Variant report

Variant	rs28623383
Chromosome Location	chr4:174341381-174341382
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	chr4:174341300-174341450	HRE	kidney:	n/a	n/a
2	SMC3	chr4:174341283-174342438	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr4:174341321-174342011	A549	lung:	n/a	chr4:174341634-174341650 chr4:174341633-174341651 chr4:174341635-174341656
4	RAD21	chr4:174341241-174342481	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr4:174341216-174342579	SK-N-SH	brain:	n/a	chr4:174341634-174341650 chr4:174341633-174341651 chr4:174341635-174341656
6	CTCF	chr4:174341260-174341410	GM12874	blood:	n/a	n/a
7	CTCF	chr4:174341300-174341450	GM12878	blood:	n/a	n/a
8	CTCF	chr4:174341300-174341450	HPF	lung:	n/a	n/a
9	CTCF	chr4:174341374-174341897	MCF-7	breast:	n/a	chr4:174341634-174341650 chr4:174341633-174341651 chr4:174341635-174341656
10	CTCF	chr4:174341375-174341962	IMR90	lung:	n/a	chr4:174341634-174341650 chr4:174341633-174341651 chr4:174341635-174341656
11	CTCF	chr4:174341340-174341490	BJ	skin:	n/a	n/a
12	CTCF	chr4:174341240-174341510	WI-38	lung:	n/a	n/a
13	CTCF	chr4:174341320-174341470	GM12864	blood:	n/a	n/a
14	CTCF	chr4:174341333-174341418	GM10266	blood:	n/a	n/a
15	RAD21	chr4:174341332-174341929	HCT-116	colon:	n/a	n/a
16	CTCF	chr4:174341320-174341470	HRPEpiC	eye:	n/a	n/a
17	CTCF	chr4:174341319-174341946	HCT-116	colon:	n/a	chr4:174341634-174341650 chr4:174341633-174341651 chr4:174341635-174341656
18	CTCF	chr4:174341320-174341470	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr4:174341340-174341490	HFF-Myc	foreskin:	n/a	n/a
20	CTCF	chr4:174341280-174341430	HCPEpiC	choroid plexus:	n/a	n/a
21	CTCF	chr4:174341260-174341410	AG04449	skin:	n/a	n/a
22	CTCF	chr4:174341260-174341410	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr4:174341140-174341390	AG09309	skin:	n/a	n/a
24	ZKSCAN1	chr4:174341363-174341824	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr4:174341320-174341470	GM12868	blood:	n/a	n/a
26	RAD21	chr4:174341381-174341950	HCT-116	colon:	n/a	n/a
27	RAD21	chr4:174341368-174341969	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:174253487..174255950-chr4:174341236..174343023,2	MCF-7	breast:
2	chr4:174249343..174251576-chr4:174340147..174342867,2	MCF-7	breast:

Variant related genes	Relation type
RPL5P11	TF binding region
ENSG00000164104	Chromatin interaction
ENSG00000248774	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10004826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010027	1.00[EUR][1000 genomes]
rs10026947	1.00[EUR][1000 genomes]
rs13137653	1.00[EUR][1000 genomes]
rs1481119	1.00[EUR][1000 genomes]
rs28444875	1.00[EUR][1000 genomes]
rs28664683	1.00[EUR][1000 genomes]
rs28820378	1.00[EUR][1000 genomes]
rs4695834	1.00[EUR][1000 genomes]
rs4696070	1.00[EUR][1000 genomes]
rs4696074	1.00[EUR][1000 genomes]
rs56989541	1.00[EUR][1000 genomes]
rs57940169	1.00[EUR][1000 genomes]
rs6823255	1.00[EUR][1000 genomes]
rs6848013	1.00[EUR][1000 genomes]
rs6848866	1.00[EUR][1000 genomes]
rs6852086	1.00[EUR][1000 genomes]
rs7675319	1.00[EUR][1000 genomes]
rs7687292	1.00[EUR][1000 genomes]
rs7690040	1.00[EUR][1000 genomes]
rs7695846	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461841	chr4:174330663-174423013	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv596233	chr4:174330663-174423013	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv967814	chr4:174339447-174341974	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174294200-174341600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:174294800-174341800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr4:174319600-174341800	Weak transcription	NHDF-Ad	bronchial
4	chr4:174320800-174347000	Weak transcription	Aorta	Aorta
5	chr4:174321000-174341800	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:174321000-174341800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:174324600-174346200	Weak transcription	HSMMtube	muscle
8	chr4:174324800-174345600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:174325800-174341800	Weak transcription	Brain Germinal Matrix	brain
10	chr4:174327400-174341600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:174331600-174346600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:174331600-174357400	Weak transcription	Left Ventricle	heart
13	chr4:174333800-174354600	Weak transcription	Lung	lung
14	chr4:174333800-174357800	Weak transcription	Pancreas	Pancrea
15	chr4:174334000-174368800	Weak transcription	Fetal Stomach	stomach
16	chr4:174334600-174341600	Weak transcription	Dnd41	blood
17	chr4:174335800-174341600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:174336000-174341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:174336200-174346600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:174336400-174341600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:174337000-174345600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:174337600-174341600	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:174337600-174366600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:174338000-174341400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:174338200-174341600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:174338200-174341800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:174338200-174348600	Weak transcription	Brain Substantia Nigra	brain
28	chr4:174338400-174341600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:174338400-174341600	Weak transcription	Fetal Lung	lung
30	chr4:174338400-174341800	Weak transcription	Fetal Brain Male	brain
31	chr4:174338600-174341400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr4:174338600-174341600	Weak transcription	Brain Angular Gyrus	brain
33	chr4:174338600-174341600	Weak transcription	Brain Anterior Caudate	brain
34	chr4:174338600-174341600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:174338600-174341600	Weak transcription	Osteobl	bone
36	chr4:174339800-174341600	Weak transcription	Stomach Mucosa	stomach
37	chr4:174339800-174352400	Weak transcription	Ovary	ovary
38	chr4:174340200-174342200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:174340600-174341600	Weak transcription	HUVEC	blood vessel
40	chr4:174340600-174341800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:174341200-174341600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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