Variant report

Variant	rs559679402
Chromosome Location	chr4:95679489-95679490
allele	C/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	POLR2A	chr4:95679404-95679710	HUVEC	blood vessel:	n/a	n/a
2	MAX	chr4:95679346-95680179	A549	lung:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
3	MXI1	chr4:95677488-95681982	SK-N-SH	brain:	n/a	chr4:95679721-95679730
4	MAX	chr4:95678600-95680454	A549	lung:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
5	ZBTB7A	chr4:95679462-95679921	ECC-1	luminal epithelium:	n/a	n/a
6	USF1	chr4:95679342-95679797	ECC-1	luminal epithelium:	n/a	chr4:95679535-95679551 chr4:95679537-95679553 chr4:95679540-95679556 chr4:95679534-95679550
7	MYC	chr4:95679460-95679611	MCF-7	breast:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
8	E2F6	chr4:95679308-95679784	A549	lung:	n/a	chr4:95679542-95679552 chr4:95679544-95679553 chr4:95679618-95679630 chr4:95679539-95679549
9	MXI1	chr4:95678575-95680180	IMR90	lung:	n/a	chr4:95679721-95679730
10	POLR2A	chr4:95679179-95679750	H1-neurons	neurons:	n/a	n/a
11	MYC	chr4:95679378-95679710	H1-hESC	embryonic stem cell:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
12	MYC	chr4:95678911-95679831	MCF10A-Er-Src	breast:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
13	POLR2A	chr4:95679042-95679843	A549	lung:	n/a	n/a
14	RAD21	chr4:95679377-95679935	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:95679034-95679845	A549	lung:	n/a	n/a
16	HA-E2F1	chr4:95678701-95680381	MCF-7	breast:	n/a	chr4:95679542-95679552 chr4:95679544-95679553 chr4:95680197-95680204 chr4:95679618-95679630 chr4:95679539-95679549
17	POLR2A	chr4:95678205-95680130	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr4:95679270-95679613	MCF-7	breast:	n/a	n/a
19	MAX	chr4:95679291-95679831	SK-N-SH	brain:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
20	MAX	chr4:95679292-95679677	HepG2	liver:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
21	TEAD4	chr4:95679367-95679772	H1-hESC	embryonic stem cell:	n/a	n/a
22	TEAD4	chr4:95679433-95679849	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr4:95679337-95679773	SK-N-SH	brain:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
24	POLR2A	chr4:95679102-95679864	MCF-7	breast:	n/a	n/a
25	CTBP2	chr4:95678812-95680327	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF143	chr4:95679304-95680279	H1-hESC	embryonic stem cell:	n/a	chr4:95679720-95679738
27	MYC	chr4:95679133-95679814	MCF-7	breast:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
28	POLR2A	chr4:95679009-95679844	A549	lung:	n/a	n/a
29	POLR2A	chr4:95678719-95680358	A549	lung:	n/a	n/a
30	POLR2A	chr4:95679005-95679905	A549	lung:	n/a	n/a
31	POLR2A	chr4:95678919-95679972	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr4:95678828-95679924	HEK293	kidney:	n/a	n/a
33	TCF12	chr4:95679460-95681991	A549	lung:	n/a	chr4:95679721-95679731
34	TAF1	chr4:95678798-95679739	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr4:95679416-95679672	SK-N-SH_RA	brain:	n/a	chr4:95679535-95679551 chr4:95679537-95679553 chr4:95679540-95679556 chr4:95679534-95679550
36	MAX	chr4:95678728-95679877	ECC-1	luminal epithelium:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
37	GABPA	chr4:95679182-95679665	H1-hESC	embryonic stem cell:	n/a	chr4:95679516-95679525
38	CHD1	chr4:95677993-95680028	IMR90	lung:	n/a	chr4:95679126-95679136 chr4:95679131-95679141
39	MAX	chr4:95679452-95679713	H1-hESC	embryonic stem cell:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
40	USF1	chr4:95679376-95679695	H1-hESC	embryonic stem cell:	n/a	chr4:95679535-95679551 chr4:95679537-95679553 chr4:95679540-95679556 chr4:95679534-95679550
41	MYC	chr4:95679165-95680339	A549	lung:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
42	YY1	chr4:95679462-95679713	H1-hESC	embryonic stem cell:	n/a	chr4:95679533-95679544 chr4:95679545-95679556 chr4:95679539-95679550 chr4:95679544-95679553 chr4:95679539-95679553 chr4:95679541-95679555 chr4:95679541-95679550 chr4:95679535-95679549
43	RAD21	chr4:95679440-95679739	H1-hESC	embryonic stem cell:	n/a	n/a
44	USF1	chr4:95679484-95679697	SK-N-SH	brain:	n/a	chr4:95679535-95679551 chr4:95679537-95679553 chr4:95679540-95679556 chr4:95679534-95679550
45	MAX	chr4:95679260-95679861	ECC-1	luminal epithelium:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
46	FOXP2	chr4:95679032-95679849	PFSK-1	brain:	n/a	n/a
47	USF1	chr4:95679415-95679644	H1-hESC	embryonic stem cell:	n/a	chr4:95679535-95679551 chr4:95679537-95679553 chr4:95679540-95679556 chr4:95679534-95679550
48	POLR2A	chr4:95678486-95680216	MCF10A-Er-Src	breast:	n/a	n/a
