Variant report

Variant	nsv965168
Chromosome Location	chr3:52409425-52416848
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52409800-52409950	GM12864	blood:	n/a	n/a
2	CTCF	chr3:52409938-52409946	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr3:52409880-52410030	HRE	kidney:	n/a	n/a
4	CTCF	chr3:52409900-52410020	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:52409954-52409962	NHEK	skin:	n/a	n/a
6	CTCF	chr3:52409920-52410070	WERI-Rb-1	eye:	n/a	n/a
7	E2F6	chr3:52409782-52410260	H1-hESC	embryonic stem cell:	n/a	chr3:52410022-52410034
8	MYC	chr3:52415797-52415905	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:52409875-52409935	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:52416044-52416089	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:52414822-52414848	K562	blood:	n/a	n/a
12	POLR2A	chr3:52416053-52416131	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr3:52413516-52413576	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:52413695-52413743	MCF-7	breast:	n/a	n/a
15	POLR2A	chr3:52415786-52415851	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:52416296-52416320	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:52407749-52410627	K562	blood:	n/a	n/a
18	POLR2A	chr3:52414966-52414976	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr3:52411969-52412069	K562	blood:	n/a	n/a
20	POLR2A	chr3:52411356-52411363	K562	blood:	n/a	n/a
21	POLR2A	chr3:52416169-52416314	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:52414905-52414925	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:52414839-52414888	HUVEC	blood vessel:	n/a	n/a
24	RAD21	chr3:52409811-52410138	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAL1	chr3:52414273-52414449	K562	blood:	n/a	chr3:52414342-52414360
26	TBP	chr3:52409927-52410069	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52413424..52415334-chr3:52416038..52418225,2	K562	blood:
2	chr3:52378872..52380816-chr3:52409313..52412087,2	MCF-7	breast:
3	chr3:52392990..52395897-chr3:52410208..52412825,2	K562	blood:
4	chr3:52413424..52415334-chr3:52416038..52418225,2	K562	blood:
5	chr3:52410804..52413361-chr3:52413563..52417960,4	K562	blood:
6	chr3:52321701..52324169-chr3:52414914..52417195,2	MCF-7	breast:
7	chr3:52406883..52409184-chr3:52415694..52419355,3	K562	blood:
8	chr3:52384981..52388271-chr3:52408939..52411277,3	K562	blood:
9	chr3:52409891..52412947-chr3:52429055..52433083,4	K562	blood:
10	chr3:52399836..52402473-chr3:52409418..52411150,2	K562	blood:
11	chr3:52410804..52413361-chr3:52413563..52417960,4	K562	blood:
12	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
13	chr3:52409617..52410373-chr3:52418918..52419802,2	MCF-7	breast:
14	chr3:52413340..52415440-chr3:52417250..52419187,2	MCF-7	breast:

No data

Variant related genes	Relation type
DNAH1	TF binding region
ENSG00000164091	chromatin interactions
ENSG00000168237	chromatin interactions
ENSG00000114841	chromatin interactions
ENSG00000239557	chromatin interactions

Extended variants
information (count: 321 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:321 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553449428	chr3:52409445-52409446	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs373909408	chr3:52409462-52409463	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs573596887	chr3:52409468-52409469	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs56347145	chr3:52409499-52409500	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs535938145	chr3:52409537-52409538	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs552563776	chr3:52409553-52409554	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs576239199	chr3:52409746-52409747	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs368508444	chr3:52409755-52409756	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs148066970	chr3:52409783-52409784	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs565902583	chr3:52409785-52409786	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs572199173	chr3:52409825-52409826	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs541324976	chr3:52409829-52409830	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs561100052	chr3:52409874-52409875	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs143374293	chr3:52409888-52409889	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs543490188	chr3:52409914-52409915	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs376808664	chr3:52409927-52409928	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs371247102	chr3:52409931-52409932	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs374196749	chr3:52409932-52409933	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs375970084	chr3:52409938-52409939	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs532517936	chr3:52409956-52409957	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs200988349	chr3:52409998-52409999	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs201299120	chr3:52410004-52410005	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs61738522	chr3:52410008-52410009	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs367692811	chr3:52410010-52410011	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs548883682	chr3:52410013-52410014	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs568686978	chr3:52410017-52410018	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs372381282	chr3:52410024-52410025	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs536228512	chr3:52410029-52410030	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs375469702	chr3:52410048-52410049	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs569761986	chr3:52410065-52410066	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs368557819	chr3:52410084-52410085	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs372472597	chr3:52410087-52410088	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs117056392	chr3:52410099-52410100	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs558742783	chr3:52410103-52410104	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs572229436	chr3:52410106-52410107	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs540899009	chr3:52410110-52410111	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs554836403	chr3:52410145-52410146	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs375128845	chr3:52410155-52410156	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs543409472	chr3:52410177-52410178	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs374576660	chr3:52410196-52410197	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs532431041	chr3:52410202-52410203	Weak transcription Strong transcription Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs114433304	chr3:52410223-52410224	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs559661858	chr3:52410251-52410252	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs561711234	chr3:52410294-52410295	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs528662175	chr3:52410300-52410301	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs547242928	chr3:52410391-52410392	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs568726734	chr3:52410392-52410393	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs531153220	chr3:52410394-52410395	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs140393855	chr3:52410397-52410398	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs569676452	chr3:52410409-52410410	Weak transcription Strong transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:97)

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
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD

Chromatin state (count:168 , 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	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
7	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
9	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
10	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
11	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:52407200-52413800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:52407200-52422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:52407600-52412400	Weak transcription	Thymus	Thymus
16	chr3:52407600-52413800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:52407600-52420800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:52407800-52421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:52408000-52409600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:52408000-52412000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:52408000-52419200	Weak transcription	Fetal Thymus	thymus
22	chr3:52408000-52421800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
25	chr3:52408600-52411200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:52408600-52421000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:52408800-52414000	Weak transcription	K562	blood
28	chr3:52409000-52410400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:52409000-52411000	Strong transcription	Primary T cells from cord blood	blood
30	chr3:52409000-52411000	Strong transcription	Liver	Liver
31	chr3:52409200-52409600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:52409200-52409800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr3:52409200-52410000	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:52409200-52410200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr3:52409200-52410400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:52409200-52410400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr3:52409200-52410400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:52409200-52410400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:52409200-52410600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:52409200-52410600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:52409200-52410600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:52409200-52410600	Strong transcription	Brain Substantia Nigra	brain
43	chr3:52409200-52410600	Strong transcription	Fetal Intestine Large	intestine
44	chr3:52409200-52410600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:52409200-52410800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:52409200-52410800	Strong transcription	Spleen	Spleen
47	chr3:52409200-52411000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:52409200-52411000	Strong transcription	Lung	lung
49	chr3:52409200-52411000	Strong transcription	Pancreas	Pancrea
50	chr3:52409200-52411400	Strong transcription	Placenta	Placenta

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