Variant report

Variant	nsv4341
Chromosome Location	chr4:55172085-55217655
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	ATF2	chr4:55181558-55182409	GM12878	blood:	n/a	n/a
2	ATF2	chr4:55181588-55182175	GM12878	blood:	n/a	n/a
3	BATF	chr4:55181674-55182115	GM12878	blood:	n/a	n/a
4	BATF	chr4:55181689-55182109	GM12878	blood:	n/a	n/a
5	BCL11A	chr4:55181702-55182144	GM12878	blood:	n/a	chr4:55181946-55181955
6	BCL11A	chr4:55181711-55182026	GM12878	blood:	n/a	chr4:55181946-55181955
7	BCL3	chr4:55181745-55182079	GM12878	blood:	n/a	chr4:55181946-55181955
8	BCLAF1	chr4:55181640-55182170	GM12878	blood:	n/a	chr4:55181946-55181955
9	BCLAF1	chr4:55181591-55182237	GM12878	blood:	n/a	chr4:55181946-55181955 chr4:55182172-55182181
10	BHLHE40	chr4:55188978-55189397	K562	blood:	n/a	n/a
11	BHLHE40	chr4:55192525-55192667	K562	blood:	n/a	n/a
12	BHLHE40	chr4:55181644-55182222	GM12878	blood:	n/a	n/a
13	CEBPB	chr4:55199981-55200082	H1-hESC	embryonic stem cell:	n/a	chr4:55200007-55200024
14	CEBPB	chr4:55185113-55185347	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPD	chr4:55179465-55179869	K562	blood:	n/a	n/a
16	CTCF	chr4:55204920-55205070	HBMEC	blood vessel:	n/a	n/a
17	CTCF	chr4:55188840-55188990	GM06990	blood:	n/a	n/a
18	CTCF	chr4:55185127-55185403	GM12878	blood:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
19	CTCF	chr4:55189043-55189322	K562	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
20	CTCF	chr4:55185180-55185330	Hela-S3	cervix:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
21	CTCF	chr4:55185200-55185350	HMEC	breast:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
22	CTCF	chr4:55185160-55185310	HAc	cerebellar:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
23	CTCF	chr4:55185200-55185350	HVMF	connective:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
24	CTCF	chr4:55189120-55189270	HMEC	breast:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
25	CTCF	chr4:55185180-55185330	K562	blood:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
26	CTCF	chr4:55189100-55189250	HRE	kidney:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
27	CTCF	chr4:55189037-55189294	H1-hESC	embryonic stem cell:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
28	CTCF	chr4:55189030-55189351	K562	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
29	CTCF	chr4:55189081-55189299	Kidney_OC	kidney:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
30	CTCF	chr4:55189100-55189250	HBMEC	blood vessel:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
31	CTCF	chr4:55189062-55189312	GM10266	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
32	CTCF	chr4:55189100-55189250	HMF	breast:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
33	CTCF	chr4:55189100-55189250	K562	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
34	CTCF	chr4:55185126-55185538	K562	blood:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
35	CTCF	chr4:55189022-55189380	A549	lung:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
36	CTCF	chr4:55185132-55185380	GM13977	blood:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
37	CTCF	chr4:55185180-55185330	GM12865	blood:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
38	CTCF	chr4:55189020-55189170	A549	lung:	n/a	n/a
39	CTCF	chr4:55185123-55185368	GM19238	blood:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
40	CTCF	chr4:55185200-55185350	MCF-7	breast:	n/a	chr4:55185255-55185276 chr4:55185256-55185269
41	CTCF	chr4:55189120-55189270	GM12866	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
42	CTCF	chr4:55189080-55189230	GM12865	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
43	CTCF	chr4:55189100-55189250	GM12865	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
44	CTCF	chr4:55189067-55189325	T-47D	breast:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
45	CTCF	chr4:55189120-55189270	GM12867	blood:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
46	CTCF	chr4:55172260-55172410	HCFaa	heart:	n/a	n/a
47	CTCF	chr4:55188974-55189402	HepG2	liver:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
48	CTCF	chr4:55184660-55184810	WI-38	lung:	n/a	n/a
49	CTCF	chr4:55189029-55189330	MCF-7	breast:	n/a	chr4:55189176-55189197 chr4:55189174-55189192
50	CTCF	chr4:55185200-55185350	Hela-S3	cervix:	n/a	chr4:55185255-55185276 chr4:55185256-55185269