49	MYC	chr4:95679460-95679786	MCF10A-Er-Src	breast:	n/a	chr4:95679555-95679566 chr4:95679555-95679566 chr4:95679555-95679565 chr4:95679554-95679567
50	TAF1	chr4:95679397-95680588	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95679187..95680719-chr4:95971290..95974263,2	MCF-7	breast:
2	chr4:95678678..95680883-chr4:96023985..96026151,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249599	TF binding region
ENSG00000138696	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv1833916	chr4:95673181-95679741	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3407255	chr4:95677954-95680802	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv12742	chr4:95678933-95679943	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv594902	chr4:95679013-95679796	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv594903	chr4:95679154-95679741	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv594904	chr4:95679154-95679796	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv594905	chr4:95679344-95679852	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95677800-95681800	Active TSS	A549	lung
2	chr4:95678000-95680000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:95678000-95680200	Active TSS	NH-A	brain
4	chr4:95678000-95682000	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:95678200-95679600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
6	chr4:95678200-95680000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:95678200-95680400	Active TSS	Aorta	Aorta
8	chr4:95678200-95680400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr4:95678200-95680400	Active TSS	HMEC	breast
10	chr4:95678400-95679600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:95678400-95679600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:95678400-95679600	Active TSS	Fetal Brain Female	brain
13	chr4:95678400-95679800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:95678400-95679800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:95678400-95680000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:95678400-95680000	Bivalent/Poised TSS	Thymus	Thymus
17	chr4:95678400-95680200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:95678400-95680200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:95678400-95680400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr4:95678400-95680600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr4:95678400-95680600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:95678400-95680600	Active TSS	Ovary	ovary
23	chr4:95678400-95680800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:95678400-95680800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr4:95678600-95679600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:95678600-95679600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:95678600-95679600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:95678600-95679600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
29	chr4:95678600-95679600	Active TSS	Fetal Kidney	kidney
30	chr4:95678600-95679600	Active TSS	Right Atrium	heart
31	chr4:95678600-95679800	Active TSS	Brain Angular Gyrus	brain
32	chr4:95678600-95679800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
33	chr4:95678600-95680000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:95678600-95680000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr4:95678600-95680000	Bivalent/Poised TSS	Left Ventricle	heart
36	chr4:95678600-95680200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr4:95678600-95680200	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr4:95678600-95680200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
39	chr4:95678600-95680400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:95678600-95680400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:95678600-95680400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:95678600-95680400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
43	chr4:95678600-95680400	Active TSS	Brain Substantia Nigra	brain
44	chr4:95678600-95680400	Bivalent/Poised TSS	Fetal Stomach	stomach
45	chr4:95678600-95680400	Active TSS	Pancreas	Pancrea
46	chr4:95678600-95680600	Active TSS	Brain Anterior Caudate	brain
47	chr4:95678600-95680600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr4:95678600-95680600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
49	chr4:95678800-95679600	Bivalent/Poised TSS	Esophagus	oesophagus
50	chr4:95678800-95679600	Active TSS	Lung	lung

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