Variant report

Variant	esv3371910
Chromosome Location	chr3:195607136-195607610
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:195607307-195607309	K562	blood:	n/a	n/a
2	POLR2A	chr3:195607468-195607864	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:195606986-195607153	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:195607489-195607573	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:195607445-195607868	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:195607506-195607773	K562	blood:	n/a	n/a
7	POLR2A	chr3:195607214-195607367	H1-hESC	embryonic stem cell:	n/a	n/a
8	POU2F2	chr3:195607532-195607858	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195601233..195610120-chr3:195632410..195638442,11	MCF-7	breast:

Variant related genes	Relation type
TNK2	TF binding region
ENSG00000061938	chromatin interactions
ENSG00000224614	chromatin interactions

Extended variants
information (count: 31 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs548984901	chr3:195607194-195607195	Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs138222609	chr3:195607195-195607196	Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs534798295	chr3:195607212-195607213	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs553476430	chr3:195607236-195607237	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs578025395	chr3:195607240-195607241	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs539650359	chr3:195607243-195607244	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs200417022	chr3:195607259-195607260	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs557643570	chr3:195607275-195607276	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs576426336	chr3:195607308-195607309	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs2550260	chr3:195607328-195607329	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs2432529	chr3:195607343-195607344	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs2550259	chr3:195607346-195607347	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs200939790	chr3:195607349-195607350	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs372700993	chr3:195607382-195607383	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs11708930	chr3:195607387-195607388	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs56230425	chr3:195607391-195607392	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs2620626	chr3:195607407-195607408	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs561674887	chr3:195607418-195607419	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs374088509	chr3:195607425-195607426	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs567694119	chr3:195607438-195607439	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs538503532	chr3:195607439-195607440	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs28719688	chr3:195607448-195607449	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs9824499	chr3:195607458-195607459	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs540661054	chr3:195607490-195607491	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs12487966	chr3:195607495-195607496	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs539234162	chr3:195607505-195607506	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs2620625	chr3:195607510-195607511	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs532865936	chr3:195607525-195607526	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs185193031	chr3:195607557-195607558	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs111283176	chr3:195607559-195607560	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs200369999	chr3:195607594-195607595	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:179 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195586800-195608600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:195589000-195612000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:195589400-195621800	Weak transcription	Small Intestine	intestine
4	chr3:195589800-195616200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:195589800-195618800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:195589800-195619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:195590000-195607200	Strong transcription	Thymus	Thymus
8	chr3:195590000-195607400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:195590000-195615600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:195590200-195607400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:195590200-195615800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:195590600-195617000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:195592200-195615800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:195592200-195616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:195592400-195607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:195592600-195607200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:195593200-195607200	Strong transcription	Fetal Thymus	thymus
18	chr3:195595600-195608800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:195595600-195618800	Weak transcription	Fetal Kidney	kidney
20	chr3:195597400-195611800	Strong transcription	Fetal Stomach	stomach
21	chr3:195601200-195614600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:195601400-195608800	Weak transcription	Osteobl	bone
23	chr3:195601400-195611600	Weak transcription	NH-A	brain
24	chr3:195602000-195607200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:195602200-195607200	Strong transcription	Adipose Nuclei	Adipose
26	chr3:195602200-195607400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:195602200-195607400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:195602400-195607200	Strong transcription	Primary T cells from cord blood	blood
29	chr3:195602400-195607200	Strong transcription	Fetal Brain Female	brain
30	chr3:195602400-195607200	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr3:195602400-195607400	Strong transcription	Liver	Liver
32	chr3:195602400-195607600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:195602600-195607200	Genic enhancers	Fetal Muscle Leg	muscle
34	chr3:195602600-195607200	Strong transcription	Right Ventricle	heart
35	chr3:195602600-195616000	Weak transcription	Fetal Brain Male	brain
36	chr3:195602600-195616800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:195602800-195607200	Genic enhancers	Placenta	Placenta
38	chr3:195602800-195607200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr3:195603000-195607200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:195603000-195607200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:195603000-195607200	Strong transcription	Dnd41	blood
42	chr3:195603200-195607400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:195603200-195607400	Strong transcription	Brain Hippocampus Middle	brain
44	chr3:195603200-195607400	Strong transcription	Brain Substantia Nigra	brain
45	chr3:195603400-195607200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:195603600-195607200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr3:195603800-195607200	Strong transcription	Spleen	Spleen
48	chr3:195604000-195607200	Strong transcription	Brain Cingulate Gyrus	brain
49	chr3:195604000-195607200	Strong transcription	Fetal Intestine Large	intestine
50	chr3:195604000-195607200	Strong transcription	Fetal Lung	lung

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