Variant report

Variant	nsv4352
Chromosome Location	chr4:59925782-59966004
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	CEBPB	chr4:59930191-59930393	A549	lung:	n/a	chr4:59930311-59930322
2	CEBPB	chr4:59926170-59926547	ECC-1	luminal epithelium:	n/a	n/a
3	CEBPB	chr4:59930192-59930433	HepG2	liver:	n/a	chr4:59930311-59930322
4	CEBPB	chr4:59963185-59963406	A549	lung:	n/a	chr4:59963289-59963300
5	CEBPB	chr4:59926151-59926570	ECC-1	luminal epithelium:	n/a	n/a
6	CEBPB	chr4:59925618-59926106	ECC-1	luminal epithelium:	n/a	n/a
7	CEBPB	chr4:59963157-59963401	HepG2	liver:	n/a	chr4:59963289-59963300
8	CEBPB	chr4:59963316-59963362	K562	blood:	n/a	n/a
9	CEBPB	chr4:59957078-59957161	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr4:59960240-59960390	GM12871	blood:	n/a	chr4:59960336-59960344
11	CTCF	chr4:59960320-59960470	HEK293	kidney:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
12	CTCF	chr4:59960360-59960510	Caco-2	colon:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
13	CTCF	chr4:59926659-59926953	GM12878	blood:	n/a	n/a
14	CTCF	chr4:59960360-59960510	RPTEC	kidney:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
15	CTCF	chr4:59926781-59926897	GM13977	blood:	n/a	n/a
16	CTCF	chr4:59960339-59960444	GM13977	blood:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
17	CTCF	chr4:59926821-59926856	GM10266	blood:	n/a	n/a
18	CTCF	chr4:59960320-59960470	WERI-Rb-1	eye:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
19	CTCF	chr4:59960360-59960510	MCF-7	breast:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
20	CTCF	chr4:59960336-59960463	HepG2	liver:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
21	CTCF	chr4:59926660-59926810	GM12875	blood:	n/a	n/a
22	CTCF	chr4:59960284-59960485	GM12878	blood:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
23	CTCF	chr4:59960311-59960458	HepG2	liver:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
24	CTCF	chr4:59926740-59926890	HEK293	kidney:	n/a	n/a
25	CTCF	chr4:59960307-59960458	MCF-7	breast:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
26	CTCF	chr4:59926760-59926910	A549	lung:	n/a	n/a
27	CTCF	chr4:59926899-59926902	GM13977	blood:	n/a	n/a
28	CTCF	chr4:59960360-59960510	HepG2	liver:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
29	CTCF	chr4:59926752-59926835	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr4:59960300-59960450	HepG2	liver:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
31	CTCF	chr4:59960300-59960450	WERI-Rb-1	eye:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
32	CTCF	chr4:59960300-59960450	GM12875	blood:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
33	CTCF	chr4:59926720-59926870	WERI-Rb-1	eye:	n/a	n/a
34	CTCF	chr4:59960309-59960473	MCF-7	breast:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
35	CTCF	chr4:59960220-59960370	GM12872	blood:	n/a	chr4:59960336-59960344
36	CTCF	chr4:59960320-59960470	A549	lung:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
37	CTCF	chr4:59960340-59960490	Hela-S3	cervix:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
38	CTCF	chr4:59960340-59960490	GM12878	blood:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
39	CTCF	chr4:59960340-59960490	GM12874	blood:	n/a	chr4:59960397-59960415 chr4:59960399-59960420
40	CTCF	chr4:59960193-59960512	H1-hESC	embryonic stem cell:	n/a	chr4:59960397-59960415 chr4:59960336-59960344 chr4:59960399-59960420
41	E2F4	chr4:59964064-59965037	MCF10A-Er-Src	breast:	n/a	n/a
42	E2F4	chr4:59963380-59963597	MCF10A-Er-Src	breast:	n/a	n/a
43	E2F4	chr4:59928701-59928783	MCF10A-Er-Src	breast:	n/a	n/a
44	EP300	chr4:59925676-59926577	ECC-1	luminal epithelium:	n/a	chr4:59925770-59925784
45	EP300	chr4:59925494-59926599	ECC-1	luminal epithelium:	n/a	chr4:59925770-59925784
46	ESR1	chr4:59925639-59926474	ECC-1	luminal epithelium:	n/a	n/a
47	ESR1	chr4:59925610-59926609	ECC-1	luminal epithelium:	n/a	n/a
48	ESR1	chr4:59925741-59926474	ECC-1	luminal epithelium:	n/a	n/a
49	FOS	chr4:59928985-59929153	MCF10A-Er-Src	breast:	n/a	chr4:59928992-59928999
50	FOS	chr4:59957580-59957698	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:59952219..59954148-chr4:59969899..59971579,2	K562	blood:
2	chr4:59959700..59961456-chr4:59961992..59964536,2	MCF-7	breast:
3	chr4:59959700..59961456-chr4:59961992..59964536,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IGFBP7-6	chr4:59940898-59940974	ENSG00000250375
2	lnc-IGFBP7-6	chr4:59940898-59940960	XLOC_003963

