Variant report

Variant	rs539170738
Chromosome Location	chr4:129730695-129730696
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:488)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:488 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:129730542-129731475	HL-60	blood:	n/a	n/a
2	RAD21	chr4:129730402-129731208	H1-hESC	embryonic stem cell:	n/a	chr4:129730800-129730814 chr4:129730771-129730780
3	CHD1	chr4:129730550-129733472	H1-hESC	embryonic stem cell:	n/a	chr4:129732389-129732399 chr4:129733422-129733432 chr4:129733260-129733270 chr4:129733062-129733072
4	MXI1	chr4:129730257-129734736	IMR90	lung:	n/a	n/a
5	POLR2A	chr4:129730532-129734022	HCT-116	colon:	n/a	n/a
6	HEY1	chr4:129730588-129731480	K562	blood:	n/a	chr4:129730719-129730734
7	POLR2A	chr4:129730570-129731542	SK-N-SH	brain:	n/a	n/a
8	EP300	chr4:129730561-129731081	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr4:129730679-129730972	MCF-7	breast:	n/a	chr4:129730800-129730813
10	POLR2A	chr4:129730561-129734095	K562	blood:	n/a	n/a
11	FOXA2	chr4:129730655-129731033	A549	lung:	n/a	n/a
12	ZNF143	chr4:129730648-129730983	Hela-S3	cervix:	n/a	n/a
13	TAF1	chr4:129730594-129731431	K562	blood:	n/a	n/a
14	CTCF	chr4:129730660-129730810	AG04450	lung:	n/a	n/a
15	MAX	chr4:129730552-129731070	SK-N-SH	brain:	n/a	n/a
16	GTF2F1	chr4:129730632-129730973	K562	blood:	n/a	n/a
17	EP300	chr4:129730611-129730988	SK-N-SH_RA	brain:	n/a	n/a
18	POLR2A	chr4:129730506-129734115	K562	blood:	n/a	n/a
19	PBX3	chr4:129730581-129731515	SK-N-SH	brain:	n/a	n/a
20	REST	chr4:129730404-129731586	H1-neurons	neurons:	n/a	chr4:129730675-129730688
21	FOS	chr4:129730687-129730969	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:129730508-129731416	U87	brain:	n/a	n/a
23	TAF1	chr4:129730568-129731511	SK-N-SH	brain:	n/a	n/a
24	RAD21	chr4:129730576-129731051	GM12878	blood:	n/a	chr4:129730800-129730814 chr4:129730771-129730780
25	ZBTB7A	chr4:129730462-129731678	ECC-1	luminal epithelium:	n/a	chr4:129731474-129731488
26	SP4	chr4:129730618-129731014	H1-hESC	embryonic stem cell:	n/a	chr4:129730765-129730776 chr4:129730751-129730762
27	POLR2A	chr4:129730599-129734478	GM18505	blood:	n/a	n/a
28	ELF1	chr4:129730664-129731112	K562	blood:	n/a	chr4:129730675-129730687
29	NFIC	chr4:129730449-129731042	ECC-1	luminal epithelium:	n/a	n/a
30	CREB1	chr4:129730516-129731599	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr4:129730619-129731085	ECC-1	luminal epithelium:	n/a	n/a
32	RELA	chr4:129730601-129734033	GM12891	blood:	n/a	n/a
33	POLR2A	chr4:129730637-129734008	GM12878	blood:	n/a	n/a
34	ELF1	chr4:129730534-129731252	GM12878	blood:	n/a	chr4:129730675-129730687
35	MAX	chr4:129730513-129731090	SK-N-SH	brain:	n/a	n/a
36	UBTF	chr4:129730658-129731441	K562	blood:	n/a	n/a
37	POLR2A	chr4:129730510-129734063	Raji	blood:	n/a	n/a
38	MYC	chr4:129730657-129731023	HUVEC	blood vessel:	n/a	n/a
39	MAX	chr4:129730540-129731387	K562	blood:	n/a	n/a
40	NFATC1	chr4:129730504-129731060	GM12878	blood:	n/a	n/a
41	MYC	chr4:129730573-129733589	Hela-S3	cervix:	n/a	chr4:129732622-129732632 chr4:129732621-129732632 chr4:129732618-129732633 chr4:129732623-129732630 chr4:129732622-129732631 chr4:129732396-129732406 chr4:129733335-129733345 chr4:129733276-129733286
42	PAX5	chr4:129730595-129731119	GM12878	blood:	n/a	chr4:129730620-129730647
43	EP300	chr4:129730595-129731018	SK-N-SH_RA	brain:	n/a	n/a
44	POLR2A	chr4:129730519-129731751	PBDE	blood:	n/a	n/a
45	RCOR1	chr4:129730574-129731509	K562	blood:	n/a	n/a
46	FOXM1	chr4:129730376-129731041	GM12878	blood:	n/a	n/a
47	TAF7	chr4:129730630-129731079	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr4:129730680-129730830	GM12870	blood:	n/a	chr4:129730800-129730813
49	TCF7L2	chr4:129730648-129730997	Hela-S3	cervix:	n/a	n/a
50	HDAC2	chr4:129730487-129731209	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:129730670-129730720	CMK	blood:	n/a
2	chr4:129730670-129730720	GM19239	blood:	n/a
3	chr4:129730670-129730720	T-47D	breast:	n/a
