Variant report

Variant	nsv964025
Chromosome Location	chr4:3535969-3544867
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:63)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:63 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr4:3538736-3538904	GM12878	blood:	n/a	n/a
2	CTCF	chr4:3536561-3536627	Kidney_OC	kidney:	n/a	n/a
3	CTCF	chr4:3542526-3542604	GM10266	blood:	n/a	n/a
4	CTCF	chr4:3543557-3543614	Lung_OC	lung:	n/a	n/a
5	CTCF	chr4:3543428-3543512	GM13976	blood:	n/a	n/a
6	CTCF	chr4:3537323-3537378	GM13976	blood:	n/a	n/a
7	EP300	chr4:3538783-3538963	GM12878	blood:	n/a	n/a
8	EP300	chr4:3538610-3539081	GM12878	blood:	n/a	n/a
9	EP300	chr4:3543980-3544761	GM12878	blood:	n/a	n/a
10	FOSL2	chr4:3538691-3539178	HepG2	liver:	n/a	chr4:3539054-3539065
11	FOSL2	chr4:3538727-3539036	HepG2	liver:	n/a	n/a
12	GABPA	chr4:3538749-3538863	Hela-S3	cervix:	n/a	n/a
13	GABPA	chr4:3544049-3544782	Hela-S3	cervix:	n/a	n/a
14	GABPA	chr4:3538691-3539052	Hela-S3	cervix:	n/a	n/a
15	GATA2	chr4:3542389-3542660	K562	blood:	n/a	n/a
16	HEY1	chr4:3538759-3539035	K562	blood:	n/a	n/a
17	IRF4	chr4:3543918-3544829	GM12878	blood:	n/a	n/a
18	IRF4	chr4:3538696-3539081	GM12878	blood:	n/a	n/a
19	IRF4	chr4:3538765-3539092	GM12878	blood:	n/a	n/a
20	JUND	chr4:3538790-3538983	HepG2	liver:	n/a	n/a
21	JUND	chr4:3538804-3538941	HepG2	liver:	n/a	n/a
22	KAP1	chr4:3539310-3539502	U2OS	brain:	n/a	n/a
23	KAP1	chr4:3539476-3539488	HEK293	kidney:	n/a	n/a
24	NR2F2	chr4:3539562-3539983	K562	blood:	n/a	n/a
25	NR2F2	chr4:3542336-3542649	K562	blood:	n/a	n/a
26	NR2F2	chr4:3539535-3539992	K562	blood:	n/a	n/a
27	PAX5	chr4:3541149-3541472	GM12878	blood:	n/a	n/a
28	PAX5	chr4:3542474-3543205	GM12878	blood:	n/a	n/a
29	PAX5	chr4:3541197-3541406	GM12878	blood:	n/a	n/a
30	PAX5	chr4:3537677-3537904	GM12878	blood:	n/a	n/a
31	PAX5	chr4:3543928-3545116	GM12878	blood:	n/a	n/a
32	PAX5	chr4:3543975-3544795	GM12878	blood:	n/a	n/a
33	PAX5	chr4:3543880-3544777	GM12878	blood:	n/a	n/a
34	PAX5	chr4:3538693-3539069	GM12878	blood:	n/a	n/a
35	PAX5	chr4:3538789-3539148	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:3543227-3543587	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:3538768-3538974	Hela-S3	cervix:	n/a	n/a
38	POU2F2	chr4:3538665-3539194	GM12878	blood:	n/a	n/a
39	POU2F2	chr4:3542917-3543484	GM12878	blood:	n/a	n/a
40	POU2F2	chr4:3544003-3544815	GM12878	blood:	n/a	n/a
41	RXRA	chr4:3542764-3543116	HepG2	liver:	n/a	n/a
42	SETDB1	chr4:3539295-3539510	U2OS	brain:	n/a	n/a
43	SIN3AK20	chr4:3538845-3538960	HepG2	liver:	n/a	n/a
44	SIN3AK20	chr4:3543922-3544049	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr4:3544062-3544725	HepG2	liver:	n/a	n/a
46	SIX5	chr4:3538732-3539225	K562	blood:	n/a	n/a
47	SIX5	chr4:3538840-3539151	GM12878	blood:	n/a	n/a
48	SIX5	chr4:3542875-3543136	K562	blood:	n/a	n/a
49	SP1	chr4:3544517-3544785	GM12878	blood:	n/a	n/a
50	SP1	chr4:3538674-3538940	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3536906-3536956	Caco-2	colon:	n/a
2	chr4:3536906-3536956	HCM	heart:	n/a
3	chr4:3536906-3536956	HCT-116	colon:	n/a
4	chr4:3536906-3536956	HAEpiC	amniotic membrane:	n/a
5	chr4:3536906-3536956	MCF-7	breast:	n/a
6	chr4:3536906-3536956	PANC-1	pancreas:	n/a
7	chr4:3536906-3536956	HPAEpiC	pulmonary alveolar:	n/a
8	chr4:3536906-3536956	HL-60	blood:	n/a
9	chr4:3536906-3536956	Hela-S3	cervix:	n/a
10	chr4:3536906-3536956	Hepatocyte	liver:	n/a
11	chr4:3536906-3536956	HCF	heart:	n/a
12	chr4:3536906-3536956	AG04449	skin:	fetal
13	chr4:3536906-3536956	GM12891	blood:	n/a
14	chr4:3536906-3536956	HRPEpiC	eye:	n/a
15	chr4:3536906-3536956	NHDF-neo	bronchial:	n/a
16	chr4:3536906-3536956	HIPEpiC	eye:	n/a
17	chr4:3536906-3536956	T-47D	breast:	n/a
18	chr4:3536906-3536956	NH-A	brain:	n/a
19	chr4:3536906-3536956	K562	blood:	n/a
20	chr4:3536906-3536956	RPTEC	kidney:	n/a
21	chr4:3536906-3536956	CMK	blood:	n/a
22	chr4:3536906-3536956	HEEpiC	esophagus:	n/a
23	chr4:3536906-3536956	AG04450	lung:	fetal
24	chr4:3536906-3536956	AG09309	skin:	n/a
25	chr4:3536906-3536956	PrEC	prostate:	n/a
26	chr4:3536906-3536956	GM06990	blood:	n/a
27	chr4:3536906-3536956	HMEC	breast:	n/a
28	chr4:3536906-3536956	LNCaP	prostate:	n/a
29	chr4:3536906-3536956	ECC-1	luminal epithelium:	n/a
30	chr4:3536906-3536956	HNPCEpiC	eye:	n/a
31	chr4:3536906-3536956	GM19239	blood:	n/a
32	chr4:3536906-3536956	HUVEC	blood vessel:	n/a
33	chr4:3536906-3536956	GM12878	blood:	n/a
34	chr4:3536906-3536956	SK-N-SH	brain:	n/a
35	chr4:3536906-3536956	NB4	blood:	n/a
36	chr4:3536906-3536956	ovcar-3	ovarian:	n/a
37	chr4:3536906-3536956	MCF10A-Er-Src	breast:	n/a
38	chr4:3536906-3536956	GM12892	blood:	n/a
39	chr4:3536906-3536956	U87	brain:	n/a
40	chr4:3536906-3536956	NHBE	bronchial:	n/a
41	chr4:3536906-3536956	Jurkat	blood:	n/a
42	chr4:3536906-3536956	SAEC	small airway:	n/a
43	chr4:3536906-3536956	NT2-D1	testis:	n/a
44	chr4:3536906-3536956	SKMC	muscle:	n/a
45	chr4:3536906-3536956	H1-hESC	embryonic stem cell:	embryo
46	chr4:3536906-3536956	AG10803	skin:	n/a
47	chr4:3536906-3536956	PFSK-1	brain:	n/a
48	chr4:3536906-3536956	BE2_C	brain:	n/a
49	chr4:3536906-3536956	BJ	skin:	n/a
50	chr4:3536906-3536956	SK-N-SH_RA	brain:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3532686..3534345-chr4:3544776..3546772,2	MCF-7	breast:
2	chr4:3485927..3488368-chr4:3533732..3536345,3	MCF-7	breast:

