Variant report

Variant	nsv1000280
Chromosome Location	chr3:53742736-53770588
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53764321..53765834-chr3:53878970..53881230,2	MCF-7	breast:
2	chr3:53711180..53712168-chr3:53743924..53744920,6	MCF-7	breast:
3	chr3:53698054..53699675-chr3:53742176..53745087,2	MCF-7	breast:
4	chr3:53763032..53764866-chr3:53879026..53880653,2	MCF-7	breast:
5	chr3:53751914..53753667-chr3:53878854..53881213,2	MCF-7	breast:
6	chr3:53764419..53766196-chr3:53767205..53769405,2	MCF-7	breast:
7	chr3:53764419..53766196-chr3:53767205..53769405,2	MCF-7	breast:
8	chr3:53741820..53744207-chr3:53806615..53808159,2	MCF-7	breast:
9	chr3:53711186..53712122-chr3:53743953..53744837,3	MCF-7	breast:
10	chr3:53747075..53750039-chr3:53753263..53755603,3	MCF-7	breast:
11	chr3:53758884..53760805-chr3:53761482..53763140,2	MCF-7	breast:
12	chr3:53409192..53409694-chr3:53743902..53744640,2	K562	blood:
13	chr3:53565964..53566939-chr3:53744231..53744799,2	MCF-7	breast:
14	chr3:53740542..53743254-chr3:53751040..53753856,2	MCF-7	breast:
15	chr3:53754923..53757308-chr3:53878657..53881028,2	MCF-7	breast:
16	chr3:53740542..53743254-chr3:53751040..53753856,2	MCF-7	breast:
17	chr3:53747075..53750039-chr3:53753263..53755603,3	MCF-7	breast:
18	chr3:53749411..53751208-chr3:54008710..54010882,2	K562	blood:
19	chr3:53758884..53760805-chr3:53761482..53763140,2	MCF-7	breast:
20	chr3:53527140..53529678-chr3:53742465..53744402,2	MCF-7	breast:
21	chr3:53711493..53712139-chr3:53742078..53742918,2	MCF-7	breast:
22	chr3:53763487..53764052-chr3:53807744..53808528,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000056736	chromatin interactions
ENSG00000157388	chromatin interactions
ENSG00000016391	chromatin interactions

Extended variants
information (count: 1174 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:1174 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6445598	chr3:53742736-53742737	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs115748911	chr3:53742780-53742781	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs35657034	chr3:53742800-53742801	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs116409054	chr3:53742804-53742805	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs537909814	chr3:53742822-53742823	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs79370913	chr3:53742828-53742829	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs545824512	chr3:53742842-53742843	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs573304922	chr3:53742945-53742946	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs145723175	chr3:53742946-53742947	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs562458134	chr3:53742982-53742983	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs574686888	chr3:53743050-53743051	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs544954137	chr3:53743108-53743109	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs13074345	chr3:53743112-53743113	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs193027209	chr3:53743126-53743127	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs547917403	chr3:53743144-53743145	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs148924769	chr3:53743154-53743155	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs530130536	chr3:53743250-53743251	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs550167199	chr3:53743252-53743253	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs570041848	chr3:53743254-53743255	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs539373071	chr3:53743291-53743292	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs552584484	chr3:53743344-53743345	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs183434309	chr3:53743383-53743384	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs534858863	chr3:53743406-53743407	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs147686120	chr3:53743429-53743430	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs74350446	chr3:53743436-53743437	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs535865901	chr3:53743439-53743440	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs142178165	chr3:53743472-53743473	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs2612014	chr3:53743567-53743568	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs575617362	chr3:53743576-53743577	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs545328525	chr3:53743588-53743589	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs546201510	chr3:53743594-53743595	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs558573356	chr3:53743617-53743618	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs62253776	chr3:53743643-53743644	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs531341183	chr3:53743657-53743658	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs540829615	chr3:53743704-53743705	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs561386898	chr3:53743714-53743715	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs146037196	chr3:53743718-53743719	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs543916027	chr3:53743768-53743769	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs138826538	chr3:53743911-53743912	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs373015476	chr3:53743951-53743952	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs552835268	chr3:53744032-53744033	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs376473118	chr3:53744048-53744049	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs528699294	chr3:53744083-53744084	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs543532502	chr3:53744085-53744086	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs548346006	chr3:53744105-53744106	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs188952246	chr3:53744106-53744107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs529063225	chr3:53744115-53744116	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs544598676	chr3:53744151-53744152	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs535977088	chr3:53744171-53744172	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs570562004	chr3:53744182-53744183	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:93)

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
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
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Chronic lymphocytic leukemia	20421269	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
Adrenocortical carcinoma	18281524	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:369 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53723200-53743400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:53726600-53744000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:53726800-53743400	Weak transcription	Spleen	Spleen
5	chr3:53736800-53744000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:53737400-53747800	Weak transcription	Fetal Brain Male	brain
7	chr3:53738800-53744000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:53739000-53743400	Enhancers	Fetal Lung	lung
9	chr3:53739800-53742800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr3:53739800-53744400	Enhancers	Fetal Heart	heart
11	chr3:53740000-53744200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:53740200-53743000	Weak transcription	Right Ventricle	heart
13	chr3:53740200-53764400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:53740400-53745400	Weak transcription	Right Atrium	heart
15	chr3:53740600-53744000	Weak transcription	Fetal Thymus	thymus
16	chr3:53740600-53744200	Weak transcription	Brain Anterior Caudate	brain
17	chr3:53741000-53744600	Enhancers	Liver	Liver
18	chr3:53741200-53743200	Enhancers	Fetal Intestine Small	intestine
19	chr3:53741200-53743800	Enhancers	Lung	lung
20	chr3:53741200-53751400	Weak transcription	Fetal Brain Female	brain
21	chr3:53741400-53742800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:53741400-53743800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:53741600-53742800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:53741600-53743000	Enhancers	Fetal Intestine Large	intestine
25	chr3:53741800-53744400	Enhancers	Left Ventricle	heart
26	chr3:53742400-53743000	Weak transcription	Primary B cells from cord blood	blood
27	chr3:53742600-53743600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:53742600-53744000	Weak transcription	Stomach Mucosa	stomach
29	chr3:53742600-53744000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:53742600-53744200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:53742600-53744200	Weak transcription	HepG2	liver
32	chr3:53742600-53744800	Enhancers	A549	lung
33	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
34	chr3:53742800-53743000	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr3:53742800-53743200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:53743000-53743600	Enhancers	Primary B cells from cord blood	blood
37	chr3:53743000-53743600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:53743000-53744000	Weak transcription	Fetal Intestine Large	intestine
39	chr3:53743000-53744400	Enhancers	Right Ventricle	heart
40	chr3:53743200-53743400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:53743200-53744000	Weak transcription	Fetal Intestine Small	intestine
42	chr3:53743400-53743600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:53743400-53743600	Enhancers	Spleen	Spleen
44	chr3:53743400-53744000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:53743400-53744600	Genic enhancers	Fetal Lung	lung
46	chr3:53743600-53743800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:53743600-53744000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:53743600-53744000	Weak transcription	Spleen	Spleen
49	chr3:53743600-53744200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr3:53743800-53744200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links