Variant report

Variant	nsv590294
Chromosome Location	chr3:52089941-52090744
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:455)
CpG islands
(count:245)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:455 , 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	BACH1	chr3:52089565-52090065	H1-hESC	embryonic stem cell:	n/a	n/a
2	BACH1	chr3:52090669-52092031	H1-hESC	embryonic stem cell:	n/a	n/a
3	BHLHE40	chr3:52090014-52090259	GM12878	blood:	n/a	n/a
4	BHLHE40	chr3:52090492-52090850	GM12878	blood:	n/a	chr3:52090590-52090606
5	BHLHE40	chr3:52089955-52090163	K562	blood:	n/a	n/a
6	BHLHE40	chr3:52090568-52091738	K562	blood:	n/a	chr3:52091498-52091514 chr3:52090590-52090606
7	BRCA1	chr3:52090153-52090187	Hela-S3	cervix:	n/a	n/a
8	CCNT2	chr3:52089689-52090249	K562	blood:	n/a	n/a
9	CCNT2	chr3:52090536-52091099	K562	blood:	n/a	chr3:52090909-52090918
10	CEBPB	chr3:52090025-52090132	Hela-S3	cervix:	n/a	n/a
11	CEBPD	chr3:52090478-52090797	HepG2	liver:	n/a	n/a
12	CHD2	chr3:52090664-52090890	K562	blood:	n/a	n/a
13	CHD2	chr3:52089502-52090307	Hela-S3	cervix:	n/a	n/a
14	CHD2	chr3:52090621-52091791	GM12878	blood:	n/a	chr3:52090988-52090998 chr3:52090658-52090665
15	CHD2	chr3:52090025-52090207	GM12878	blood:	n/a	n/a
16	CHD2	chr3:52090566-52091794	Hela-S3	cervix:	n/a	chr3:52090988-52090998 chr3:52090658-52090665
17	CREB1	chr3:52089895-52090385	A549	lung:	n/a	n/a
18	CREB1	chr3:52090713-52091930	H1-hESC	embryonic stem cell:	n/a	n/a
19	CREB1	chr3:52090526-52090768	A549	lung:	n/a	n/a
20	CTCF	chr3:52090080-52090230	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr3:52089944-52090293	GM19238	blood:	n/a	n/a
22	CTCF	chr3:52090120-52090270	GM12873	blood:	n/a	n/a
23	CTCF	chr3:52090100-52090250	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr3:52090060-52090210	AG04450	lung:	n/a	n/a
25	CTCF	chr3:52090100-52090250	HA-sp	spinal cord:	n/a	n/a
26	CTCF	chr3:52090100-52090250	GM12864	blood:	n/a	n/a
27	CTCF	chr3:52090070-52090072	GM12891	blood:	n/a	n/a
28	CTCF	chr3:52090080-52090230	GM06990	blood:	n/a	n/a
29	CTCF	chr3:52090131-52090241	A549	lung:	n/a	n/a
30	CTCF	chr3:52090165-52090237	HUVEC	blood vessel:	n/a	n/a
31	CTCF	chr3:52090060-52090210	GM12873	blood:	n/a	n/a
32	CTCF	chr3:52090040-52090190	GM12873	blood:	n/a	n/a
33	CTCF	chr3:52090040-52090190	RPTEC	kidney:	n/a	n/a
34	CTCF	chr3:52090100-52090250	GM12872	blood:	n/a	n/a
35	CTCF	chr3:52090073-52090279	GM12891	blood:	n/a	n/a
36	CTCF	chr3:52090005-52090011	MCF-7	breast:	n/a	n/a
37	CTCF	chr3:52090140-52090290	GM12871	blood:	n/a	n/a
38	CTCF	chr3:52090100-52090250	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr3:52090100-52090268	MCF-7	breast:	n/a	n/a
40	CTCF	chr3:52090100-52090250	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr3:52090201-52090234	GM13976	blood:	n/a	n/a
42	CTCF	chr3:52090160-52090310	GM12868	blood:	n/a	n/a
43	CTCF	chr3:52090080-52090230	HepG2	liver:	n/a	n/a
44	CTCF	chr3:52090128-52090260	MCF-7	breast:	n/a	n/a
45	CTCF	chr3:52090022-52090280	Pancreas_OC	pancreas:	n/a	n/a
46	CTCF	chr3:52090060-52090210	SAEC	small airway:	n/a	n/a
47	CTCF	chr3:52090080-52090230	GM12874	blood:	n/a	n/a
48	CTCF	chr3:52090080-52090230	HA-sp	spinal cord:	n/a	n/a
49	CTCF	chr3:52090170-52090261	GM20000	blood:	n/a	n/a
50	CTCF	chr3:52090080-52090230	K562	blood:	n/a	n/a