4	chr4:129730670-129730720	Hela-S3	cervix:	n/a
5	chr4:129730670-129730720	AG09319	gingival:	n/a
6	chr4:129730670-129730720	HIPEpiC	eye:	n/a
7	chr4:129730670-129730720	U87	brain:	n/a
8	chr4:129730670-129730720	AG10803	skin:	n/a
9	chr4:129730670-129730720	SKMC	muscle:	n/a
10	chr4:129730670-129730720	GM06990	blood:	n/a
11	chr4:129730670-129730720	PFSK-1	brain:	n/a
12	chr4:129730670-129730720	GM12878	blood:	n/a
13	chr4:129730670-129730720	LNCaP	prostate:	n/a
14	chr4:129730670-129730720	BJ	skin:	n/a
15	chr4:129730670-129730720	ECC-1	luminal epithelium:	n/a
16	chr4:129730670-129730720	NHBE	bronchial:	n/a
17	chr4:129730670-129730720	Jurkat	blood:	n/a
18	chr4:129730670-129730720	PrEC	prostate:	n/a
19	chr4:129730670-129730720	AG04449	skin:	fetal
20	chr4:129730670-129730720	HRPEpiC	eye:	n/a
21	chr4:129730670-129730720	HNPCEpiC	eye:	n/a
22	chr4:129730670-129730720	HAEpiC	amniotic membrane:	n/a
23	chr4:129730670-129730720	AG04450	lung:	fetal
24	chr4:129730670-129730720	HRCEpiC	kidney:	n/a
25	chr4:129730670-129730720	MCF10A-Er-Src	breast:	n/a
26	chr4:129730670-129730720	ProgFib	skin:	n/a
27	chr4:129730670-129730720	K562	blood:	n/a
28	chr4:129730670-129730720	HPAEpiC	pulmonary alveolar:	n/a
29	chr4:129730670-129730720	IMR90	lung:	fetal
30	chr4:129730670-129730720	SAEC	small airway:	n/a
31	chr4:129730670-129730720	Hepatocyte	liver:	n/a
32	chr4:129730670-129730720	GM12891	blood:	n/a
33	chr4:129730670-129730720	NH-A	brain:	n/a
34	chr4:129730670-129730720	HCT-116	colon:	n/a
35	chr4:129730670-129730720	NB4	blood:	n/a
36	chr4:129730670-129730720	MCF-7	breast:	n/a
37	chr4:129730670-129730720	AG09309	skin:	n/a
38	chr4:129730670-129730720	SK-N-MC	brain:	n/a
39	chr4:129730670-129730720	HEEpiC	esophagus:	n/a
40	chr4:129730670-129730720	HUVEC	blood vessel:	n/a
41	chr4:129730670-129730720	RPTEC	kidney:	n/a
42	chr4:129730670-129730720	H1-hESC	embryonic stem cell:	embryo
43	chr4:129730670-129730720	BE2_C	brain:	n/a
44	chr4:129730670-129730720	HMEC	breast:	n/a
45	chr4:129730670-129730720	SK-N-SH_RA	brain:	n/a
46	chr4:129730670-129730720	NHDF-neo	bronchial:	n/a
47	chr4:129730670-129730720	GM12892	blood:	n/a
48	chr4:129730670-129730720	AoSMC	blood vessel:	n/a
49	chr4:129730670-129730720	HepG2	liver:	n/a
50	chr4:129730670-129730720	HCPEpiC	choroid plexus:	n/a

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:129375160..129378617-chr4:129730147..129733611,3	MCF-7	breast:
2	chr4:128980795..128984031-chr4:129730059..129735028,7	K562	blood:
3	chr4:129374782..129377512-chr4:129729521..129732215,3	K562	blood:
4	chr4:129472709..129474756-chr4:129728389..129731319,2	MCF-7	breast:
5	chr4:128980795..128982891-chr4:129730267..129732892,3	K562	blood:
6	chr4:129730688..129731418-chr6:24720530..24721134,2	Hela-S3	cervix:
7	chr4:129491375..129494260-chr4:129730648..129733095,2	MCF-7	breast:
8	chr4:129518963..129527383-chr4:129727996..129735335,14	K562	blood:
9	chr4:129206178..129209105-chr4:129728853..129732712,4	K562	blood:
10	chr4:129473168..129475213-chr4:129730479..129732295,2	K562	blood:
11	chr4:129209335..129213237-chr4:129730288..129733311,3	K562	blood:
12	chr4:129730547..129732304-chr4:129732580..129735331,2	MCF-7	breast:
13	chr4:129730646..129731365-chr6:31939370..31940250,2	Hela-S3	cervix:
14	chr4:129376012..129378140-chr4:129729596..129731686,2	K562	blood:
15	chr4:129207558..129209105-chr4:129728853..129730896,2	K562	blood:
16	chr4:129472659..129478043-chr4:129729703..129733779,4	K562	blood:
17	chr4:129730340..129733748-chr4:130013373..130016609,5	K562	blood:
18	chr4:129348880..129349601-chr4:129730054..129731203,4	MCF-7	breast:

No data

Variant related genes	Relation type
JADE1	TF binding region
JADE1	CpG island
ENSG00000273077	Chromatin interaction
ENSG00000151466	Chromatin interaction
ENSG00000251432	Chromatin interaction
ENSG00000164040	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000204344	Chromatin interaction
ENSG00000248187	Chromatin interaction
