Variant report

Variant	nsv979834
Chromosome Location	chr3:52407592-52408592
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52408256-52408453	GM12878	blood:	n/a	n/a
2	CTCF	chr3:52408353-52408438	GM19238	blood:	n/a	n/a
3	CTCF	chr3:52408260-52408410	HRE	kidney:	n/a	n/a
4	CTCF	chr3:52408260-52408410	GM12875	blood:	n/a	n/a
5	CTCF	chr3:52408360-52408510	GM12872	blood:	n/a	n/a
6	CTCF	chr3:52408127-52408176	GM20000	blood:	n/a	n/a
7	CTCF	chr3:52408343-52408431	LNCaP	prostate:	n/a	n/a
8	CTCF	chr3:52408293-52408455	K562	blood:	n/a	n/a
9	CTCF	chr3:52408280-52408430	HPAF	blood vessel:	n/a	n/a
10	CTCF	chr3:52408280-52408430	AG10803	skin:	n/a	n/a
11	CTCF	chr3:52408345-52408439	Gliobla	brain:	n/a	n/a
12	CTCF	chr3:52408337-52408459	NHEK	skin:	n/a	n/a
13	CTCF	chr3:52408066-52408651	A549	lung:	n/a	n/a
14	CTCF	chr3:52408300-52408450	Caco-2	colon:	n/a	n/a
15	CTCF	chr3:52408355-52408415	MCF-7	breast:	n/a	n/a
16	CTCF	chr3:52408340-52408490	A549	lung:	n/a	n/a
17	CTCF	chr3:52408340-52408490	GM12869	blood:	n/a	n/a
18	CTCF	chr3:52408282-52408460	HepG2	liver:	n/a	n/a
19	CTCF	chr3:52408300-52408450	HCFaa	heart:	n/a	n/a
20	CTCF	chr3:52408300-52408450	BJ	skin:	n/a	n/a
21	CTCF	chr3:52408340-52408490	GM12864	blood:	n/a	n/a
22	CTCF	chr3:52408320-52408470	GM12873	blood:	n/a	n/a
23	CTCF	chr3:52408360-52408510	GM12874	blood:	n/a	n/a
24	CTCF	chr3:52408240-52408390	GM12866	blood:	n/a	n/a
25	CTCF	chr3:52408260-52408410	HFF-Myc	foreskin:	n/a	n/a
26	CTCF	chr3:52408320-52408470	RPTEC	kidney:	n/a	n/a
27	CTCF	chr3:52408365-52408387	GM19239	blood:	n/a	n/a
28	CTCF	chr3:52408301-52408449	IMR90	lung:	n/a	n/a
29	CTCF	chr3:52408300-52408450	GM06990	blood:	n/a	n/a
30	CTCF	chr3:52408300-52408450	SAEC	small airway:	n/a	n/a
31	CTCF	chr3:52408300-52408450	HEK293	kidney:	n/a	n/a
32	CTCF	chr3:52408260-52408410	GM06990	blood:	n/a	n/a
33	CTCF	chr3:52408335-52408454	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:52408347-52408459	GM10266	blood:	n/a	n/a
35	CTCF	chr3:52408260-52408410	HCT-116	colon:	n/a	n/a
36	CTCF	chr3:52408202-52408544	K562	blood:	n/a	n/a
37	CTCF	chr3:52408274-52408423	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr3:52408360-52408510	GM12878	blood:	n/a	n/a
39	CTCF	chr3:52408360-52408510	GM12864	blood:	n/a	n/a
40	CTCF	chr3:52408248-52408466	K562	blood:	n/a	n/a
41	CTCF	chr3:52408320-52408470	GM12878	blood:	n/a	n/a
42	CTCF	chr3:52408282-52408468	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr3:52408280-52408430	HMEC	breast:	n/a	n/a
44	CTCF	chr3:52408310-52408445	GM13977	blood:	n/a	n/a
45	CTCF	chr3:52408300-52408450	GM12868	blood:	n/a	n/a
46	CTCF	chr3:52408300-52408450	GM12864	blood:	n/a	n/a
47	CTCF	chr3:52408320-52408470	GM12871	blood:	n/a	n/a
48	CTCF	chr3:52408300-52408450	HCT-116	colon:	n/a	n/a
49	CTCF	chr3:52408280-52408430	AG09309	skin:	n/a	n/a
50	CTCF	chr3:52408320-52408470	GM12865	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
2	chr3:52321755..52323526-chr3:52405745..52408434,2	K562	blood:
3	chr3:52406883..52409184-chr3:52415694..52419355,3	K562	blood:
4	chr3:52408372..52408995-chr3:52419399..52420367,2	MCF-7	breast:
5	chr3:52272390..52274822-chr3:52406008..52407949,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239557	TF binding region
ENSG00000243224	chromatin interactions
ENSG00000114841	chromatin interactions
ENSG00000239732	chromatin interactions
ENSG00000164091	chromatin interactions
ENSG00000247596	chromatin interactions
ENSG00000168237	chromatin interactions

