Variant report

Variant	nsv972293
Chromosome Location	chr9:6633517-6640353
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	chr9:6640333-6640626	HepG2	liver:	n/a	n/a
2	CEBPB	chr9:6637416-6637577	MCF-7	breast:	n/a	chr9:6637505-6637516
3	CEBPB	chr9:6640287-6640673	HepG2	liver:	n/a	chr9:6640489-6640498
4	CEBPB	chr9:6637458-6637625	Hela-S3	cervix:	n/a	chr9:6637505-6637516
5	CEBPB	chr9:6637423-6637632	HepG2	liver:	n/a	chr9:6637505-6637516
6	CEBPB	chr9:6640280-6640653	HepG2	liver:	n/a	chr9:6640489-6640498
7	CTCF	chr9:6639104-6639207	MCF-7	breast:	n/a	n/a
8	CTCF	chr9:6639060-6639224	A549	lung:	n/a	n/a
9	CTCF	chr9:6638980-6639130	HepG2	liver:	n/a	n/a
10	CTCF	chr9:6639127-6639174	HepG2	liver:	n/a	n/a
11	CTCF	chr9:6639022-6639188	HepG2	liver:	n/a	n/a
12	CTCF	chr9:6639179-6639224	LNCaP	prostate:	n/a	n/a
13	CTCF	chr9:6639347-6639398	K562	blood:	n/a	n/a
14	E2F4	chr9:6634438-6634750	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr9:6634519-6634748	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr9:6634505-6634695	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr9:6640327-6640727	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr9:6634495-6634738	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr9:6640335-6640663	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr9:6640329-6640669	MCF10A-Er-Src	breast:	n/a	n/a
21	FOXA2	chr9:6640338-6640595	HepG2	liver:	n/a	n/a
22	FOXA2	chr9:6639342-6639532	HepG2	liver:	n/a	n/a
23	GATA2	chr9:6635087-6635413	SH-SY5Y	brain:	n/a	chr9:6635240-6635247 chr9:6635240-6635247 chr9:6635334-6635343 chr9:6635240-6635247
24	GATA3	chr9:6634952-6635446	MCF-7	breast:	n/a	chr9:6635240-6635247 chr9:6635240-6635247 chr9:6635334-6635343 chr9:6635240-6635247
25	GATA3	chr9:6635078-6635398	T-47D	breast:	n/a	chr9:6635240-6635247 chr9:6635240-6635247 chr9:6635334-6635343 chr9:6635240-6635247
26	GATA3	chr9:6635125-6635415	SH-SY5Y	brain:	n/a	chr9:6635240-6635247 chr9:6635240-6635247 chr9:6635334-6635343 chr9:6635240-6635247
27	GATA3	chr9:6639711-6640027	T-47D	breast:	n/a	n/a
28	GATA3	chr9:6639740-6640049	T-47D	breast:	n/a	n/a
29	GATA3	chr9:6639830-6639980	SH-SY5Y	brain:	n/a	n/a
30	MAFK	chr9:6634568-6634766	K562	blood:	n/a	n/a
31	MEF2A	chr9:6639695-6640026	GM12878	blood:	n/a	n/a
32	MTA3	chr9:6632363-6633621	GM12878	blood:	n/a	n/a
33	MYC	chr9:6634514-6634695	MCF10A-Er-Src	breast:	n/a	n/a
34	MYC	chr9:6639947-6640140	MCF10A-Er-Src	breast:	n/a	n/a
35	MYC	chr9:6634627-6634719	MCF10A-Er-Src	breast:	n/a	n/a
36	PBX3	chr9:6633463-6633658	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:6636564-6636681	HepG2	liver:	n/a	n/a
38	POLR2A	chr9:6640200-6640370	HepG2	liver:	n/a	n/a
39	POLR2A	chr9:6640281-6640544	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr9:6633706-6633815	HepG2	liver:	n/a	n/a
41	POLR2A	chr9:6636800-6636821	HepG2	liver:	n/a	n/a
42	RAD21	chr9:6638956-6639359	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr9:6639092-6639292	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr9:6639040-6639247	H1-hESC	embryonic stem cell:	n/a	n/a
45	STAT3	chr9:6639754-6639954	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT3	chr9:6634452-6634765	MCF10A-Er-Src	breast:	n/a	chr9:6634613-6634624
47	STAT3	chr9:6634426-6634791	MCF10A-Er-Src	breast:	n/a	chr9:6634613-6634624
48	STAT3	chr9:6634452-6634766	MCF10A-Er-Src	breast:	n/a	chr9:6634613-6634624
49	STAT3	chr9:6640276-6640673	MCF10A-Er-Src	breast:	n/a	chr9:6640489-6640497
50	STAT3	chr9:6634453-6634750	MCF10A-Er-Src	breast:	n/a	chr9:6634613-6634624

