Variant report

Variant	nsv594204
Chromosome Location	chr4:56266973-56268507
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:56268055-56268112	GM13977	blood:	n/a	n/a
2	GTF2F1	chr4:56267234-56267272	K562	blood:	n/a	n/a
3	NRF1	chr4:56267652-56267803	K562	blood:	n/a	n/a
4	POLR2A	chr4:56268360-56274870	K562	blood:	n/a	n/a
5	POLR2A	chr4:56267055-56267867	K562	blood:	n/a	n/a
6	POLR2A	chr4:56268244-56268530	K562	blood:	n/a	n/a
7	POLR2A	chr4:56268074-56268234	K562	blood:	n/a	n/a
8	POLR2A	chr4:56267894-56268099	K562	blood:	n/a	n/a
9	POLR2A	chr4:56267444-56267718	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr4:56267578-56267745	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr4:56267004-56267374	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr4:56268475-56270582	IMR90	lung:	n/a	n/a
13	RCOR1	chr4:56267074-56267077	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
2	chr4:56210761..56214527-chr4:56265668..56271169,8	K562	blood:
3	chr4:56266067..56267699-chr4:56271922..56273908,2	MCF-7	breast:
4	chr4:56206647..56208292-chr4:56265434..56267347,2	MCF-7	breast:
5	chr4:56211242..56218739-chr4:56258356..56267013,28	MCF-7	breast:
6	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
7	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:

No data

Variant related genes	Relation type
SRD5A3-AS1	TF binding region
TMEM165	TF binding region
ENSG00000249700	chromatin interactions
ENSG00000134851	chromatin interactions
ENSG00000251111	chromatin interactions
ENSG00000128039	chromatin interactions

Extended variants
information (count: 52 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:52 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs572205827	chr4:56266973-56266974	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs534892270	chr4:56267004-56267005	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs557890093	chr4:56267008-56267009	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs578207698	chr4:56267010-56267011	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs115620278	chr4:56267011-56267012	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs544969694	chr4:56267044-56267045	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs189872823	chr4:56267121-56267122	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs11729403	chr4:56267182-56267183	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs182432312	chr4:56267276-56267277	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs559534337	chr4:56267318-56267319	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs528155405	chr4:56267372-56267373	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs113948049	chr4:56267380-56267381	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs139151670	chr4:56267388-56267389	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs75920719	chr4:56267401-56267402	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs550637029	chr4:56267452-56267453	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs561523596	chr4:56267458-56267459	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs12641881	chr4:56267473-56267474	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs187879253	chr4:56267506-56267507	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs547275903	chr4:56267509-56267510	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs565844251	chr4:56267550-56267551	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs77008311	chr4:56267589-56267590	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs367858144	chr4:56267605-56267606	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs571819981	chr4:56267608-56267609	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs558350475	chr4:56267780-56267781	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs571775165	chr4:56267816-56267817	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
26	rs149918639	chr4:56267823-56267824	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
27	rs571256825	chr4:56267870-56267871	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs12331161	chr4:56267871-56267872	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs191147135	chr4:56267887-56267888	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs145108268	chr4:56267899-56267900	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
31	rs542645212	chr4:56267927-56267928	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
32	rs573566774	chr4:56267970-56267971	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
33	rs183360502	chr4:56268009-56268010	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
34	rs545154968	chr4:56268019-56268020	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
35	rs149107904	chr4:56268021-56268022	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
36	rs372762803	chr4:56268022-56268023	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
37	rs377561722	chr4:56268035-56268036	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
38	rs113513890	chr4:56268049-56268050	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
39	rs199765539	chr4:56268066-56268067	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
40	rs188719383	chr4:56268146-56268147	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
41	rs544393497	chr4:56268209-56268210	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
42	rs561030220	chr4:56268211-56268212	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
43	rs370149153	chr4:56268259-56268260	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
44	rs370288685	chr4:56268286-56268287	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
45	rs77062036	chr4:56268287-56268288	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
46	rs71194551	chr4:56268298-56268299	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
47	rs192541720	chr4:56268340-56268341	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
48	rs548980909	chr4:56268368-56268369	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
49	rs565709056	chr4:56268410-56268411	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
50	rs398092379	chr4:56268436-56268437	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

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
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
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
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	22183965	CNVD
Autism	22543975	CNVD
Breast cancer	21785460	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:256 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264200-56267400	Enhancers	Small Intestine	intestine
2	chr4:56264200-56269800	Weak transcription	Spleen	Spleen
3	chr4:56264200-56270200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:56264200-56273000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:56264600-56270000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:56264800-56269800	Weak transcription	Fetal Kidney	kidney
7	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:56265000-56267000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:56265000-56273200	Weak transcription	Gastric	stomach
11	chr4:56265400-56273400	Weak transcription	Aorta	Aorta
12	chr4:56265600-56267000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:56265600-56267000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:56265600-56267200	Weak transcription	HepG2	liver
15	chr4:56265600-56268200	Strong transcription	HSMM	muscle
16	chr4:56265600-56269200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:56265600-56269200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:56265600-56269200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:56265600-56269200	Weak transcription	HSMMtube	muscle
20	chr4:56265600-56269800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:56265600-56269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:56265600-56269800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:56265600-56269800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:56265600-56269800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:56265600-56270200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:56265600-56270200	Weak transcription	Lung	lung
27	chr4:56265600-56270200	Weak transcription	Thymus	Thymus
28	chr4:56265600-56271400	Weak transcription	Psoas Muscle	Psoas
29	chr4:56265600-56271800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:56265600-56272000	Weak transcription	Esophagus	oesophagus
31	chr4:56265600-56272200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:56265600-56273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:56265600-56273800	Weak transcription	Stomach Mucosa	stomach
34	chr4:56265600-56275600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
37	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
38	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:56265800-56267000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:56265800-56267000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:56265800-56267000	Weak transcription	Adipose Nuclei	Adipose
43	chr4:56265800-56267000	Weak transcription	Liver	Liver
44	chr4:56265800-56267000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:56265800-56267000	Weak transcription	A549	lung
46	chr4:56265800-56267000	Weak transcription	Hela-S3	cervix
47	chr4:56265800-56267800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:56265800-56267800	Strong transcription	Osteobl	bone
49	chr4:56265800-56268000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:56265800-56269400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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