Extended variants
information (count: 36 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs576705265	chr3:52407626-52407627	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
2	rs543793548	chr3:52407664-52407665	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs140481308	chr3:52407668-52407669	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
4	rs13096571	chr3:52407725-52407726	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs539958804	chr3:52407744-52407745	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
6	rs373022589	chr3:52407783-52407784	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
7	rs13076508	chr3:52407805-52407806	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs181102959	chr3:52407869-52407870	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
9	rs533369838	chr3:52407889-52407890	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
10	rs373145611	chr3:52407892-52407893	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
11	rs531686089	chr3:52407897-52407898	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
12	rs13076890	chr3:52407933-52407934	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs563807957	chr3:52407953-52407954	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs571676208	chr3:52408003-52408004	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs534251522	chr3:52408033-52408034	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs184020562	chr3:52408039-52408040	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs567773121	chr3:52408100-52408101	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs536426452	chr3:52408114-52408115	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs556756265	chr3:52408134-52408135	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs576323218	chr3:52408156-52408157	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs545307849	chr3:52408158-52408159	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs138276682	chr3:52408193-52408194	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs577243800	chr3:52408208-52408209	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs539872598	chr3:52408213-52408214	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs559976863	chr3:52408235-52408236	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs529025816	chr3:52408238-52408239	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs141318204	chr3:52408263-52408264	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs1802864	chr3:52408281-52408282	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs188796620	chr3:52408414-52408415	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs537135103	chr3:52408504-52408505	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs531595235	chr3:52408505-52408506	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs551714277	chr3:52408535-52408536	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs565252088	chr3:52408545-52408546	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs181599571	chr3:52408560-52408561	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs532478999	chr3:52408574-52408575	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs567642241	chr3:52408575-52408576	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:91)

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
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:151 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
4	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
6	chr3:52395400-52409400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
8	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
10	chr3:52399000-52409400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52399400-52409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:52400200-52409200	Weak transcription	Right Ventricle	heart
13	chr3:52401000-52409400	Weak transcription	Esophagus	oesophagus
14	chr3:52401200-52409400	Weak transcription	Colonic Mucosa	Colon
15	chr3:52403000-52407600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52403200-52407600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:52404800-52409200	Weak transcription	Pancreas	Pancrea
19	chr3:52405000-52408400	Weak transcription	Brain Substantia Nigra	brain
20	chr3:52405000-52409200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:52405000-52409200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:52405000-52409400	Weak transcription	Brain Angular Gyrus	brain
23	chr3:52405000-52409400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
25	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:52405600-52409200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:52405600-52409200	Weak transcription	Lung	lung
28	chr3:52406200-52409200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:52406200-52409400	Enhancers	GM12878-XiMat	blood
30	chr3:52406400-52407600	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr3:52406400-52407600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:52406400-52408000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:52406400-52408000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr3:52406400-52408000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:52406400-52409400	Weak transcription	Brain Anterior Caudate	brain
36	chr3:52406400-52409400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:52406600-52407600	Weak transcription	Primary T cells from cord blood	blood
39	chr3:52406600-52407600	Enhancers	Thymus	Thymus
40	chr3:52406600-52407800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:52406600-52407800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:52406600-52408000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr3:52406600-52408000	Enhancers	Fetal Thymus	thymus
44	chr3:52406600-52409000	Weak transcription	Liver	Liver
45	chr3:52406600-52409200	Weak transcription	Placenta	Placenta
46	chr3:52406600-52409400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:52406600-52409400	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:52406600-52409400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:52406600-52409400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:52406800-52407600	Enhancers	Fetal Muscle Trunk	muscle

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