No data

Variant related genes	Relation type
LRPAP1	TF binding region
ENSG00000270090	TF binding region
LRPAP1	CpG island
ENSG00000270090	CpG island
ENSG00000163956	chromatin interactions
ENSG00000175920	chromatin interactions

Extended variants
information (count: 185 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:185 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs189133058	chr4:3535994-3535995	Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs193299792	chr4:3535997-3535998	Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs7672287	chr4:3536002-3536003	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs558964897	chr4:3536029-3536030	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs528071656	chr4:3536034-3536035	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs368838714	chr4:3536070-3536071	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs563931147	chr4:3536095-3536096	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs2073502	chr4:3536112-3536113	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs544263291	chr4:3536118-3536119	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs151134666	chr4:3536146-3536147	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs531024789	chr4:3536161-3536162	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs185471753	chr4:3536162-3536163	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs2073503	chr4:3536176-3536177	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs536906747	chr4:3536180-3536181	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs200994626	chr4:3536193-3536194	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs566902014	chr4:3536240-3536241	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs539022969	chr4:3536253-3536254	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs367708522	chr4:3536265-3536266	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs1794431	chr4:3536329-3536330	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs10937932	chr4:3536505-3536506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs189209774	chr4:3536506-3536507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs374980323	chr4:3536514-3536515	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs369180359	chr4:3536531-3536532	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs573746539	chr4:3536538-3536539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs181654264	chr4:3536564-3536565	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs559199685	chr4:3536573-3536574	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs572539456	chr4:3536574-3536575	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs62272719	chr4:3536575-3536576	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs564658160	chr4:3536576-3536577	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs3108671	chr4:3536588-3536589	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs530579413	chr4:3536629-3536630	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs550901662	chr4:3536635-3536636	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs561567910	chr4:3536637-3536638	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs530213909	chr4:3536693-3536694	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs185990343	chr4:3536707-3536708	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs149890013	chr4:3536723-3536724	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs59393260	chr4:3536732-3536733	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs201400261	chr4:3536823-3536824	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs375154543	chr4:3536829-3536830	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs199610860	chr4:3536830-3536831	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs552559078	chr4:3536844-3536845	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs11736573	chr4:3536882-3536883	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs76961379	chr4:3536889-3536890	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs149593055	chr4:3536895-3536896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs181126540	chr4:3536942-3536943	Weak transcription	CpG island	1 gene(s)	Overlapped CNVs	n/a
46	rs373940515	chr4:3536962-3536963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs144876544	chr4:3537000-3537001	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs186261495	chr4:3537040-3537041	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs376896377	chr4:3537053-3537054	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs190685700	chr4:3537054-3537055	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Ependymoma	20639864	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3535000-3536000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
2	chr4:3535000-3536800	Weak transcription	Lung	lung
3	chr4:3535400-3536000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:3535400-3537000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:3537000-3537200	Enhancers	Lung	lung
6	chr4:3537000-3537400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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