Variant report

Variant	nsv965164
Chromosome Location	chr3:48485079-48485579
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:48485422-48485461	LNCaP	prostate:	n/a	n/a
2	POLR2A	chr3:48484670-48485413	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:48485447-48486613	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:48485085-48485317	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:48485218-48485238	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:48485050-48485245	K562	blood:	n/a	n/a
7	POLR2A	chr3:48485436-48488575	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:48484863-48485286	GM12891	blood:	n/a	n/a
9	POLR2A	chr3:48485006-48485247	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:48484896-48485106	K562	blood:	n/a	n/a
11	POLR2A	chr3:48485546-48486547	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:48485047-48485298	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:48484919-48485229	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:48485480-48488528	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr3:48485060-48485350	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:48485461-48485860	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:48485476-48485838	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:48485188-48485208	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:48485350-48488730	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr3:48485458-48485868	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:48485442-48485455	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:48485560-48487612	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr3:48485523-48485889	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:48484036-48485400	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:48485244-48485263	MCF-7	breast:	n/a	n/a
26	POLR2A	chr3:48484910-48485345	GM12892	blood:	n/a	n/a
27	POLR2A	chr3:48484988-48485196	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:48484943-48485879	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:48485160-48485179	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:48485446-48488566	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:48485097-48485114	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:48484059-48485410	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:48484948-48485307	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:48484973-48485239	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr3:48485493-48489452	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:
2	chr3:48228273..48230987-chr3:48484727..48487110,2	K562	blood:
3	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
4	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
5	chr3:48461352..48463314-chr3:48484246..48486227,2	MCF-7	breast:
6	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
7	chr3:48485232..48487898-chr3:48541366..48542951,2	K562	blood:
8	chr3:48472201..48473721-chr3:48483082..48485224,2	MCF-7	breast:

No data

Variant related genes	Relation type
ATRIP	TF binding region
CCDC51	TF binding region
ENSG00000164051	chromatin interactions
ENSG00000213689	chromatin interactions
ENSG00000164045	chromatin interactions
ENSG00000114268	chromatin interactions
ENSG00000164050	chromatin interactions
ENSG00000232112	chromatin interactions
ENSG00000164054	chromatin interactions

Extended variants
information (count: 29 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs565444965	chr3:48485125-48485126	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
2	rs549643140	chr3:48485128-48485129	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs151146971	chr3:48485135-48485136	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
4	rs548383797	chr3:48485157-48485158	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
5	rs569813626	chr3:48485162-48485163	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
6	rs537336702	chr3:48485209-48485210	Weak transcription Strong transcription	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
7	rs549957558	chr3:48485214-48485215	Weak transcription Strong transcription	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
8	rs558920262	chr3:48485250-48485251	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
9	rs578066508	chr3:48485259-48485260	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
10	rs375127083	chr3:48485261-48485262	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
11	rs367740188	chr3:48485275-48485276	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
12	rs539074977	chr3:48485301-48485302	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
13	rs375880978	chr3:48485344-48485345	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
14	rs554268815	chr3:48485347-48485348	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
15	rs572507761	chr3:48485356-48485357	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
16	rs542826372	chr3:48485375-48485376	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
17	rs140064569	chr3:48485381-48485382	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
18	rs576596946	chr3:48485416-48485417	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
19	rs11552877	chr3:48485431-48485432	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
20	rs369760515	chr3:48485433-48485434	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
21	rs565737200	chr3:48485436-48485437	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
22	rs373553505	chr3:48485438-48485439	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
23	rs7126	chr3:48485493-48485494	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs531938710	chr3:48485502-48485503	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
25	rs138163950	chr3:48485522-48485523	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
26	rs558992283	chr3:48485528-48485529	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
27	rs141110854	chr3:48485532-48485533	Weak transcription Strong transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
28	rs112430504	chr3:48485557-48485558	Weak transcription Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
29	rs548012930	chr3:48485558-48485559	Weak transcription Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:100)

Disease	PMID	Source
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
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
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	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
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48482600-48487200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48482600-48487200	Weak transcription	Right Atrium	heart
3	chr3:48482600-48487400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:48482600-48487600	Weak transcription	Ovary	ovary
5	chr3:48483200-48487200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:48483400-48485200	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr3:48483400-48486200	Strong transcription	Gastric	stomach
8	chr3:48483400-48486200	Strong transcription	Left Ventricle	heart
9	chr3:48483400-48486200	Strong transcription	Osteobl	bone
10	chr3:48483400-48486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:48483400-48486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:48483400-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:48483400-48486400	Strong transcription	Brain Anterior Caudate	brain
14	chr3:48483400-48486400	Strong transcription	Esophagus	oesophagus
15	chr3:48483400-48487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:48483400-48487200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:48483400-48487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:48483400-48487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:48483600-48485200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:48483600-48485200	Strong transcription	Fetal Lung	lung
21	chr3:48483600-48485200	Strong transcription	Right Ventricle	heart
22	chr3:48483600-48486000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:48483600-48486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:48483600-48486200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:48483600-48486200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:48483600-48486200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:48483600-48486200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:48483600-48486200	Strong transcription	Fetal Thymus	thymus
29	chr3:48483600-48486200	Strong transcription	Lung	lung
30	chr3:48483600-48486400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:48483600-48486400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:48483600-48486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:48483600-48486400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:48483600-48486400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:48483600-48486400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:48483600-48486400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:48483600-48486400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:48483600-48486400	Strong transcription	Adipose Nuclei	Adipose
39	chr3:48483600-48486400	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:48483600-48486400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr3:48483600-48486400	Strong transcription	Colon Smooth Muscle	Colon
42	chr3:48483600-48486400	Strong transcription	Placenta	Placenta
43	chr3:48483600-48486400	Strong transcription	Pancreas	Pancrea
44	chr3:48483600-48486400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:48483600-48486400	Strong transcription	NH-A	brain
46	chr3:48483600-48486600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:48483600-48486600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:48483600-48486600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:48483600-48486600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:48483600-48487000	Strong transcription	Brain Germinal Matrix	brain

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