Variant report

Variant	rs62272388
Chromosome Location	chr3:134514292-134514293
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:134513722-134514332	GM19239	blood:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
2	TBL1XR1	chr3:134513666-134514438	GM12878	blood:	n/a	n/a
3	TAF1	chr3:134513901-134514318	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:134513759-134516964	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr3:134513837-134514363	HEK293	kidney:	n/a	n/a
6	EGR1	chr3:134514220-134514365	GM12878	blood:	n/a	chr3:134514320-134514329 chr3:134514269-134514283 chr3:134514318-134514331 chr3:134514319-134514329 chr3:134514317-134514331 chr3:134514315-134514329 chr3:134514319-134514330 chr3:134514319-134514329 chr3:134514317-134514332 chr3:134514312-134514325 chr3:134514313-134514335 chr3:134514318-134514331 chr3:134514319-134514330 chr3:134514318-134514331 chr3:134514319-134514328
7	POLR2A	chr3:134513965-134514384	GM12878	blood:	n/a	n/a
8	RAD21	chr3:134513573-134514292	HCT-116	colon:	n/a	chr3:134513885-134513904
9	RAD21	chr3:134513422-134514439	SK-N-SH	brain:	n/a	chr3:134513885-134513904
10	TAF1	chr3:134513950-134514297	GM12878	blood:	n/a	n/a
11	REST	chr3:134513559-134517109	H1-neurons	neurons:	n/a	chr3:134515459-134515469 chr3:134513816-134513824 chr3:134514415-134514428 chr3:134515274-134515284 chr3:134515272-134515292 chr3:134514323-134514336 chr3:134514680-134514693 chr3:134514418-134514436 chr3:134515452-134515465
12	POLR2A	chr3:134513932-134514490	HUVEC	blood vessel:	n/a	n/a
13	KAP1	chr3:134513742-134514811	HEK293	kidney:	n/a	chr3:134514607-134514615
14	POLR2A	chr3:134514060-134514326	Gliobla	brain:	n/a	n/a
15	ELF1	chr3:134513694-134514338	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:134514019-134514339	MCF-7	breast:	n/a	n/a
17	POLR2A	chr3:134513918-134514614	GM15510	blood:	n/a	n/a
18	POLR2A	chr3:134513836-134514611	GM12878	blood:	n/a	n/a
19	SP1	chr3:134513672-134514405	GM12878	blood:	n/a	chr3:134514316-134514326 chr3:134514082-134514096 chr3:134513988-134514009 chr3:134514052-134514063
20	EGR1	chr3:134513694-134514571	MCF-7	breast:	n/a	chr3:134514320-134514329 chr3:134514269-134514283 chr3:134514318-134514331 chr3:134514319-134514329 chr3:134514317-134514331 chr3:134514315-134514329 chr3:134514319-134514330 chr3:134514319-134514329 chr3:134514317-134514332 chr3:134514312-134514325 chr3:134514313-134514335 chr3:134514318-134514331 chr3:134514319-134514330 chr3:134514318-134514331 chr3:134514319-134514328
21	POLR2A	chr3:134513627-134514412	GM12878	blood:	n/a	n/a
22	E2F6	chr3:134513703-134514394	H1-hESC	embryonic stem cell:	n/a	chr3:134514359-134514366 chr3:134514359-134514366 chr3:134514358-134514366 chr3:134513999-134514008 chr3:134514359-134514366
23	MAZ	chr3:134513746-134514492	GM12878	blood:	n/a	chr3:134514294-134514303 chr3:134514084-134514094
24	YY1	chr3:134513717-134514472	H1-hESC	embryonic stem cell:	n/a	n/a
25	ATF2	chr3:134513732-134514414	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F6	chr3:134513903-134514407	A549	lung:	n/a	chr3:134514359-134514366 chr3:134514359-134514366 chr3:134514358-134514366 chr3:134513999-134514008 chr3:134514359-134514366
27	SIN3A	chr3:134513789-134514794	GM12878	blood:	n/a	chr3:134514415-134514428
28	BHLHE40	chr3:134513763-134514400	GM12878	blood:	n/a	n/a
29	TAF7	chr3:134513784-134514432	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD2	chr3:134513819-134514374	H1-hESC	embryonic stem cell:	n/a	n/a
31	TAF1	chr3:134513944-134514561	H1-neurons	neurons:	n/a	n/a
32	ZNF143	chr3:134513713-134514521	GM12878	blood:	n/a	chr3:134514401-134514419 chr3:134514423-134514433
33	POLR2A	chr3:134513784-134516025	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr3:134513967-134514328	H1-hESC	embryonic stem cell:	n/a	n/a
35	RELA	chr3:134513778-134514404	GM19099	blood:	n/a	n/a
36	EGR1	chr3:134514166-134514389	K562	blood:	n/a	chr3:134514320-134514329 chr3:134514269-134514283 chr3:134514318-134514331 chr3:134514319-134514329 chr3:134514317-134514331 chr3:134514315-134514329 chr3:134514319-134514330 chr3:134514319-134514329 chr3:134514317-134514332 chr3:134514312-134514325 chr3:134514313-134514335 chr3:134514318-134514331 chr3:134514319-134514330 chr3:134514318-134514331 chr3:134514319-134514328
37	MYC	chr3:134514018-134514546	GM12878	blood:	n/a	chr3:134514294-134514303 chr3:134514084-134514094
38	SMC3	chr3:134513477-134514759	SK-N-SH	brain:	n/a	chr3:134514713-134514727 chr3:134513886-134513900 chr3:134513886-134513894
39	POLR2A	chr3:134513847-134515016	GM12878	blood:	n/a	n/a
40	EGR1	chr3:134513950-134514511	ECC-1	luminal epithelium:	n/a	chr3:134514320-134514329 chr3:134514269-134514283 chr3:134514318-134514331 chr3:134514319-134514329 chr3:134514317-134514331 chr3:134514315-134514329 chr3:134514319-134514330 chr3:134514319-134514329 chr3:134514317-134514332 chr3:134514312-134514325 chr3:134514313-134514335 chr3:134514318-134514331 chr3:134514319-134514330 chr3:134514318-134514331 chr3:134514319-134514328
41	CTCF	chr3:134513661-134514292	GM12878	blood:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
42	TBP	chr3:134513839-134514348	GM12878	blood:	n/a	n/a
43	TCF12	chr3:134513636-134514517	ECC-1	luminal epithelium:	n/a	n/a
44	STAT1	chr3:134513864-134514324	GM12878	blood:	n/a	chr3:134514193-134514205
45	CTCF	chr3:134513529-134514345	SK-N-SH	brain:	n/a	chr3:134513884-134513902 chr3:134513886-134513907 chr3:134513885-134513901 chr3:134513887-134513900
46	TAF1	chr3:134513729-134514709	H1-neurons	neurons:	n/a	n/a
47	CTCF	chr3:134514240-134514390	HCM	heart:	n/a	n/a
48	EBF1	chr3:134513766-134514478	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:134514004-134514353	MCF-7	breast:	n/a	n/a
50	SIN3A	chr3:134513803-134515698	H1-hESC	embryonic stem cell:	n/a	chr3:134514415-134514428 chr3:134515536-134515544 chr3:134515452-134515465 chr3:134515544-134515555