No.	Distal block	Cell Line	Cell type
1	chr4:55188755..55189636-chr4:55299369..55300499,5	MCF-7	breast:
2	chr4:55188829..55189372-chr4:55706928..55707723,2	MCF-7	breast:
3	chr4:55189198..55189880-chr4:55837437..55838307,2	MCF-7	breast:
4	chr4:55188651..55189879-chr4:55299577..55300637,10	MCF-7	breast:
5	chr4:55214457..55216740-chr4:55222463..55224435,2	MCF-7	breast:
6	chr4:55199239..55202091-chr4:55236220..55238051,2	MCF-7	breast:
7	chr4:55184839..55185711-chr4:55827240..55827767,2	MCF-7	breast:
8	chr4:55188876..55189604-chr4:55241739..55242312,2	MCF-7	breast:
9	chr4:55184800..55185406-chr4:55706810..55707325,2	MCF-7	breast:
10	chr4:55184744..55185734-chr4:55306461..55307691,6	MCF-7	breast:
11	chr4:55188990..55189633-chr4:55827285..55828214,3	K562	blood:
12	chr4:55188742..55189647-chr4:55306683..55307683,5	K562	blood:
13	chr4:55188935..55189678-chr4:55232967..55233845,2	MCF-7	breast:
14	chr4:55185299..55185879-chr4:55250478..55251050,2	MCF-7	breast:
15	chr4:55184812..55185387-chr4:55827256..55827776,2	K562	blood:
16	chr4:55188790..55189653-chr4:55306542..55307230,3	MCF-7	breast:
17	chr4:55188871..55189578-chr4:55299616..55300145,2	K562	blood:
18	chr4:55188891..55189478-chr4:55307244..55307822,2	MCF-7	breast:
19	chr4:55188918..55189432-chr4:55241699..55242360,2	MCF-7	breast:
20	chr4:55184927..55185737-chr4:55306931..55307659,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDGFRA-1	chr4:55199037-55199101	XLOC_003539

Variant related genes	Relation type
ENSG00000248184	TF binding region
ENSG00000248518	chromatin interactions

