Variant report

Variant	nsv585733
Chromosome Location	chr20:24410195-24431225
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	BCL3	chr20:24415916-24416156	GM12878	blood:	n/a	n/a
2	BCL3	chr20:24415845-24416289	GM12878	blood:	n/a	n/a
3	CEBPB	chr20:24413312-24413524	A549	lung:	n/a	n/a
4	CEBPB	chr20:24413325-24413519	HepG2	liver:	n/a	n/a
5	CEBPB	chr20:24429436-24429573	A549	lung:	n/a	n/a
6	CHD2	chr20:24426201-24426353	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr20:24424019-24424652	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr20:24423614-24425184	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr20:24428948-24429051	MCF-7	breast:	n/a	chr20:24428991-24429012
10	CTCF	chr20:24428940-24429033	GM12878	blood:	n/a	chr20:24428991-24429012
11	CTCF	chr20:24428911-24429092	H1-hESC	embryonic stem cell:	n/a	chr20:24428991-24429012
12	CTCF	chr20:24412740-24412890	HCPEpiC	choroid plexus:	n/a	n/a
13	CTCF	chr20:24412603-24412891	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr20:24412760-24412910	HBMEC	blood vessel:	n/a	n/a
15	CTCF	chr20:24428900-24429050	WERI-Rb-1	eye:	n/a	chr20:24428991-24429012
16	CTCF	chr20:24428911-24429108	H1-hESC	embryonic stem cell:	n/a	chr20:24428991-24429012
17	CTCF	chr20:24412720-24412870	HEK293	kidney:	n/a	n/a
18	CTCF	chr20:24412700-24412850	HepG2	liver:	n/a	n/a
19	CTCF	chr20:24428932-24429038	Pancreas_OC	pancreas:	n/a	chr20:24428991-24429012
20	CTCF	chr20:24428940-24429090	GM12872	blood:	n/a	chr20:24428991-24429012
21	CTCF	chr20:24412680-24412830	BE2_C	brain:	n/a	n/a
22	CTCF	chr20:24412700-24412850	WERI-Rb-1	eye:	n/a	n/a
23	CTCF	chr20:24414479-24414482	GM10248	blood:	n/a	n/a
24	CTCF	chr20:24414494-24414507	GM10248	blood:	n/a	n/a
25	CTCF	chr20:24412820-24412970	GM12871	blood:	n/a	n/a
26	CTCF	chr20:24412620-24412770	SAEC	small airway:	n/a	n/a
27	CTCF	chr20:24412660-24412810	GM12871	blood:	n/a	n/a
28	CTCF	chr20:24428983-24428999	MCF-7	breast:	n/a	n/a
29	CTCF	chr20:24428880-24429030	HCPEpiC	choroid plexus:	n/a	chr20:24428991-24429012
30	CTCF	chr20:24430641-24430720	Spleen_OC	spleen:	n/a	n/a
31	CTCF	chr20:24412580-24412730	RPTEC	kidney:	n/a	n/a
32	CTCF	chr20:24428880-24429030	GM06990	blood:	n/a	chr20:24428991-24429012
33	CTCF	chr20:24412720-24412870	GM12873	blood:	n/a	n/a
34	CTCF	chr20:24423760-24423910	GM12869	blood:	n/a	n/a
35	CTCF	chr20:24412671-24412928	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr20:24428940-24429090	HRE	kidney:	n/a	chr20:24428991-24429012
37	CTCF	chr20:24414463-24414478	GM10248	blood:	n/a	n/a
38	CTCF	chr20:24412640-24412790	GM06990	blood:	n/a	n/a
39	CTCF	chr20:24412680-24412830	HepG2	liver:	n/a	n/a
40	CTCF	chr20:24412840-24412990	Caco-2	colon:	n/a	n/a
41	CTCF	chr20:24428947-24429047	MCF-7	breast:	n/a	chr20:24428991-24429012
42	CTCF	chr20:24428979-24428981	MCF-7	breast:	n/a	n/a
43	CTCF	chr20:24412660-24412810	GM12869	blood:	n/a	n/a
44	CTCF	chr20:24412752-24412763	MCF-7	breast:	n/a	n/a
45	CTCF	chr20:24412640-24412790	HA-sp	spinal cord:	n/a	n/a
46	CTCF	chr20:24428969-24429033	GM12891	blood:	n/a	chr20:24428991-24429012
47	CTCF	chr20:24428960-24429110	GM12878	blood:	n/a	chr20:24428991-24429012
48	CTCF	chr20:24412520-24412670	A549	lung:	n/a	n/a
49	CTCF	chr20:24428939-24429050	GM12892	blood:	n/a	chr20:24428991-24429012
50	CTCF	chr20:24412700-24412850	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24420874..24424389-chr20:24442088..24445319,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNDIG1-5	chr20:24426027-24426950	NONHSAT079109

