Variant report

Variant	nsv962568
Chromosome Location	chr20:25460648-25462141
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	CEBPB	chr20:25461288-25461454	HepG2	liver:	n/a	chr20:25461356-25461367
2	NR2F2	chr20:25462141-25462645	MCF-7	breast:	n/a	n/a
3	POLR2A	chr20:25461196-25461317	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr20:25461149-25461165	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:25460985-25461012	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:25461397-25461416	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr20:25462013-25462088	HepG2	liver:	n/a	n/a
8	POLR2A	chr20:25461403-25461695	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:25462067-25462365	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
NINL	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:64 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs376679743	chr20:25460665-25460666	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs558831024	chr20:25460707-25460708	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs34345105	chr20:25460725-25460726	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs62211496	chr20:25460779-25460780	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs364722	chr20:25460806-25460807	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs62211497	chr20:25460827-25460828	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs147804078	chr20:25460857-25460858	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs200438908	chr20:25460859-25460860	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs148838435	chr20:25460860-25460861	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs35054550	chr20:25460861-25460862	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs368992672	chr20:25460904-25460905	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs143430964	chr20:25460912-25460913	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs113029948	chr20:25460925-25460926	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs375274008	chr20:25460938-25460939	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs369648201	chr20:25460954-25460955	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs546078802	chr20:25460988-25460989	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs146727303	chr20:25461066-25461067	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs76976017	chr20:25461086-25461087	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs541790300	chr20:25461120-25461121	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs77295497	chr20:25461175-25461176	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs527348364	chr20:25461187-25461188	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs547091731	chr20:25461189-25461190	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs111596069	chr20:25461212-25461213	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs186111555	chr20:25461255-25461256	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs115748952	chr20:25461257-25461258	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs552398548	chr20:25461269-25461270	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs140320698	chr20:25461318-25461319	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs113582755	chr20:25461373-25461374	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs538190746	chr20:25461378-25461379	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs548527436	chr20:25461410-25461411	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs557933410	chr20:25461427-25461428	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs568382946	chr20:25461440-25461441	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs534238900	chr20:25461441-25461442	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs372939355	chr20:25461464-25461465	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs192020538	chr20:25461465-25461466	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs573295963	chr20:25461480-25461481	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs114143303	chr20:25461481-25461482	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs539641636	chr20:25461559-25461560	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs145579184	chr20:25461584-25461585	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs576273591	chr20:25461602-25461603	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs541776916	chr20:25461616-25461617	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs540584969	chr20:25461627-25461628	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs561675542	chr20:25461675-25461676	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs571952696	chr20:25461694-25461695	Weak transcription Strong transcription Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs138103288	chr20:25461707-25461708	Weak transcription Strong transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs376202097	chr20:25461716-25461717	Weak transcription Strong transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs183336214	chr20:25461722-25461723	Weak transcription Strong transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs562376081	chr20:25461735-25461736	Weak transcription Strong transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs529653832	chr20:25461838-25461839	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs6050640	chr20:25461840-25461841	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
2	chr20:25429400-25463200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
4	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:25434400-25460800	Weak transcription	Fetal Heart	heart
6	chr20:25435800-25465600	Weak transcription	NH-A	brain
7	chr20:25436200-25465200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr20:25438600-25466200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr20:25438800-25472600	Strong transcription	HepG2	liver
10	chr20:25440600-25466600	Weak transcription	Left Ventricle	heart
11	chr20:25446000-25466600	Weak transcription	NHDF-Ad	bronchial
12	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
14	chr20:25447000-25477600	Strong transcription	Fetal Muscle Leg	muscle
15	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr20:25448800-25464600	Weak transcription	HUVEC	blood vessel
18	chr20:25448800-25480800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr20:25450000-25463000	Strong transcription	Liver	Liver
20	chr20:25451000-25461800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr20:25451000-25462000	Weak transcription	Colonic Mucosa	Colon
22	chr20:25451200-25461400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:25451200-25474000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr20:25451400-25460800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr20:25451400-25468400	Weak transcription	Osteobl	bone
26	chr20:25451400-25488800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr20:25451600-25470000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr20:25451800-25468000	Weak transcription	HSMMtube	muscle
29	chr20:25453200-25463000	Strong transcription	Fetal Brain Female	brain
30	chr20:25453400-25462800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
32	chr20:25453600-25467200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:25455200-25465200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr20:25455800-25462800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr20:25455800-25462800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr20:25455800-25462800	Strong transcription	Ovary	ovary
37	chr20:25456200-25462400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr20:25456200-25463000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr20:25456200-25463000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr20:25456200-25466200	Strong transcription	Fetal Intestine Small	intestine
41	chr20:25456400-25461200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:25456400-25462800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr20:25456400-25462800	Strong transcription	Aorta	Aorta
44	chr20:25456400-25462800	Strong transcription	Gastric	stomach
45	chr20:25456400-25463000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr20:25456400-25470800	Strong transcription	Fetal Lung	lung
47	chr20:25456400-25472600	Strong transcription	Fetal Intestine Large	intestine
48	chr20:25456600-25462600	Strong transcription	Dnd41	blood
49	chr20:25456600-25462800	Strong transcription	Spleen	Spleen
50	chr20:25456600-25463000	Strong transcription	Placenta Amnion	Placenta Amnion

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