Variant report

Variant	esv2439697
Chromosome Location	chr4:54564973-54568229
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	chr4:54567735-54567808	K562	blood:	n/a	n/a
2	CTCF	chr4:54568220-54568370	AG04450	lung:	n/a	n/a
3	EBF1	chr4:54567546-54568140	GM12878	blood:	n/a	chr4:54567725-54567736
4	EBF1	chr4:54565597-54565982	GM12878	blood:	n/a	chr4:54565795-54565806
5	EBF1	chr4:54567557-54567828	GM12878	blood:	n/a	chr4:54567725-54567736
6	EBF1	chr4:54566665-54566963	GM12878	blood:	n/a	chr4:54566807-54566818 chr4:54566789-54566800
7	EBF1	chr4:54567547-54567866	GM12878	blood:	n/a	chr4:54567725-54567736
8	EP300	chr4:54567557-54567619	GM12878	blood:	n/a	n/a
9	MYC	chr4:54567496-54567626	K562	blood:	n/a	n/a
10	PAX5	chr4:54565457-54565726	GM12878	blood:	n/a	n/a
11	PAX5	chr4:54565483-54565717	GM12878	blood:	n/a	n/a
12	PAX5	chr4:54567407-54567694	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:54567873-54569548	GM12878	blood:	n/a	n/a
14	SETDB1	chr4:54567485-54567818	U2OS	brain:	n/a	n/a
15	SPI1	chr4:54567472-54567722	GM12878	blood:	n/a	n/a
16	STAT1	chr4:54567996-54567999	GM12878	blood:	n/a	n/a
17	WRNIP1	chr4:54568086-54568134	GM12878	blood:	n/a	n/a
18	ZNF384	chr4:54564962-54565162	K562	blood:	n/a	n/a
19	ZNF384	chr4:54564988-54565171	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54568125..54570977-chr4:54571339..54573651,2	K562	blood:
2	chr4:54486968..54487480-chr4:54567881..54568820,2	MCF-7	breast:

Variant related genes	Relation type
LNX1	TF binding region

Extended variants
information (count: 123 )
Associated
traits (count: 101 )

Variant overlapped rSNPs/rCNVs (count:123 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs530270224	chr4:54565033-54565034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs111866480	chr4:54565062-54565063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs368648943	chr4:54565067-54565068	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs375611003	chr4:54565091-54565092	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs2590815	chr4:54565092-54565093	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs367903945	chr4:54565093-54565094	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs2616442	chr4:54565098-54565099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs547211819	chr4:54565131-54565132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs567210490	chr4:54565235-54565236	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs568314272	chr4:54565266-54565267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs368124171	chr4:54565275-54565276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs532837434	chr4:54565298-54565299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs373972770	chr4:54565322-54565323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs375864552	chr4:54565365-54565366	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs537972958	chr4:54565392-54565393	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs370803415	chr4:54565394-54565395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs555008983	chr4:54565395-54565396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs567354200	chr4:54565405-54565406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs531051819	chr4:54565415-54565416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs536091417	chr4:54565440-54565441	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs80116193	chr4:54565499-54565500	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs115834022	chr4:54565548-54565549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs572836520	chr4:54565622-54565623	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs544882169	chr4:54565656-54565657	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs558283735	chr4:54565765-54565766	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs112602814	chr4:54565811-54565812	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs545815682	chr4:54565875-54565876	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs557818357	chr4:54565878-54565879	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs200044938	chr4:54565894-54565895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs561082969	chr4:54565898-54565899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs529803137	chr4:54565956-54565957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs540861269	chr4:54565960-54565961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs182671555	chr4:54565962-54565963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs532874909	chr4:54566165-54566166	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs576030974	chr4:54566168-54566169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs112154424	chr4:54566183-54566184	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs531687176	chr4:54566184-54566185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs2668547	chr4:54566185-54566186	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs187528474	chr4:54566243-54566244	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs141005599	chr4:54566268-54566269	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs192825897	chr4:54566288-54566289	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs2590814	chr4:54566331-54566332	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs116061448	chr4:54566333-54566334	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs372166164	chr4:54566349-54566350	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs184116616	chr4:54566350-54566351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs549473001	chr4:54566394-54566395	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs544234862	chr4:54566395-54566396	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs559218656	chr4:54566412-54566413	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs376898616	chr4:54566427-54566428	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs554250887	chr4:54566430-54566431	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:101)

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	21525872	CNVD
Glioblastoma multiforme	19115005	CNVD
Wilms tumour	21544195	CNVD
Cancer	20164919	CNVD
Gastrointestinal stromal cancer	17527083	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17209131	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164920	CNVD

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54555600-54568600	Weak transcription	Right Atrium	heart
2	chr4:54560400-54568000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:54560400-54568600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:54561600-54568400	Weak transcription	Fetal Brain Male	brain
5	chr4:54562000-54568600	Weak transcription	Placenta	Placenta
6	chr4:54562200-54566600	Weak transcription	Spleen	Spleen
7	chr4:54562200-54568600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:54562400-54568600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:54564600-54568000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:54564800-54568400	Weak transcription	NHDF-Ad	bronchial
11	chr4:54564800-54568600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:54564800-54568600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:54566200-54566800	Enhancers	Gastric	stomach
14	chr4:54566400-54568800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:54566600-54566800	Enhancers	Spleen	Spleen
16	chr4:54566800-54568600	Weak transcription	Gastric	stomach
17	chr4:54566800-54568600	Weak transcription	Spleen	Spleen
18	chr4:54567600-54568400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:54567600-54568600	Enhancers	Primary B cells from peripheral blood	blood
20	chr4:54567800-54568000	Enhancers	GM12878-XiMat	blood
21	chr4:54568000-54568600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:54568000-54568600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:54568000-54568600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:54568000-54568600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:54568000-54568600	Enhancers	Fetal Muscle Leg	muscle
26	chr4:54568000-54569000	Enhancers	Fetal Lung	lung
27	chr4:54568000-54569600	Flanking Active TSS	GM12878-XiMat	blood
28	chr4:54568000-54569800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:54568200-54568400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:54568200-54568400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:54568200-54568400	Enhancers	Liver	Liver
32	chr4:54568200-54568400	Enhancers	Brain Substantia Nigra	brain
33	chr4:54568200-54568400	Enhancers	Hela-S3	cervix
34	chr4:54568200-54568600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:54568200-54568600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr4:54568200-54568600	Enhancers	A549	lung
37	chr4:54568200-54568600	Enhancers	NHLF	lung
38	chr4:54568200-54568800	Enhancers	Primary B cells from cord blood	blood
39	chr4:54568200-54568800	Enhancers	Fetal Heart	heart

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