Variant report

Variant	rs542379239
Chromosome Location	chr4:57773785-57773786
allele	A/T
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	E2F6	chr4:57773623-57775591	K562	blood:	n/a	chr4:57774165-57774175 chr4:57774582-57774592 chr4:57774574-57774584
2	SP4	chr4:57773590-57774022	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773953 chr4:57773938-57773954 chr4:57773940-57773956
3	ZNF384	chr4:57773528-57773810	GM12878	blood:	n/a	n/a
4	SP1	chr4:57773313-57773965	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773954 chr4:57773939-57773953 chr4:57773943-57773953 chr4:57773944-57773953 chr4:57773942-57773953 chr4:57773943-57773953 chr4:57773942-57773954 chr4:57773944-57773953 chr4:57773943-57773952
5	MAX	chr4:57773747-57775766	HepG2	liver:	n/a	n/a
6	CTBP2	chr4:57773280-57774131	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:57773738-57775553	NB4	blood:	n/a	n/a
8	POLR2A	chr4:57773716-57774376	ECC-1	luminal epithelium:	n/a	n/a
9	PAX5	chr4:57773781-57774262	GM12892	blood:	n/a	n/a
10	SIN3AK20	chr4:57773562-57773835	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr4:57773691-57774315	MCF10A-Er-Src	breast:	n/a	n/a
12	EP300	chr4:57773486-57773995	K562	blood:	n/a	n/a
13	HA-E2F1	chr4:57773647-57775798	MCF-7	breast:	n/a	chr4:57774165-57774175 chr4:57774582-57774592 chr4:57774574-57774584
14	CHD2	chr4:57773765-57773965	GM12878	blood:	n/a	chr4:57773944-57773954
15	SIN3AK20	chr4:57773768-57774314	K562	blood:	n/a	n/a
16	MAX	chr4:57773756-57775706	NB4	blood:	n/a	n/a
17	MXI1	chr4:57773345-57776166	IMR90	lung:	n/a	n/a
18	TBP	chr4:57773376-57774951	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr4:57773482-57774002	SK-N-MC	brain:	n/a	n/a
20	EP300	chr4:57773581-57773945	H1-hESC	embryonic stem cell:	n/a	n/a
21	HDAC2	chr4:57773694-57773998	H1-hESC	embryonic stem cell:	n/a	n/a
22	EP300	chr4:57773767-57773933	HepG2	liver:	n/a	n/a
23	POLR2A	chr4:57773726-57774251	U87	brain:	n/a	n/a
24	MXI1	chr4:57773723-57775676	HepG2	liver:	n/a	n/a
25	POLR2A	chr4:57773675-57773988	SK-N-MC	brain:	n/a	n/a
26	BCL11A	chr4:57773599-57773878	H1-hESC	embryonic stem cell:	n/a	n/a
27	TEAD4	chr4:57773105-57774259	H1-hESC	embryonic stem cell:	n/a	chr4:57774088-57774097
28	MAX	chr4:57773763-57775621	K562	blood:	n/a	n/a
29	TBL1XR1	chr4:57773767-57773941	K562	blood:	n/a	n/a
30	GTF2F1	chr4:57773548-57773806	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOXP2	chr4:57773773-57774032	SK-N-MC	brain:	n/a	n/a
32	NANOG	chr4:57773256-57774100	H1-hESC	embryonic stem cell:	n/a	n/a
33	MXI1	chr4:57773663-57773858	K562	blood:	n/a	n/a
34	ELF1	chr4:57773783-57775651	GM12878	blood:	n/a	chr4:57775032-57775041 chr4:57774652-57774661 chr4:57775031-57775042 chr4:57774439-57774451
35	ZNF143	chr4:57773032-57773971	H1-hESC	embryonic stem cell:	n/a	n/a
36	MYC	chr4:57773776-57776081	NB4	blood:	n/a	n/a
37	YY1	chr4:57773524-57773876	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr4:57773760-57773910	SK-N-SH_RA	brain:	n/a	n/a
39	SP4	chr4:57773550-57774029	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773953 chr4:57773938-57773954 chr4:57773940-57773956
40	ZBTB7A	chr4:57773702-57775485	ECC-1	luminal epithelium:	n/a	chr4:57773897-57773906 chr4:57775068-57775076 chr4:57775067-57775075 chr4:57775231-57775239
41	POLR2A	chr4:57773732-57774353	HCT-116	colon:	n/a	n/a
42	MAX	chr4:57773547-57774129	SK-N-SH	brain:	n/a	n/a
43	JUND	chr4:57773728-57775607	K562	blood:	n/a	chr4:57774863-57774873 chr4:57774862-57774874
44	SIN3A	chr4:57773767-57775671	GM12878	blood:	n/a	chr4:57774969-57774978 chr4:57774574-57774587 chr4:57774972-57774985 chr4:57774938-57774951 chr4:57774480-57774493 chr4:57774388-57774401 chr4:57774851-57774862
45	CTCF	chr4:57773760-57773910	HEEpiC	esophagus:	n/a	n/a