(count:245 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52090647-52090697	MCF-7	breast:	n/a
2	chr3:52090647-52090697	MCF-7	breast:	n/a
3	chr3:52090125-52090175	AG04449	skin:	fetal
4	chr3:52090732-52090782	CMK	blood:	n/a
5	chr3:52090125-52090175	HPAEpiC	pulmonary alveolar:	n/a
6	chr3:52090647-52090697	PANC-1	pancreas:	n/a
7	chr3:52090732-52090782	SK-N-SH_RA	brain:	n/a
8	chr3:52090125-52090175	Hela-S3	cervix:	n/a
9	chr3:52090142-52090192	NHBE	bronchial:	n/a
10	chr3:52090142-52090192	SK-N-SH_RA	brain:	n/a
11	chr3:52090142-52090192	LNCaP	prostate:	n/a
12	chr3:52090647-52090697	GM12878	blood:	n/a
13	chr3:52090142-52090192	HRE	kidney:	n/a
14	chr3:52090732-52090782	Hepatocyte	liver:	n/a
15	chr3:52090125-52090175	HCT-116	colon:	n/a
16	chr3:52090125-52090175	SK-N-SH_RA	brain:	n/a
17	chr3:52090732-52090782	HEEpiC	esophagus:	n/a
18	chr3:52090142-52090192	IMR90	lung:	fetal
19	chr3:52090142-52090192	AG09309	skin:	n/a
20	chr3:52090125-52090175	HIPEpiC	eye:	n/a
21	chr3:52090142-52090192	HepG2	liver:	n/a
22	chr3:52090125-52090175	NT2-D1	testis:	n/a
23	chr3:52090125-52090175	MCF10A-Er-Src	breast:	n/a
24	chr3:52090125-52090175	HRCEpiC	kidney:	n/a
25	chr3:52090647-52090697	Caco-2	colon:	n/a
26	chr3:52090125-52090175	ProgFib	skin:	n/a
27	chr3:52090732-52090782	SK-N-SH	brain:	n/a
28	chr3:52090647-52090697	H1-hESC	embryonic stem cell:	embryo
29	chr3:52090732-52090782	LNCaP	prostate:	n/a
30	chr3:52090647-52090697	Jurkat	blood:	n/a
31	chr3:52090142-52090192	HPAEpiC	pulmonary alveolar:	n/a
32	chr3:52090125-52090175	PANC-1	pancreas:	n/a
33	chr3:52090647-52090697	NH-A	brain:	n/a
34	chr3:52090142-52090192	HIPEpiC	eye:	n/a
35	chr3:52090142-52090192	HRPEpiC	eye:	n/a
36	chr3:52090142-52090192	Caco-2	colon:	n/a
37	chr3:52090125-52090175	U87	brain:	n/a
38	chr3:52090647-52090697	BJ	skin:	n/a
39	chr3:52090732-52090782	GM12891	blood:	n/a
40	chr3:52090732-52090782	HCT-116	colon:	n/a
41	chr3:52090125-52090175	SAEC	small airway:	n/a
42	chr3:52090732-52090782	HMEC	breast:	n/a
43	chr3:52090142-52090192	NH-A	brain:	n/a
44	chr3:52090142-52090192	GM12892	blood:	n/a
45	chr3:52090732-52090782	BJ	skin:	n/a
46	chr3:52090732-52090782	HepG2	liver:	n/a
47	chr3:52090142-52090192	Hela-S3	cervix:	n/a
48	chr3:52090142-52090192	AG04449	skin:	fetal
49	chr3:52090647-52090697	HIPEpiC	eye:	n/a
50	chr3:52090647-52090697	HPAEpiC	pulmonary alveolar:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52015921..52019600-chr3:52088214..52092499,4	K562	blood:
2	chr3:52088419..52090155-chr3:52113932..52115849,2	K562	blood:
3	chr19:12901888..12902868-chr3:52090426..52090997,2	Hela-S3	cervix:
4	chr1:149222699..149225112-chr3:52088904..52091700,2	MCF-7	breast:
5	chr3:52026823..52031380-chr3:52087204..52091486,4	K562	blood:
6	chr3:52028061..52031321-chr3:52088873..52092735,5	MCF-7	breast:
7	chr3:52088633..52090447-chr3:52187469..52189147,2	MCF-7	breast:
8	chr3:52089534..52090129-chr5:139554580..139555447,2	Hela-S3	cervix:
9	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:
10	chr3:52089814..52091351-chr3:52187528..52189873,2	K562	blood:
11	chr3:52016320..52018909-chr3:52089400..52091632,2	MCF-7	breast:
12	chr3:51975919..51976628-chr3:52090698..52091583,2	K562	blood:
13	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:

No data

Variant related genes	Relation type
DUSP7	TF binding region
DUSP7	CpG island
ENSG00000114779	chromatin interactions
ENSG00000164087	chromatin interactions
ENSG00000206737	chromatin interactions
ENSG00000114767	chromatin interactions
ENSG00000162244	chromatin interactions
ENSG00000171223	chromatin interactions
ENSG00000243989	chromatin interactions
ENSG00000120306	chromatin interactions
ENSG00000041880	chromatin interactions
ENSG00000256097	chromatin interactions

Extended variants
information (count: 12 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs571458726	chr3:52089997-52089998	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
2	rs374933715	chr3:52090053-52090054	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
3	rs148092517	chr3:52090158-52090159	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
4	rs538765819	chr3:52090276-52090277	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
5	rs553815117	chr3:52090290-52090291	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
6	rs572009424	chr3:52090326-52090327	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
7	rs534175599	chr3:52090503-52090504	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
8	rs541808196	chr3:52090531-52090532	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
9	rs542627967	chr3:52090581-52090582	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
10	rs554218405	chr3:52090588-52090589	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
11	rs574001754	chr3:52090625-52090626	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
12	rs370131035	chr3:52090654-52090655	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Bladder cancer	21909424	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:189 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52083200-52090200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:52084800-52090000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:52085000-52090200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:52086200-52090000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr3:52086400-52090200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr3:52086800-52090800	Active TSS	Rectal Smooth Muscle	rectum
7	chr3:52087400-52091800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:52087600-52090800	Enhancers	Fetal Brain Male	brain
9	chr3:52088000-52090200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr3:52088200-52090200	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr3:52088400-52090000	Transcr. at gene 5' and 3'	Dnd41	blood
12	chr3:52088400-52090200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:52088400-52090200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:52088400-52090800	Active TSS	HSMM	muscle
15	chr3:52088600-52090000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:52088600-52090200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:52088600-52090200	Flanking Active TSS	Placenta	Placenta
18	chr3:52088600-52090200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr3:52088600-52090800	Active TSS	Brain Anterior Caudate	brain
20	chr3:52088600-52091200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr3:52088600-52091600	Active TSS	Psoas Muscle	Psoas
22	chr3:52088600-52091800	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr3:52088600-52091800	Active TSS	Aorta	Aorta
24	chr3:52088600-52092000	Active TSS	Fetal Kidney	kidney
25	chr3:52088600-52092000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr3:52088800-52090200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:52088800-52090200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr3:52088800-52090200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr3:52088800-52090200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:52088800-52090200	Flanking Active TSS	Colonic Mucosa	Colon
31	chr3:52088800-52090200	Flanking Active TSS	Pancreas	Pancrea
32	chr3:52088800-52090800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:52088800-52090800	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr3:52088800-52090800	Active TSS	Esophagus	oesophagus
35	chr3:52088800-52090800	Active TSS	HMEC	breast
36	chr3:52088800-52090800	Active TSS	NHDF-Ad	bronchial
37	chr3:52088800-52091400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:52088800-52091600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:52088800-52091600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:52088800-52091600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:52088800-52091600	Active TSS	Brain Substantia Nigra	brain
42	chr3:52088800-52091600	Active TSS	Gastric	stomach
43	chr3:52088800-52091600	Active TSS	Lung	lung
44	chr3:52088800-52091600	Active TSS	Osteobl	bone
45	chr3:52088800-52091800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52088800-52091800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr3:52088800-52091800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:52088800-52091800	Active TSS	Ovary	ovary
49	chr3:52088800-52091800	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr3:52088800-52091800	Active TSS	Small Intestine	intestine

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