Variant related genes	Relation type
ENSG00000250375	TF binding region

Extended variants
information (count: 352 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:352 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543911162	chr4:59925814-59925815	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs577389670	chr4:59925826-59925827	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs113889450	chr4:59925915-59925916	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs111742480	chr4:59925916-59925917	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs560172628	chr4:59925962-59925963	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs2333730	chr4:59926051-59926052	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs111392869	chr4:59926061-59926062	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs561118432	chr4:59926063-59926064	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs115026205	chr4:59926110-59926111	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs201943557	chr4:59926120-59926121	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs369835698	chr4:59926121-59926122	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs199502947	chr4:59926124-59926125	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs3034271	chr4:59926125-59926126	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs138678177	chr4:59926156-59926157	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs2088196	chr4:59926182-59926183	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs532716696	chr4:59926183-59926184	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs551507854	chr4:59926202-59926203	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs566526241	chr4:59926203-59926204	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs533647007	chr4:59926204-59926205	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs549002173	chr4:59926205-59926206	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs149327120	chr4:59926230-59926231	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs115496600	chr4:59926235-59926236	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs112464340	chr4:59926252-59926253	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs2088195	chr4:59926261-59926262	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs577425461	chr4:59926315-59926316	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs147442491	chr4:59926316-59926317	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs553550493	chr4:59926324-59926325	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs561409585	chr4:59926326-59926327	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs542742538	chr4:59926345-59926346	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs561364911	chr4:59926352-59926353	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs192425646	chr4:59926366-59926367	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs2088194	chr4:59926419-59926420	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs565079631	chr4:59926428-59926429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs532754104	chr4:59926431-59926432	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs540267609	chr4:59926443-59926444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs73194867	chr4:59926487-59926488	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs527414878	chr4:59926520-59926521	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs114486923	chr4:59926551-59926552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs142846517	chr4:59926556-59926557	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs567270435	chr4:59926557-59926558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs565279082	chr4:59926601-59926602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs534351700	chr4:59926628-59926629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs532607718	chr4:59926631-59926632	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs139767779	chr4:59926711-59926712	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs184451585	chr4:59926712-59926713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs538539440	chr4:59926728-59926729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs58833451	chr4:59926784-59926785	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs565717006	chr4:59926824-59926825	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs370970190	chr4:59926838-59926839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs551109168	chr4:59926893-59926894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

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	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
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	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
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
Colorectal cancer	16272173	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute monocytic leukemia	16498392	CNVD
Prostate cancer	16573809	CNVD
Osteoporosis	18992858	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:59925800-59926200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:59925800-59926400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:59926000-59926400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:59926400-59927000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:59928800-59929400	Enhancers	Fetal Heart	heart
6	chr4:59929000-59930400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr4:59934400-59935400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:59952200-59952600	Enhancers	Brain Hippocampus Middle	brain
9	chr4:59952600-59953000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:59957000-59957200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:59957000-59958000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:59957000-59958200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:59957200-59957400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:59957200-59957600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:59957200-59957600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:59957200-59957800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:59957200-59958000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr4:59957200-59958200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr4:59957400-59958000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:59957800-59958200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr4:59963600-59964200	Active TSS	A549	lung

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