No.	Distal block	Cell Line	Cell type
1	chr9:6639721..6642651-chr9:6680043..6682884,2	MCF-7	breast:
2	chr9:6627812..6629680-chr9:6632614..6635740,3	MCF-7	breast:
3	chr9:6639393..6643031-chr9:6644244..6646064,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206147	TF binding region
ENSG00000236924	chromatin interactions
ENSG00000178445	chromatin interactions

Extended variants
information (count: 397 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:397 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs549131088	chr9:6633529-6633530	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs567467188	chr9:6633539-6633540	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs534954242	chr9:6633542-6633543	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs546469971	chr9:6633617-6633618	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs147596333	chr9:6633653-6633654	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs72695582	chr9:6633664-6633665	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs181952340	chr9:6633689-6633690	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs575253206	chr9:6633700-6633701	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs186549923	chr9:6633718-6633719	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs545223526	chr9:6633729-6633730	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs555178951	chr9:6633737-6633738	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs555720407	chr9:6633766-6633767	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs377111094	chr9:6633820-6633821	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs113928846	chr9:6633853-6633854	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance
15	rs111875513	chr9:6633869-6633870	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance
16	rs138601777	chr9:6633893-6633894	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs7853194	chr9:6633922-6633923	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs544568851	chr9:6633930-6633931	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs562990002	chr9:6633942-6633943	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs530177877	chr9:6633988-6633989	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs368870545	chr9:6633993-6633994	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs548380117	chr9:6634020-6634021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs561166530	chr9:6634031-6634032	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs112401513	chr9:6634051-6634052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs377753166	chr9:6634080-6634081	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs113306420	chr9:6634112-6634113	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs571169497	chr9:6634119-6634120	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs531983912	chr9:6634126-6634127	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs550133248	chr9:6634161-6634162	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs568744946	chr9:6634193-6634194	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs369995449	chr9:6634199-6634200	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs536374235	chr9:6634259-6634260	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs554363583	chr9:6634290-6634291	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs540341224	chr9:6634307-6634308	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs567092608	chr9:6634310-6634311	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs534347609	chr9:6634320-6634321	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs148297126	chr9:6634338-6634339	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs565295555	chr9:6634356-6634357	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs544630397	chr9:6634372-6634373	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs556558143	chr9:6634386-6634387	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs575692469	chr9:6634390-6634391	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs542357720	chr9:6634418-6634419	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs560375046	chr9:6634433-6634434	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs369824302	chr9:6634440-6634441	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs373758330	chr9:6634483-6634484	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs10117019	chr9:6634512-6634513	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs532240975	chr9:6634522-6634523	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs368084515	chr9:6634525-6634526	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs371811317	chr9:6634526-6634527	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs375156048	chr9:6634527-6634528	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:106)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Developmental delay	21147756	CNVD
Lung cancer	18438408	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Metastatic melanoma	18483359	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	16783165	CNVD
Dyslexia	22102821	CNVD
T-cell lymphomas	22341440	CNVD
Breast cancer	22522925	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Ependymoma	20639864	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Schizophrenia	21346763	CNVD

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6628000-6633600	Enhancers	NHEK	skin
2	chr9:6629000-6634600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:6629200-6640200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:6630400-6633600	Enhancers	Primary B cells from peripheral blood	blood
5	chr9:6631400-6641200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:6632400-6633600	Enhancers	Fetal Kidney	kidney
7	chr9:6632400-6633600	Flanking Active TSS	GM12878-XiMat	blood
8	chr9:6632600-6633600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:6632600-6634400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:6632800-6633600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:6632800-6633600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr9:6632800-6633600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:6632800-6633600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr9:6632800-6633600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr9:6632800-6633800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:6633000-6633600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr9:6633000-6634200	Weak transcription	Placenta	Placenta
18	chr9:6633200-6633600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr9:6633200-6634400	Enhancers	HepG2	liver
20	chr9:6633200-6635400	Weak transcription	Fetal Intestine Large	intestine
21	chr9:6633200-6640400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr9:6633400-6633600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:6633400-6633800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr9:6633400-6635000	Weak transcription	Liver	Liver
25	chr9:6633400-6635400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:6633400-6639800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr9:6633600-6634200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:6633600-6634400	Enhancers	GM12878-XiMat	blood
29	chr9:6633600-6634600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:6633600-6639800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:6633600-6640000	Weak transcription	Fetal Kidney	kidney
32	chr9:6633600-6641000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:6633600-6641000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:6633600-6641200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr9:6633600-6641200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:6633600-6642600	Weak transcription	NHEK	skin
37	chr9:6633600-6643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:6633800-6634800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:6633800-6644200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:6634200-6635800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:6634200-6637800	Enhancers	Placenta	Placenta
42	chr9:6634400-6636200	Weak transcription	GM12878-XiMat	blood
43	chr9:6634400-6639000	Weak transcription	HepG2	liver
44	chr9:6634600-6635800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:6634600-6637000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:6634800-6635200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr9:6634800-6635200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:6634800-6635400	Enhancers	K562	blood
49	chr9:6634800-6635800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:6635000-6635600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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