46	E2F4	chr4:57773739-57773939	MCF10A-Er-Src	breast:	n/a	n/a
47	EP300	chr4:57773508-57774125	H1-hESC	embryonic stem cell:	n/a	chr4:57774097-57774113
48	SP1	chr4:57773236-57774607	H1-hESC	embryonic stem cell:	n/a	chr4:57773942-57773954 chr4:57773939-57773953 chr4:57773943-57773953 chr4:57773944-57773953 chr4:57773942-57773953 chr4:57773943-57773953 chr4:57773942-57773954 chr4:57773944-57773953 chr4:57773943-57773952 chr4:57774283-57774297
49	ELF1	chr4:57773710-57774252	GM12878	blood:	n/a	n/a
50	NANOG	chr4:57773469-57773947	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:57773768-57773818	GM06990	blood:	n/a
2	chr4:57773768-57773818	BE2_C	brain:	n/a
3	chr4:57773768-57773818	LNCaP	prostate:	n/a
4	chr4:57773768-57773818	Hepatocyte	liver:	n/a
5	chr4:57773768-57773818	HRE	kidney:	n/a
6	chr4:57773768-57773818	HEK293	kidney:	embryo
7	chr4:57773768-57773818	NHDF-neo	bronchial:	n/a
8	chr4:57773768-57773818	GM12878	blood:	n/a
9	chr4:57773768-57773818	A549	lung:	n/a
10	chr4:57773768-57773818	AG09309	skin:	n/a
11	chr4:57773768-57773818	HCF	heart:	n/a
12	chr4:57773768-57773818	AG04449	skin:	fetal
13	chr4:57773768-57773818	GM19239	blood:	n/a
14	chr4:57773768-57773818	HAEpiC	amniotic membrane:	n/a
15	chr4:57773768-57773818	SK-N-SH	brain:	n/a
16	chr4:57773768-57773818	GM12892	blood:	n/a
17	chr4:57773768-57773818	PFSK-1	brain:	n/a
18	chr4:57773768-57773818	Hela-S3	cervix:	n/a
19	chr4:57773768-57773818	HPAEpiC	pulmonary alveolar:	n/a
20	chr4:57773768-57773818	HCPEpiC	choroid plexus:	n/a
21	chr4:57773768-57773818	HUVEC	blood vessel:	n/a
22	chr4:57773768-57773818	ECC-1	luminal epithelium:	n/a
23	chr4:57773768-57773818	HIPEpiC	eye:	n/a
24	chr4:57773768-57773818	AoSMC	blood vessel:	n/a
25	chr4:57773768-57773818	ProgFib	skin:	n/a
26	chr4:57773768-57773818	T-47D	breast:	n/a
27	chr4:57773768-57773818	NHBE	bronchial:	n/a
28	chr4:57773768-57773818	RPTEC	kidney:	n/a
29	chr4:57773768-57773818	SAEC	small airway:	n/a
30	chr4:57773768-57773818	U87	brain:	n/a
31	chr4:57773768-57773818	HCT-116	colon:	n/a
32	chr4:57773768-57773818	HCM	heart:	n/a
33	chr4:57773768-57773818	HRCEpiC	kidney:	n/a
34	chr4:57773768-57773818	BJ	skin:	n/a
35	chr4:57773768-57773818	AG04450	lung:	fetal
36	chr4:57773768-57773818	GM12891	blood:	n/a
37	chr4:57773768-57773818	SKMC	muscle:	n/a
38	chr4:57773768-57773818	NT2-D1	testis:	n/a
39	chr4:57773768-57773818	NB4	blood:	n/a
40	chr4:57773768-57773818	HEEpiC	esophagus:	n/a
41	chr4:57773768-57773818	HNPCEpiC	eye:	n/a
42	chr4:57773768-57773818	HMEC	breast:	n/a
43	chr4:57773768-57773818	HepG2	liver:	n/a
44	chr4:57773768-57773818	NH-A	brain:	n/a
45	chr4:57773768-57773818	IMR90	lung:	fetal
46	chr4:57773768-57773818	MCF10A-Er-Src	breast:	n/a
47	chr4:57773768-57773818	AG09319	gingival:	n/a
48	chr4:57773768-57773818	K562	blood:	n/a
49	chr4:57773768-57773818	PANC-1	pancreas:	n/a
50	chr4:57773768-57773818	HRPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57772988..57775343-chr4:57776220..57778579,3	MCF-7	breast:
2	chr19:1248083..1248884-chr4:57773766..57774545,2	Hela-S3	cervix:
3	chr4:57772839..57777394-chr4:57841397..57848240,17	K562	blood:
4	chr4:57301355..57303854-chr4:57773620..57776020,4	MCF-7	breast:
5	chr4:57302175..57303989-chr4:57773484..57775623,2	MCF-7	breast:
6	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:
7	chr4:57299951..57301849-chr4:57773604..57776000,3	K562	blood:
8	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:

Variant related genes	Relation type
REST	TF binding region
REST	CpG island
