Variant report

Variant	rs3772678
Chromosome Location	chr3:134514760-134514761
allele	A/G
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	GABPA	chr3:134514414-134514962	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chr3:134514524-134514896	H1-hESC	embryonic stem cell:	n/a	chr3:134514634-134514652 chr3:134514752-134514771 chr3:134514802-134514812
3	CTCF	chr3:134514620-134514770	GM12875	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
4	CTCF	chr3:134514620-134514770	GM12878	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
5	POLR2A	chr3:134513759-134516964	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr3:134514620-134514770	GM12864	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
7	CTCF	chr3:134514640-134514790	AG04449	skin:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
8	CTCF	chr3:134514660-134514810	AG09319	gingival:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
9	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
10	CTCF	chr3:134514653-134514795	SK-N-SH_RA	brain:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
11	KAP1	chr3:134513742-134514811	HEK293	kidney:	n/a	chr3:134514607-134514615
12	CTCF	chr3:134514620-134514770	HAc	cerebellar:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
13	CTCF	chr3:134514640-134514790	BJ	skin:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
14	CTCF	chr3:134514620-134514770	BJ	skin:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
15	CTCF	chr3:134514635-134514791	GM12891	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
16	SIN3A	chr3:134513789-134514794	GM12878	blood:	n/a	chr3:134514415-134514428
17	CTCF	chr3:134514636-134514805	GM19239	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
18	CTCF	chr3:134514620-134514770	HRPEpiC	eye:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
19	CTCF	chr3:134514600-134514830	GM12872	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
20	POLR2A	chr3:134513784-134516025	H1-neurons	neurons:	n/a	n/a
21	CTCF	chr3:134514660-134514810	GM12868	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
22	POLR2A	chr3:134513847-134515016	GM12878	blood:	n/a	n/a
23	CTCF	chr3:134514614-134514789	ProgFib	skin:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
24	CTCF	chr3:134514760-134514910	HA-sp	spinal cord:	n/a	n/a
25	MAZ	chr3:134514713-134515879	GM12878	blood:	n/a	n/a
26	CTCF	chr3:134514666-134514834	GM12878	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
27	CTCF	chr3:134514680-134514830	RPTEC	kidney:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
28	SIN3A	chr3:134513803-134515698	H1-hESC	embryonic stem cell:	n/a	chr3:134514415-134514428 chr3:134515536-134515544 chr3:134515452-134515465 chr3:134515544-134515555
29	CHD1	chr3:134513715-134515047	GM12878	blood:	n/a	n/a
30	CTCF	chr3:134514680-134514830	HFF	foreskin:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
31	CTCF	chr3:134514640-134514790	GM12873	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
32	CTCF	chr3:134514680-134514830	GM06990	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
33	CTCF	chr3:134514660-134514801	Fibrobl	skin:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
34	CTCF	chr3:134514680-134514830	GM12874	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
35	CTCF	chr3:134514620-134514770	HRE	kidney:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
36	CTCF	chr3:134514620-134514770	AG09319	gingival:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
37	TBP	chr3:134513817-134515119	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:134514640-134514790	GM12871	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
39	RAD21	chr3:134513517-134515198	H1-hESC	embryonic stem cell:	n/a	chr3:134514713-134514727 chr3:134514709-134514728 chr3:134513885-134513904
40	CTCF	chr3:134514533-134514920	GM12878	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
41	GABPA	chr3:134514419-134514847	H1-hESC	embryonic stem cell:	n/a	n/a
42	MXI1	chr3:134513762-134514857	GM12878	blood:	n/a	n/a
43	CTCF	chr3:134514720-134514870	HRE	kidney:	n/a	n/a
44	CTBP2	chr3:134513919-134515868	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:134513731-134515872	GM18526	blood:	n/a	n/a
46	CTCF	chr3:134514620-134514770	HUVEC	blood vessel:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
47	CTCF	chr3:134514606-134514808	GM19238	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
48	CTCF	chr3:134514660-134514810	GM12875	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
49	CTCF	chr3:134514660-134514810	GM12867	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726
50	CTCF	chr3:134514620-134514770	GM12872	blood:	n/a	chr3:134514711-134514729 chr3:134514713-134514726

Variant related genes	Relation type
EPHB1	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12487566	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12488253	1.00[ASW][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12494279	1.00[EUR][1000 genomes]
rs61273084	1.00[EUR][1000 genomes]
rs72982119	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643763	1.00[EUR][1000 genomes]
rs7648884	0.90[GIH][hapmap];1.00[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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134513600-134514800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:134513600-134515000	Active TSS	GM12878-XiMat	blood
3	chr3:134513600-134515200	Active TSS	Brain Anterior Caudate	brain
4	chr3:134513600-134515600	Enhancers	Fetal Heart	heart
5	chr3:134513600-134516000	Bivalent/Poised TSS	HSMM	muscle
6	chr3:134513800-134514800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:134513800-134514800	Bivalent/Poised TSS	A549	lung
8	chr3:134513800-134514800	Active TSS	HSMMtube	muscle
9	chr3:134513800-134515000	Active TSS	Ovary	ovary
10	chr3:134513800-134515600	Active TSS	Fetal Brain Female	brain
11	chr3:134513800-134515800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:134513800-134515800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:134513800-134515800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:134513800-134515800	Active TSS	Brain Cingulate Gyrus	brain
15	chr3:134513800-134516000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:134513800-134516000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
17	chr3:134513800-134516200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:134513800-134516800	Active TSS	Brain Angular Gyrus	brain
19	chr3:134514000-134514800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr3:134514000-134514800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:134514000-134514800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
22	chr3:134514000-134514800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
23	chr3:134514000-134514800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:134514000-134514800	Bivalent/Poised TSS	Fetal Stomach	stomach
25	chr3:134514000-134514800	Active TSS	Rectal Smooth Muscle	rectum
26	chr3:134514000-134515000	Flanking Active TSS	Liver	Liver
27	chr3:134514000-134515000	Flanking Active TSS	Spleen	Spleen
28	chr3:134514000-134515000	Flanking Bivalent TSS/Enh	HMEC	breast
29	chr3:134514000-134515000	Active TSS	NHLF	lung
30	chr3:134514000-134515000	Active TSS	Osteobl	bone
31	chr3:134514000-134515200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr3:134514000-134515200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:134514000-134515200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr3:134514000-134515200	Flanking Active TSS	Gastric	stomach
35	chr3:134514000-134515400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:134514000-134515400	Flanking Active TSS	Pancreas	Pancrea
37	chr3:134514000-134515600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:134514000-134515600	Bivalent/Poised TSS	Thymus	Thymus
39	chr3:134514000-134515600	Active TSS	NH-A	brain
40	chr3:134514000-134515800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:134514000-134515800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:134514000-134515800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr3:134514000-134515800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:134514000-134515800	Active TSS	Aorta	Aorta
45	chr3:134514000-134515800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
46	chr3:134514000-134515800	Active TSS	Fetal Kidney	kidney
47	chr3:134514000-134516000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:134514000-134516000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr3:134514000-134516000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr3:134514000-134516000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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