ENSG00000151470	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000204348	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000248802	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv822717	chr4:129724785-129739862	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a
5	esv3340336	chr4:129730252-129734500	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129726200-129730800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:129726200-129731200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:129730000-129734000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr4:129730200-129730800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr4:129730200-129730800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr4:129730200-129734200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:129730200-129734200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr4:129730200-129734200	Active TSS	K562	blood
9	chr4:129730200-129734400	Active TSS	NHDF-Ad	bronchial
10	chr4:129730400-129730800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:129730400-129730800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr4:129730400-129730800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr4:129730400-129730800	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr4:129730400-129730800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr4:129730400-129730800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:129730400-129730800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr4:129730400-129730800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:129730400-129730800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:129730400-129730800	Flanking Active TSS	Liver	Liver
20	chr4:129730400-129730800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr4:129730400-129730800	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr4:129730400-129730800	Flanking Active TSS	Fetal Lung	lung
23	chr4:129730400-129730800	Flanking Active TSS	Dnd41	blood
24	chr4:129730400-129730800	Flanking Active TSS	HUVEC	blood vessel
25	chr4:129730400-129731000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:129730400-129731400	Active TSS	Primary hematopoietic stem cells	blood
27	chr4:129730400-129731400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:129730400-129732000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:129730400-129732000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:129730400-129732000	Active TSS	Placenta	Placenta
31	chr4:129730400-129732000	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:129730400-129732000	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr4:129730400-129732200	Active TSS	Right Atrium	heart
34	chr4:129730400-129733600	Active TSS	Primary T cells fromperipheralblood	blood
35	chr4:129730400-129733600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:129730400-129733600	Active TSS	Thymus	Thymus
37	chr4:129730400-129733800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:129730400-129733800	Active TSS	Primary T cells from cord blood	blood
39	chr4:129730400-129733800	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr4:129730400-129733800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:129730400-129733800	Active TSS	Brain Cingulate Gyrus	brain
42	chr4:129730400-129733800	Active TSS	Brain Hippocampus Middle	brain
43	chr4:129730400-129733800	Active TSS	Fetal Brain Female	brain
44	chr4:129730400-129733800	Active TSS	Fetal Kidney	kidney
45	chr4:129730400-129733800	Active TSS	Fetal Muscle Leg	muscle
46	chr4:129730400-129733800	Active TSS	Fetal Thymus	thymus
47	chr4:129730400-129733800	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr4:129730400-129733800	Active TSS	Stomach Smooth Muscle	stomach
49	chr4:129730400-129733800	Active TSS	Osteobl	bone
50	chr4:129730400-129734000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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