Variant report

Variant	nsv979494
Chromosome Location	chr20:23900040-23910180
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	BHLHE40	chr20:23909552-23909553	K562	blood:	n/a	n/a
2	CEBPB	chr20:23900611-23901506	MCF-7	breast:	n/a	chr20:23901302-23901313
3	CEBPB	chr20:23900626-23901487	MCF-7	breast:	n/a	chr20:23901302-23901313
4	CEBPB	chr20:23901279-23901335	HepG2	liver:	n/a	chr20:23901302-23901313
5	CTCF	chr20:23900840-23900990	SAEC	small airway:	n/a	n/a
6	EGR1	chr20:23900710-23901242	MCF-7	breast:	n/a	chr20:23900932-23900939 chr20:23900933-23900943
7	EGR1	chr20:23900615-23901210	MCF-7	breast:	n/a	chr20:23900932-23900939 chr20:23900933-23900943
8	FOS	chr20:23900882-23900934	MCF10A-Er-Src	breast:	n/a	chr20:23900887-23900897 chr20:23900888-23900896 chr20:23900887-23900897
9	FOSL2	chr20:23900619-23901193	MCF-7	breast:	n/a	chr20:23900887-23900897 chr20:23900888-23900896 chr20:23900887-23900897
10	GATA3	chr20:23900434-23901275	MCF-7	breast:	n/a	chr20:23900899-23900907
11	GATA3	chr20:23907690-23907971	MCF-7	breast:	n/a	n/a
12	GATA3	chr20:23901562-23901896	MCF-7	breast:	n/a	n/a
13	GATA3	chr20:23900423-23901896	MCF-7	breast:	n/a	chr20:23900899-23900907 chr20:23901399-23901409
14	GATA3	chr20:23901363-23901996	MCF-7	breast:	n/a	chr20:23901399-23901409
15	GATA3	chr20:23901538-23901815	T-47D	breast:	n/a	n/a
16	GATA3	chr20:23900593-23901319	MCF-7	breast:	n/a	chr20:23900899-23900907
17	HA-E2F1	chr20:23900557-23901284	MCF-7	breast:	n/a	n/a
18	HDAC2	chr20:23900478-23901284	MCF-7	breast:	n/a	n/a
19	HDAC2	chr20:23900625-23901409	MCF-7	breast:	n/a	n/a
20	MAX	chr20:23909456-23909702	K562	blood:	n/a	n/a
21	MAX	chr20:23901386-23901898	MCF-7	breast:	n/a	chr20:23901632-23901641 chr20:23901634-23901641 chr20:23901632-23901642 chr20:23901632-23901643 chr20:23901633-23901642
22	MAX	chr20:23909462-23909755	K562	blood:	n/a	n/a
23	MAX	chr20:23909465-23909690	NB4	blood:	n/a	n/a
24	MAX	chr20:23900419-23901268	MCF-7	breast:	n/a	n/a
25	MAX	chr20:23900317-23901190	MCF-7	breast:	n/a	n/a
26	MYC	chr20:23905690-23905761	H1-hESC	embryonic stem cell:	n/a	n/a
27	MYC	chr20:23900460-23901025	MCF-7	breast:	n/a	n/a
28	MYC	chr20:23901560-23901780	MCF-7	breast:	n/a	chr20:23901632-23901641 chr20:23901634-23901641 chr20:23901632-23901642 chr20:23901632-23901643 chr20:23901633-23901642
29	MYC	chr20:23900310-23901077	MCF-7	breast:	n/a	n/a
30	MYC	chr20:23900530-23901018	MCF-7	breast:	n/a	n/a
31	NR2F2	chr20:23900588-23901560	MCF-7	breast:	n/a	n/a
32	NR2F2	chr20:23900473-23901457	MCF-7	breast:	n/a	n/a
33	POLR2A	chr20:23900442-23900704	MCF-7	breast:	n/a	n/a
34	POLR2A	chr20:23902297-23902499	HepG2	liver:	n/a	n/a
35	SIN3AK20	chr20:23900376-23902128	MCF-7	breast:	n/a	n/a
36	SIN3AK20	chr20:23907428-23908140	MCF-7	breast:	n/a	n/a
37	TCF7L2	chr20:23900684-23901077	MCF-7	breast:	n/a	n/a
38	USF1	chr20:23909409-23909672	SK-N-SH_RA	brain:	n/a	chr20:23909578-23909589
39	USF1	chr20:23909358-23909780	H1-hESC	embryonic stem cell:	n/a	chr20:23909578-23909589
40	USF1	chr20:23909420-23909740	K562	blood:	n/a	chr20:23909578-23909589
41	USF1	chr20:23909467-23909709	HepG2	liver:	n/a	chr20:23909578-23909589
42	USF1	chr20:23909474-23909699	GM12878	blood:	n/a	chr20:23909578-23909589
43	USF1	chr20:23909426-23909765	ECC-1	luminal epithelium:	n/a	chr20:23909578-23909589
44	USF1	chr20:23909450-23909752	HCT-116	colon:	n/a	chr20:23909578-23909589
45	USF1	chr20:23909435-23909708	ECC-1	luminal epithelium:	n/a	chr20:23909578-23909589
46	USF1	chr20:23909436-23909728	K562	blood:	n/a	chr20:23909578-23909589
47	USF1	chr20:23909431-23909686	H1-hESC	embryonic stem cell:	n/a	chr20:23909578-23909589
48	USF1	chr20:23909397-23909728	A549	lung:	n/a	chr20:23909578-23909589
49	USF1	chr20:23909461-23909683	SK-N-SH_RA	brain:	n/a	chr20:23909578-23909589
50	USF1	chr20:23909467-23909641	HepG2	liver:	n/a	chr20:23909578-23909589

