Variant report

Variant	nsv1014215
Chromosome Location	chr4:88192854-88225673
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	ARID3A	chr4:88195615-88195678	HepG2	liver:	n/a	n/a
2	ARID3A	chr4:88196507-88196704	HepG2	liver:	n/a	n/a
3	ARID3A	chr4:88199339-88199978	HepG2	liver:	n/a	n/a
4	ATF3	chr4:88199339-88199930	HepG2	liver:	n/a	n/a
5	ATF3	chr4:88223744-88223892	K562	blood:	n/a	n/a
6	ATF3	chr4:88199549-88199769	HepG2	liver:	n/a	n/a
7	BHLHE40	chr4:88199507-88199750	HepG2	liver:	n/a	n/a
8	BHLHE40	chr4:88199420-88199720	HepG2	liver:	n/a	n/a
9	BHLHE40	chr4:88199328-88199876	HepG2	liver:	n/a	n/a
10	CBX3	chr4:88207920-88208188	K562	blood:	n/a	n/a
11	CBX3	chr4:88215016-88215405	K562	blood:	n/a	n/a
12	CEBPB	chr4:88222879-88223179	HepG2	liver:	n/a	chr4:88223035-88223046
13	CEBPB	chr4:88222901-88223173	A549	lung:	n/a	chr4:88223035-88223046
14	CEBPB	chr4:88222884-88223200	IMR90	lung:	n/a	chr4:88223035-88223046
15	CEBPB	chr4:88197413-88197511	HepG2	liver:	n/a	chr4:88197420-88197431
16	CEBPB	chr4:88199523-88199974	HepG2	liver:	n/a	n/a
17	CEBPB	chr4:88222910-88223189	K562	blood:	n/a	chr4:88223035-88223046
18	CEBPB	chr4:88195585-88195771	HepG2	liver:	n/a	n/a
19	CTCF	chr4:88222500-88222650	GM12873	blood:	n/a	n/a
20	CTCF	chr4:88213449-88213554	Lung_OC	lung:	n/a	n/a
21	CTCF	chr4:88207876-88207941	GM13976	blood:	n/a	n/a
22	CUX1	chr4:88202373-88202519	K562	blood:	n/a	n/a
23	E2F4	chr4:88195030-88195185	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F4	chr4:88216610-88216698	MCF10A-Er-Src	breast:	n/a	n/a
25	E2F4	chr4:88224694-88224894	MCF10A-Er-Src	breast:	n/a	n/a
26	ELF1	chr4:88202056-88202492	HCT-116	colon:	n/a	n/a
27	ELF1	chr4:88201995-88202321	K562	blood:	n/a	n/a
28	ELF1	chr4:88202116-88202347	HepG2	liver:	n/a	n/a
29	EP300	chr4:88199482-88199897	HepG2	liver:	n/a	n/a
30	EP300	chr4:88199359-88199988	HepG2	liver:	n/a	n/a
31	EP300	chr4:88199285-88200003	HepG2	liver:	n/a	n/a
32	FOS	chr4:88223072-88223076	MCF10A-Er-Src	breast:	n/a	n/a
33	FOSL2	chr4:88199486-88199887	HepG2	liver:	n/a	n/a
34	FOXA1	chr4:88196594-88196931	HepG2	liver:	n/a	chr4:88196705-88196717
35	FOXA1	chr4:88196427-88196873	HepG2	liver:	n/a	chr4:88196705-88196717
36	FOXA1	chr4:88199439-88199951	HepG2	liver:	n/a	chr4:88199711-88199723
37	FOXA1	chr4:88199330-88199997	HepG2	liver:	n/a	chr4:88199711-88199723 chr4:88199421-88199433 chr4:88199412-88199424
38	FOXA1	chr4:88195492-88195850	HepG2	liver:	n/a	n/a
39	FOXA1	chr4:88196533-88196786	T-47D	breast:	n/a	chr4:88196705-88196717
40	FOXA1	chr4:88199420-88199956	HepG2	liver:	n/a	chr4:88199711-88199723 chr4:88199421-88199433
41	FOXA1	chr4:88196402-88196939	HepG2	liver:	n/a	chr4:88196705-88196717
42	FOXA1	chr4:88196500-88196810	HepG2	liver:	n/a	chr4:88196705-88196717
43	FOXA1	chr4:88199326-88200021	HepG2	liver:	n/a	chr4:88199711-88199723 chr4:88199421-88199433 chr4:88199412-88199424
44	FOXA1	chr4:88219466-88219788	T-47D	breast:	n/a	n/a
45	FOXA2	chr4:88199420-88199979	HepG2	liver:	n/a	chr4:88199711-88199723 chr4:88199421-88199433
46	FOXA2	chr4:88199052-88200107	HepG2	liver:	n/a	chr4:88199711-88199723 chr4:88199421-88199433 chr4:88199412-88199424
47	FOXA2	chr4:88196557-88196871	HepG2	liver:	n/a	chr4:88196705-88196717
48	FOXM1	chr4:88225661-88226647	MCF-7	breast:	n/a	n/a
49	GATA3	chr4:88221013-88221290	T-47D	breast:	n/a	chr4:88221219-88221231
50	GATA3	chr4:88220983-88221306	MCF-7	breast:	n/a	chr4:88221219-88221231