Variant related genes	Relation type
GAPDHP53	TF binding region

Extended variants
information (count: 1035 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:1035 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6114718	chr20:24410195-24410196	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs545594610	chr20:24410207-24410208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs562299858	chr20:24410231-24410232	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs180923825	chr20:24410276-24410277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs559790421	chr20:24410279-24410280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs145467130	chr20:24410305-24410306	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs530368283	chr20:24410326-24410327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs73339909	chr20:24410350-24410351	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs376379015	chr20:24410395-24410396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs562003340	chr20:24410412-24410413	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs530083593	chr20:24410472-24410473	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs546971356	chr20:24410473-24410474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs115798114	chr20:24410510-24410511	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs185946269	chr20:24410527-24410528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs140320186	chr20:24410532-24410533	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs552821567	chr20:24410564-24410565	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs369980241	chr20:24410607-24410608	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs77403509	chr20:24410617-24410618	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs73610800	chr20:24410618-24410619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs6106878	chr20:24410664-24410665	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs144232456	chr20:24410748-24410749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs568726716	chr20:24410749-24410750	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs114828818	chr20:24410789-24410790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs117033997	chr20:24410790-24410791	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs6049676	chr20:24410791-24410792	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs539109117	chr20:24410807-24410808	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs6036779	chr20:24410811-24410812	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs34581494	chr20:24410818-24410819	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs114340420	chr20:24410819-24410820	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs148439499	chr20:24410826-24410827	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs112623840	chr20:24410843-24410844	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs572259378	chr20:24410846-24410847	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs540279539	chr20:24410885-24410886	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs560505591	chr20:24410886-24410887	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs532676329	chr20:24410892-24410893	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs150984448	chr20:24410928-24410929	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs562955230	chr20:24410947-24410948	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs531983075	chr20:24410960-24410961	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs548758480	chr20:24410994-24410995	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs568662276	chr20:24410995-24410996	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs527943279	chr20:24411040-24411041	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs547090574	chr20:24411041-24411042	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs6049677	chr20:24411057-24411058	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs74173645	chr20:24411066-24411067	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs6083521	chr20:24411070-24411071	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs6036780	chr20:24411080-24411081	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs569411476	chr20:24411091-24411092	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs576336995	chr20:24411099-24411100	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs535295874	chr20:24411125-24411126	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs555499554	chr20:24411193-24411194	Weak transcription Enhancers	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
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
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:208 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24401200-24412400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:24403400-24411400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:24407200-24412600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:24407400-24411600	Weak transcription	Fetal Stomach	stomach
5	chr20:24407600-24410800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr20:24407600-24413000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr20:24410800-24413600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr20:24411200-24412400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:24411400-24411600	Bivalent Enhancer	Lung	lung
10	chr20:24411400-24411800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:24411400-24411800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr20:24411400-24412400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr20:24411600-24412200	Enhancers	Fetal Stomach	stomach
14	chr20:24411600-24412600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr20:24411600-24412800	Enhancers	Gastric	stomach
16	chr20:24411600-24412800	Enhancers	Lung	lung
17	chr20:24411800-24412600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr20:24411800-24412600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr20:24411800-24412800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr20:24411800-24413600	Enhancers	Stomach Mucosa	stomach
21	chr20:24412200-24412600	Bivalent Enhancer	Fetal Stomach	stomach
22	chr20:24412200-24413600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr20:24412400-24412800	Enhancers	Duodenum Mucosa	Duodenum
24	chr20:24412400-24413000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:24412400-24413400	Enhancers	Fetal Intestine Small	intestine
26	chr20:24412400-24413400	Enhancers	Fetal Lung	lung
27	chr20:24412400-24413400	Enhancers	HepG2	liver
28	chr20:24412400-24413600	Enhancers	Fetal Intestine Large	intestine
29	chr20:24412400-24423400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr20:24412600-24412800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr20:24412600-24413000	Enhancers	Fetal Stomach	stomach
32	chr20:24412600-24413200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr20:24412600-24423600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr20:24412800-24413000	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr20:24412800-24413000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
36	chr20:24412800-24413200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr20:24412800-24417000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr20:24413000-24413400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr20:24413000-24413800	Enhancers	Fetal Kidney	kidney
40	chr20:24413000-24414200	Enhancers	Duodenum Mucosa	Duodenum
41	chr20:24413000-24416600	Weak transcription	Fetal Stomach	stomach
42	chr20:24413400-24416800	Weak transcription	Fetal Intestine Small	intestine
43	chr20:24413600-24414000	Weak transcription	Fetal Intestine Large	intestine
44	chr20:24413600-24417400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr20:24413800-24417000	Weak transcription	Fetal Kidney	kidney
46	chr20:24414000-24414200	Enhancers	Fetal Intestine Large	intestine
47	chr20:24414200-24416400	Weak transcription	Fetal Intestine Large	intestine
48	chr20:24415800-24418600	Enhancers	Fetal Muscle Leg	muscle
49	chr20:24416000-24419200	Enhancers	Fetal Brain Male	brain
50	chr20:24416200-24416400	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links