Variant report

Variant	nsv999528
Chromosome Location	chr4:94230291-94263411
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	chr4:94255240-94255511	GM12878	blood:	n/a	n/a
2	CEBPB	chr4:94238251-94238506	ECC-1	luminal epithelium:	n/a	n/a
3	CEBPB	chr4:94255145-94255295	HepG2	liver:	n/a	n/a
4	CEBPB	chr4:94238269-94238550	ECC-1	luminal epithelium:	n/a	n/a
5	CHD2	chr4:94255304-94255542	GM12878	blood:	n/a	n/a
6	CTCF	chr4:94250951-94251003	GM12878	blood:	n/a	n/a
7	CTCF	chr4:94258490-94258602	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr4:94258440-94258590	HCT-116	colon:	n/a	n/a
9	CTCF	chr4:94250920-94251070	MCF-7	breast:	n/a	n/a
10	CTCF	chr4:94258480-94258630	RPTEC	kidney:	n/a	n/a
11	CTCF	chr4:94258520-94258670	GM12872	blood:	n/a	n/a
12	CTCF	chr4:94258480-94258630	HepG2	liver:	n/a	n/a
13	CTCF	chr4:94258520-94258578	MCF-7	breast:	n/a	n/a
14	CTCF	chr4:94258440-94258590	AG09319	gingival:	n/a	n/a
15	CTCF	chr4:94258512-94258542	A549	lung:	n/a	n/a
16	CTCF	chr4:94254019-94254138	GM12878	blood:	n/a	n/a
17	CTCF	chr4:94258500-94258650	Caco-2	colon:	n/a	n/a
18	CTCF	chr4:94258440-94258590	HEK293	kidney:	n/a	n/a
19	CTCF	chr4:94250960-94251110	WI-38	lung:	n/a	n/a
20	CTCF	chr4:94258420-94258570	WERI-Rb-1	eye:	n/a	n/a
21	CUX1	chr4:94255243-94255564	GM12878	blood:	n/a	n/a
22	E2F4	chr4:94233564-94233629	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr4:94237918-94238031	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F4	chr4:94234708-94234806	MCF10A-Er-Src	breast:	n/a	n/a
25	EBF1	chr4:94257611-94257835	GM12878	blood:	n/a	n/a
26	EBF1	chr4:94255056-94255623	GM12878	blood:	n/a	n/a
27	EBF1	chr4:94250800-94250805	GM12878	blood:	n/a	n/a
28	EBF1	chr4:94254504-94255695	GM12878	blood:	n/a	n/a
29	EBF1	chr4:94253912-94254242	GM12878	blood:	n/a	n/a
30	EP300	chr4:94255225-94255587	GM12878	blood:	n/a	n/a
31	EP300	chr4:94255110-94255536	GM12878	blood:	n/a	n/a
32	EP300	chr4:94238076-94238698	ECC-1	luminal epithelium:	n/a	chr4:94238231-94238239 chr4:94238177-94238186
33	ESR1	chr4:94238244-94238456	ECC-1	luminal epithelium:	n/a	n/a
34	ESR1	chr4:94233496-94233697	ECC-1	luminal epithelium:	n/a	n/a
35	FOS	chr4:94255201-94255366	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr4:94234414-94234694	MCF10A-Er-Src	breast:	n/a	chr4:94234569-94234579 chr4:94234569-94234579
37	FOS	chr4:94238341-94239088	MCF10A-Er-Src	breast:	n/a	chr4:94238886-94238897 chr4:94238884-94238895 chr4:94238887-94238896 chr4:94238887-94238897 chr4:94238886-94238898 chr4:94238889-94238896 chr4:94238888-94238897
38	FOS	chr4:94234432-94234685	MCF10A-Er-Src	breast:	n/a	chr4:94234569-94234579 chr4:94234569-94234579
39	FOS	chr4:94238253-94239135	MCF10A-Er-Src	breast:	n/a	chr4:94238886-94238897 chr4:94238884-94238895 chr4:94238887-94238896 chr4:94238887-94238897 chr4:94238886-94238898 chr4:94238889-94238896 chr4:94238888-94238897
40	FOS	chr4:94240295-94240585	MCF10A-Er-Src	breast:	n/a	chr4:94240425-94240435 chr4:94240425-94240435 chr4:94240426-94240434 chr4:94240425-94240435 chr4:94240425-94240435
41	FOS	chr4:94240379-94240601	MCF10A-Er-Src	breast:	n/a	chr4:94240425-94240435 chr4:94240425-94240435 chr4:94240426-94240434 chr4:94240425-94240435 chr4:94240425-94240435
42	FOS	chr4:94238345-94239104	MCF10A-Er-Src	breast:	n/a	chr4:94238886-94238897 chr4:94238884-94238895 chr4:94238887-94238896 chr4:94238887-94238897 chr4:94238886-94238898 chr4:94238889-94238896 chr4:94238888-94238897
43	FOS	chr4:94238703-94239101	MCF10A-Er-Src	breast:	n/a	chr4:94238886-94238897 chr4:94238884-94238895 chr4:94238887-94238896 chr4:94238887-94238897 chr4:94238886-94238898 chr4:94238889-94238896 chr4:94238888-94238897
44	FOS	chr4:94234415-94234705	MCF10A-Er-Src	breast:	n/a	chr4:94234569-94234579 chr4:94234569-94234579
45	FOS	chr4:94240288-94240504	MCF10A-Er-Src	breast:	n/a	chr4:94240425-94240435 chr4:94240425-94240435 chr4:94240426-94240434 chr4:94240425-94240435 chr4:94240425-94240435
46	FOS	chr4:94234431-94234705	MCF10A-Er-Src	breast:	n/a	chr4:94234569-94234579 chr4:94234569-94234579
47	FOS	chr4:94238680-94239079	HUVEC	blood vessel:	n/a	chr4:94238886-94238897 chr4:94238884-94238895 chr4:94238887-94238896 chr4:94238887-94238897 chr4:94238886-94238898 chr4:94238889-94238896 chr4:94238888-94238897
48	FOXM1	chr4:94238008-94238660	ECC-1	luminal epithelium:	n/a	n/a
49	GATA2	chr4:94238754-94239079	HUVEC	blood vessel:	n/a	chr4:94238886-94238895 chr4:94238954-94238975
50	GTF2F1	chr4:94251422-94251429	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:94226949..94229265-chr4:94235078..94237239,2	K562	blood:
2	chr4:94259967..94262049-chr4:94263845..94266211,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPGDS-2	chr4:94240750-94240937	ENSG00000250908.1
2	lnc-HPGDS-2	chr4:94239774-94240026	ENSG00000250908.1