Extended variants
information (count: 1244 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:1244 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs144376342	chr4:55173847-55173848	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs148721572	chr4:55173848-55173849	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs536590762	chr4:55173865-55173866	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs186660185	chr4:55173890-55173891	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs573137688	chr4:55173901-55173902	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs75475549	chr4:55173928-55173929	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs6858442	chr4:55173933-55173934	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs575348587	chr4:55173989-55173990	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs544552254	chr4:55174017-55174018	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs561126524	chr4:55174073-55174074	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs191005328	chr4:55174127-55174128	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs151242763	chr4:55174200-55174201	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs377042632	chr4:55174259-55174260	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs74477693	chr4:55174292-55174293	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs62299408	chr4:55174367-55174368	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs140031222	chr4:55174390-55174391	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs564934127	chr4:55174506-55174507	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs183703918	chr4:55174513-55174514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs569587807	chr4:55174551-55174552	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs550548297	chr4:55174569-55174570	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs113917936	chr4:55174642-55174643	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs374437563	chr4:55174643-55174644	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs79842015	chr4:55174646-55174647	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs567191114	chr4:55174662-55174663	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs547880003	chr4:55174674-55174675	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs530408545	chr4:55174717-55174718	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs567758273	chr4:55174728-55174729	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs188329945	chr4:55174779-55174780	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs566508655	chr4:55174793-55174794	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs566848138	chr4:55174804-55174805	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs6554168	chr4:55174827-55174828	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs6554169	chr4:55174858-55174859	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs57821195	chr4:55174865-55174866	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs145441907	chr4:55174883-55174884	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs6554170	chr4:55174885-55174886	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs570189996	chr4:55174920-55174921	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs191208229	chr4:55174981-55174982	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs542920891	chr4:55175063-55175064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs553275427	chr4:55175065-55175066	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs142137445	chr4:55175067-55175068	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs545179493	chr4:55175078-55175079	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs565124443	chr4:55175169-55175170	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs530621605	chr4:55175185-55175186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs544013056	chr4:55175253-55175254	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs150170683	chr4:55175289-55175290	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs56351733	chr4:55175323-55175324	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs145658160	chr4:55175336-55175337	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs148897040	chr4:55175387-55175388	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs532667886	chr4:55175429-55175430	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs10018609	chr4:55175492-55175493	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
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
Hodgkin''s lymphoma	17606441	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
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Cancer	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	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
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	19435819	CNVD
Multiple myeloma	16616336	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
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
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Ovarian neoplasms	16753589	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21569311	CNVD
Glioblastoma	17504929	CNVD
Glioblastoma	16823502	CNVD
Melanoma	16908931	CNVD
Glioblastoma	20031968	CNVD
Medulloblastoma	19270706	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Olfactory neuroblastoma	18408657	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Rhabdomyosarcoma	16790082	CNVD
Gastrointestinal stromal cancer	17438095	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	19115005	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164920	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55173800-55175800	Enhancers	Brain Germinal Matrix	brain
2	chr4:55174400-55175400	Enhancers	Fetal Brain Female	brain
3	chr4:55180400-55180800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:55180800-55181400	Enhancers	GM12878-XiMat	blood
5	chr4:55180800-55182400	Enhancers	Primary B cells from peripheral blood	blood
6	chr4:55181200-55182400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr4:55181400-55181800	Flanking Active TSS	GM12878-XiMat	blood
8	chr4:55181400-55182600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr4:55181400-55183000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:55181400-55183400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:55181600-55182000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:55181600-55182000	Enhancers	Fetal Lung	lung
13	chr4:55181600-55182400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:55181600-55182600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:55181800-55182000	Enhancers	GM12878-XiMat	blood
16	chr4:55181800-55182800	Enhancers	Brain Cingulate Gyrus	brain
17	chr4:55181800-55182800	Enhancers	Brain Substantia Nigra	brain
18	chr4:55182000-55182400	Enhancers	Brain Angular Gyrus	brain
19	chr4:55182000-55182400	Flanking Active TSS	GM12878-XiMat	blood
20	chr4:55182000-55182600	Enhancers	Brain Hippocampus Middle	brain
21	chr4:55182000-55183000	Enhancers	Brain Anterior Caudate	brain
22	chr4:55182000-55183000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr4:55182000-55185400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:55182400-55183000	Enhancers	GM12878-XiMat	blood
25	chr4:55182400-55184800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:55183000-55184800	Weak transcription	GM12878-XiMat	blood
27	chr4:55183000-55189200	Weak transcription	Brain Anterior Caudate	brain
28	chr4:55183000-55190000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:55183400-55183800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:55183800-55184200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:55184800-55185600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:55184800-55185600	Enhancers	GM12878-XiMat	blood
33	chr4:55185400-55185600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:55185400-55185600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr4:55185400-55185600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:55185400-55185600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:55185400-55185800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:55185600-55186200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:55186200-55187200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:55186800-55187200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:55186800-55187400	Enhancers	HMEC	breast
42	chr4:55186800-55187400	Enhancers	NHEK	skin
43	chr4:55187400-55188000	Enhancers	Fetal Brain Female	brain
44	chr4:55187600-55187800	Enhancers	Fetal Brain Male	brain
45	chr4:55188000-55188800	Weak transcription	Fetal Brain Male	brain
46	chr4:55188800-55189600	Enhancers	Fetal Brain Male	brain
47	chr4:55189000-55189800	Enhancers	Brain Cingulate Gyrus	brain
48	chr4:55189200-55189400	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr4:55189200-55189400	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr4:55189200-55189800	Enhancers	Brain Substantia Nigra	brain

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