1_disc6	+	11.1	10.6	SSNGSSSSSGS
NRSF_disc9	+	11.7	11.3	GSNSDSSSNGSNSS
SRF_disc2	+	7.7	11.1	SNSVSSSVGSS
Tgif1_1	-	13.3	4.3	WHNTGACARST
Tgif1_2	-	12.5	13.6	DRBWWTGACAGSTVVBD
Znf143_known1	-	10.7	10	KCDWKGMABBMTGGRWVDKV