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23895606..23897789-chr20:23899245..23901665,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CST5-1	chr20:23909251-23909558	NONHSAT079090
2	lnc-CST5-1	chr20:23904588-23904694	NONHSAT079090

Variant related genes	Relation type
CSTP1	TF binding region

Extended variants
information (count: 460 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:460 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529835644	chr20:23900071-23900072	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs546286073	chr20:23900094-23900095	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs373335037	chr20:23900111-23900112	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs559768425	chr20:23900203-23900204	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs145312012	chr20:23900216-23900217	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs73320892	chr20:23900221-23900222	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs6036575	chr20:23900240-23900241	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs151006286	chr20:23900255-23900256	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs538141907	chr20:23900320-23900321	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs565114933	chr20:23900327-23900328	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs139699616	chr20:23900346-23900347	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs189095196	chr20:23900360-23900361	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs556482594	chr20:23900399-23900400	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs534345528	chr20:23900406-23900407	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs181711888	chr20:23900497-23900498	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs149764156	chr20:23900498-23900499	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs539862517	chr20:23900502-23900503	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs145763033	chr20:23900520-23900521	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs575528082	chr20:23900533-23900534	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs140573025	chr20:23900573-23900574	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs113578029	chr20:23900611-23900612	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs370016589	chr20:23900612-23900613	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs6036576	chr20:23900637-23900638	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs554795709	chr20:23900639-23900640	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs377097224	chr20:23900642-23900643	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs574295357	chr20:23900765-23900766	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs540004970	chr20:23900793-23900794	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs559837350	chr20:23900811-23900812	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs532056901	chr20:23900823-23900824	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
30	rs186674126	chr20:23900828-23900829	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs371469616	chr20:23900850-23900851	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs559630118	chr20:23900866-23900867	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
33	rs73905806	chr20:23900883-23900884	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs532080566	chr20:23900896-23900897	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs562034064	chr20:23900900-23900901	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs530699020	chr20:23900912-23900913	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs548372643	chr20:23900924-23900925	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs563582760	chr20:23900935-23900936	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs1797042	chr20:23900945-23900946	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs146619620	chr20:23900967-23900968	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs112314010	chr20:23900982-23900983	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs539923006	chr20:23900983-23900984	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs141337596	chr20:23900986-23900987	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs189502076	chr20:23901081-23901082	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs535793747	chr20:23901087-23901088	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs554576104	chr20:23901126-23901127	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs11908279	chr20:23901136-23901137	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs373169932	chr20:23901165-23901166	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs540065855	chr20:23901190-23901191	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs553536081	chr20:23901205-23901206	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
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
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	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
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:143 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23897400-23903000	Enhancers	Fetal Muscle Trunk	muscle
2	chr20:23897400-23903200	Enhancers	Fetal Muscle Leg	muscle
3	chr20:23898600-23903200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr20:23899000-23902600	Enhancers	Fetal Thymus	thymus
5	chr20:23899400-23903400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr20:23899600-23900400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr20:23899600-23903000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr20:23899800-23900800	Enhancers	Lung	lung
9	chr20:23899800-23902000	Enhancers	Primary T cells from cord blood	blood
10	chr20:23899800-23902000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr20:23899800-23902200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr20:23899800-23902800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr20:23900000-23900400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:23900000-23901000	Enhancers	Brain Anterior Caudate	brain
15	chr20:23900000-23902000	Enhancers	Stomach Smooth Muscle	stomach
16	chr20:23900000-23902200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr20:23900000-23902400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:23900000-23902400	Enhancers	Esophagus	oesophagus
19	chr20:23900000-23902600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr20:23900000-23902800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:23900000-23902800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr20:23900200-23900600	Enhancers	Brain Angular Gyrus	brain
23	chr20:23900200-23901000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr20:23900200-23901200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr20:23900200-23901400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr20:23900200-23901800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:23900200-23901800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr20:23900200-23901800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:23900200-23901800	Enhancers	HMEC	breast
30	chr20:23900200-23902000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr20:23900200-23902000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr20:23900200-23902200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr20:23900200-23902200	Enhancers	HSMMtube	muscle
34	chr20:23900400-23900600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr20:23900400-23900600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr20:23900400-23900600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
37	chr20:23900400-23900600	Bivalent Enhancer	Left Ventricle	heart
38	chr20:23900400-23900600	Enhancers	Right Atrium	heart
39	chr20:23900400-23900800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr20:23900400-23901000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr20:23900400-23901000	Enhancers	Gastric	stomach
42	chr20:23900400-23901000	Enhancers	Pancreas	Pancrea
43	chr20:23900400-23901200	Enhancers	Brain Cingulate Gyrus	brain
44	chr20:23900400-23901200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr20:23900400-23901200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr20:23900400-23901200	Enhancers	Thymus	Thymus
47	chr20:23900400-23901400	Enhancers	NHEK	skin
48	chr20:23900400-23901600	Enhancers	Osteobl	bone
49	chr20:23900400-23902000	Enhancers	Placenta	Placenta
50	chr20:23900400-23902200	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links