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:134514288-134514338	PrEC	prostate:	n/a
2	chr3:134514288-134514338	GM19239	blood:	n/a
3	chr3:134514288-134514338	SK-N-SH	brain:	n/a
4	chr3:134514288-134514338	BE2_C	brain:	n/a
5	chr3:134514288-134514338	HRE	kidney:	n/a
6	chr3:134514288-134514338	Jurkat	blood:	n/a
7	chr3:134514288-134514338	AG10803	skin:	n/a
8	chr3:134514288-134514338	T-47D	breast:	n/a
9	chr3:134514288-134514338	HepG2	liver:	n/a
10	chr3:134514288-134514338	AG04450	lung:	fetal
11	chr3:134514288-134514338	NB4	blood:	n/a
12	chr3:134514288-134514338	A549	lung:	n/a
13	chr3:134514288-134514338	RPTEC	kidney:	n/a
14	chr3:134514288-134514338	HL-60	blood:	n/a
15	chr3:134514288-134514338	AoSMC	blood vessel:	n/a
16	chr3:134514288-134514338	LNCaP	prostate:	n/a
17	chr3:134514288-134514338	MCF10A-Er-Src	breast:	n/a
18	chr3:134514288-134514338	AG04449	skin:	fetal
19	chr3:134514288-134514338	NH-A	brain:	n/a
20	chr3:134514288-134514338	HMEC	breast:	n/a
21	chr3:134514288-134514338	ECC-1	luminal epithelium:	n/a
22	chr3:134514288-134514338	PFSK-1	brain:	n/a
23	chr3:134514288-134514338	GM12892	blood:	n/a
24	chr3:134514288-134514338	ovcar-3	ovarian:	n/a
25	chr3:134514288-134514338	SK-N-SH_RA	brain:	n/a
26	chr3:134514288-134514338	HNPCEpiC	eye:	n/a
27	chr3:134514288-134514338	H1-hESC	embryonic stem cell:	embryo
28	chr3:134514288-134514338	GM12878	blood:	n/a
29	chr3:134514288-134514338	NT2-D1	testis:	n/a
30	chr3:134514288-134514338	SAEC	small airway:	n/a
31	chr3:134514288-134514338	HCT-116	colon:	n/a
32	chr3:134514288-134514338	PANC-1	pancreas:	n/a
33	chr3:134514288-134514338	Hepatocyte	liver:	n/a
34	chr3:134514288-134514338	CMK	blood:	n/a
35	chr3:134514288-134514338	AG09309	skin:	n/a
36	chr3:134514288-134514338	HEEpiC	esophagus:	n/a
37	chr3:134514288-134514338	NHDF-neo	bronchial:	n/a
38	chr3:134514288-134514338	HPAEpiC	pulmonary alveolar:	n/a
39	chr3:134514288-134514338	HEK293	kidney:	embryo
40	chr3:134514288-134514338	IMR90	lung:	fetal
41	chr3:134514288-134514338	BJ	skin:	n/a
42	chr3:134514288-134514338	SK-N-MC	brain:	n/a
43	chr3:134514288-134514338	AG09319	gingival:	n/a
44	chr3:134514288-134514338	HUVEC	blood vessel:	n/a
45	chr3:134514288-134514338	HCM	heart:	n/a
46	chr3:134514288-134514338	HIPEpiC	eye:	n/a
47	chr3:134514288-134514338	GM12891	blood:	n/a
48	chr3:134514288-134514338	HCPEpiC	choroid plexus:	n/a
49	chr3:134514288-134514338	GM06990	blood:	n/a
50	chr3:134514288-134514338	SKMC	muscle:	n/a