No.	Distal block	Cell Line	Cell type
1	chr4:88224415..88227242-chr4:88231505..88233396,2	K562	blood:
2	chr4:88216757..88219177-chr4:88220101..88221682,2	MCF-7	breast:
3	chr4:88216757..88219177-chr4:88220101..88221682,2	MCF-7	breast:
4	chr4:88132419..88135036-chr4:88191101..88193543,2	K562	blood:
5	chr4:88141337..88143545-chr4:88209433..88211061,2	MCF-7	breast:
6	chr4:88161337..88162947-chr4:88190418..88192890,2	K562	blood:
7	chr10:46970031..46970993-chr4:88194361..88194882,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AFF1-1	chr4:88198781-88198895	XLOC_003601
2	lnc-AFF1-1	chr4:88199776-88199855	XLOC_003601

miRNA name	Chromosome Location	mirBase accession
hsa-miR-5705	chr4:88221657-88221679	MIMAT0022499

Variant related genes	Relation type
ENSG00000250572	TF binding region
MIR5705	TF binding region
ENSG00000204176	chromatin interactions
ENSG00000145332	chromatin interactions

Extended variants
information (count: 807 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:807 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs577497366	chr4:88192855-88192856	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs541698155	chr4:88192879-88192880	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs144801828	chr4:88192880-88192881	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs574395328	chr4:88192889-88192890	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs541413893	chr4:88192915-88192916	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs563382572	chr4:88192998-88192999	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs112968889	chr4:88193007-88193008	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs115176484	chr4:88193073-88193074	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs576225478	chr4:88193125-88193126	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs190830464	chr4:88193204-88193205	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs564257671	chr4:88193238-88193239	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs368565874	chr4:88193284-88193285	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs372532921	chr4:88193304-88193305	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs528238146	chr4:88193324-88193325	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs546891749	chr4:88193356-88193357	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs139530689	chr4:88193380-88193381	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs145148235	chr4:88193392-88193393	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs543747187	chr4:88193402-88193403	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs200435131	chr4:88193445-88193446	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs199584712	chr4:88193446-88193447	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs67562357	chr4:88193447-88193448	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs35717638	chr4:88193448-88193449	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs569863205	chr4:88193475-88193476	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs183098953	chr4:88193482-88193483	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs371113339	chr4:88193572-88193573	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs112460963	chr4:88193573-88193574	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs544612912	chr4:88193602-88193603	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs562004342	chr4:88193623-88193624	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs534878762	chr4:88193660-88193661	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs551800890	chr4:88193664-88193665	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs575002413	chr4:88193692-88193693	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs147551749	chr4:88193707-88193708	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs574992734	chr4:88193714-88193715	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs6531967	chr4:88193728-88193729	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs141965762	chr4:88193758-88193759	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs575443859	chr4:88193780-88193781	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs545929756	chr4:88193819-88193820	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs111233137	chr4:88193820-88193821	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs563997353	chr4:88193963-88193964	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs144253060	chr4:88193992-88193993	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs193003047	chr4:88193997-88193998	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs182849445	chr4:88193998-88193999	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs151220161	chr4:88194001-88194002	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs140412561	chr4:88194002-88194003	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs150343780	chr4:88194004-88194005	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs530782699	chr4:88194030-88194031	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs552278156	chr4:88194068-88194069	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs59526367	chr4:88194071-88194072	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs187487947	chr4:88194074-88194075	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs553283147	chr4:88194094-88194095	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
Olfactory neuroblastoma	18408657	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Acute monocytic leukemia	16498392	CNVD
Multiple myeloma	16616336	CNVD
Esophageal adenocarcinoma	18820669	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	22522925	CNVD
Parkinson disease	20877625	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88192400-88193200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:88192400-88196000	Weak transcription	Liver	Liver
3	chr4:88192600-88193000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:88193000-88193400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:88193400-88193600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr4:88193400-88193600	Enhancers	HepG2	liver
7	chr4:88193400-88194400	Enhancers	Stomach Mucosa	stomach
8	chr4:88193600-88195400	Weak transcription	HepG2	liver
9	chr4:88194400-88196000	Weak transcription	Stomach Mucosa	stomach
10	chr4:88195400-88197000	Enhancers	HepG2	liver
11	chr4:88195800-88196400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:88196000-88196200	Enhancers	Fetal Intestine Large	intestine
13	chr4:88196000-88196400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:88196000-88196400	Enhancers	Liver	Liver
15	chr4:88196200-88196400	Enhancers	Stomach Mucosa	stomach
16	chr4:88196200-88196400	Bivalent Enhancer	NHDF-Ad	bronchial
17	chr4:88196200-88196600	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr4:88196400-88199200	Weak transcription	Liver	Liver
19	chr4:88197000-88198600	Weak transcription	HepG2	liver
20	chr4:88198600-88200800	Enhancers	HepG2	liver
21	chr4:88199200-88200200	Enhancers	Liver	Liver
22	chr4:88199600-88200000	Enhancers	Pancreas	Pancrea
23	chr4:88200200-88200400	Enhancers	Aorta	Aorta
24	chr4:88200200-88200600	Weak transcription	Liver	Liver
25	chr4:88200400-88201000	Weak transcription	Aorta	Aorta
26	chr4:88200600-88200800	Enhancers	Liver	Liver
27	chr4:88200800-88205200	Weak transcription	Liver	Liver
28	chr4:88205200-88205600	Enhancers	Liver	Liver
29	chr4:88205800-88206000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:88207800-88208400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:88208000-88208200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:88220800-88221400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:88221000-88221400	Enhancers	Liver	Liver
34	chr4:88221000-88221400	Enhancers	Fetal Lung	lung
35	chr4:88221400-88225400	Weak transcription	Liver	Liver
36	chr4:88221400-88225800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:88224000-88225600	Enhancers	Hela-S3	cervix
38	chr4:88225400-88237800	Strong transcription	Liver	Liver
39	chr4:88225600-88225800	Flanking Active TSS	Hela-S3	cervix
40	chr4:88225600-88225800	Enhancers	NHEK	skin

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