ENSG00000128059	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv12676	chr4:57772270-57775584	Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv3374947	chr4:57773220-57776168	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3389347	chr4:57773345-57775893	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv594205	chr4:57773442-57775064	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv594206	chr4:57773595-57775543	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57772800-57773800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:57772800-57773800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr4:57772800-57776200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:57773000-57773800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr4:57773000-57773800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr4:57773000-57773800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr4:57773000-57773800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr4:57773000-57773800	Enhancers	Lung	lung
9	chr4:57773000-57773800	Enhancers	Spleen	Spleen
10	chr4:57773000-57774000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr4:57773000-57774800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr4:57773000-57776000	Active TSS	Rectal Smooth Muscle	rectum
13	chr4:57773200-57773800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:57773200-57773800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr4:57773200-57773800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr4:57773200-57773800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:57773200-57773800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr4:57773200-57773800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:57773200-57773800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:57773200-57773800	Flanking Active TSS	Liver	Liver
21	chr4:57773200-57773800	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr4:57773200-57773800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr4:57773200-57773800	Enhancers	Fetal Heart	heart
24	chr4:57773200-57773800	Flanking Active TSS	Fetal Thymus	thymus
25	chr4:57773200-57773800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr4:57773200-57773800	Weak transcription	Small Intestine	intestine
27	chr4:57773200-57773800	Flanking Active TSS	Dnd41	blood
28	chr4:57773200-57773800	Flanking Active TSS	GM12878-XiMat	blood
29	chr4:57773200-57773800	Flanking Bivalent TSS/Enh	NHEK	skin
30	chr4:57773200-57774000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr4:57773200-57774600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:57773200-57775600	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr4:57773200-57775800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:57773200-57776000	Active TSS	A549	lung
35	chr4:57773200-57776000	Active TSS	HMEC	breast
36	chr4:57773200-57776200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:57773200-57776200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:57773200-57776400	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr4:57773200-57776600	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr4:57773200-57776600	Active TSS	Aorta	Aorta
41	chr4:57773200-57776800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:57773400-57773800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:57773400-57773800	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr4:57773400-57773800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr4:57773400-57773800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:57773400-57773800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:57773400-57773800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
48	chr4:57773400-57773800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr4:57773400-57773800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:57773400-57773800	Active TSS	Brain Germinal Matrix	brain

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