Variant related genes	Relation type
EPHB1	TF binding region
EPHB1	CpG island

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11924725	0.84[ASN][1000 genomes]
rs11928724	0.84[ASN][1000 genomes]
rs1374812	0.82[ASN][1000 genomes]
rs57941453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62272389	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439520	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6762299	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134513600-134514600	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr3:134513600-134514800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr3:134513600-134515000	Active TSS	GM12878-XiMat	blood
4	chr3:134513600-134515200	Active TSS	Brain Anterior Caudate	brain
5	chr3:134513600-134515600	Enhancers	Fetal Heart	heart
6	chr3:134513600-134516000	Bivalent/Poised TSS	HSMM	muscle
7	chr3:134513800-134514400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr3:134513800-134514400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
9	chr3:134513800-134514400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:134513800-134514400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr3:134513800-134514400	Active TSS	Brain Hippocampus Middle	brain
12	chr3:134513800-134514400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr3:134513800-134514400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr3:134513800-134514600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:134513800-134514600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:134513800-134514600	Active TSS	Brain Germinal Matrix	brain
17	chr3:134513800-134514600	Active TSS	Colon Smooth Muscle	Colon
18	chr3:134513800-134514600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
19	chr3:134513800-134514600	Bivalent/Poised TSS	HepG2	liver
20	chr3:134513800-134514800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:134513800-134514800	Bivalent/Poised TSS	A549	lung
22	chr3:134513800-134514800	Active TSS	HSMMtube	muscle
23	chr3:134513800-134515000	Active TSS	Ovary	ovary
24	chr3:134513800-134515600	Active TSS	Fetal Brain Female	brain
25	chr3:134513800-134515800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:134513800-134515800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:134513800-134515800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:134513800-134515800	Active TSS	Brain Cingulate Gyrus	brain
29	chr3:134513800-134516000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:134513800-134516000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr3:134513800-134516200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:134513800-134516800	Active TSS	Brain Angular Gyrus	brain
33	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
35	chr3:134514000-134514400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
37	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr3:134514000-134514400	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:134514000-134514400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:134514000-134514400	Flanking Active TSS	Fetal Brain Male	brain
42	chr3:134514000-134514400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
43	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	Placenta	Placenta
44	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
45	chr3:134514000-134514400	Flanking Bivalent TSS/Enh	NHEK	skin
46	chr3:134514000-134514600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:134514000-134514600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:134514000-134514600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr3:134514000-134514600	Bivalent/Poised TSS	Fetal Lung	lung
50	chr3:134514000-134514600	Bivalent/Poised TSS	HUVEC	blood vessel

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