Variant related genes	Relation type
ENSG00000250908	TF binding region

Extended variants
information (count: 1054 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:1054 , 50 per page) page: 1 2 3 4 5 6 7 ... 22

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs184763971	chr4:94230302-94230303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs529163617	chr4:94230340-94230341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs539229252	chr4:94230414-94230415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs367565822	chr4:94230425-94230426	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs57353227	chr4:94230440-94230441	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs537458239	chr4:94230470-94230471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs371803584	chr4:94230497-94230498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs148987638	chr4:94230506-94230507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs570903283	chr4:94230507-94230508	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs10010594	chr4:94230511-94230512	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs553490637	chr4:94230515-94230516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs573103403	chr4:94230522-94230523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs56043153	chr4:94230566-94230567	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs56775228	chr4:94230578-94230579	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs142327083	chr4:94230592-94230593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs573290475	chr4:94230593-94230594	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs146361484	chr4:94230609-94230610	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs61399215	chr4:94230629-94230630	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs571364599	chr4:94230692-94230693	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs144251678	chr4:94230693-94230694	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs578159222	chr4:94230698-94230699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs544170963	chr4:94230715-94230716	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs148314428	chr4:94230733-94230734	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs555379411	chr4:94230753-94230754	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs533039544	chr4:94230773-94230774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs572229880	chr4:94230776-94230777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs539964046	chr4:94230806-94230807	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs540308124	chr4:94230930-94230931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs72876911	chr4:94230942-94230943	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs140493025	chr4:94230978-94230979	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs549266472	chr4:94231048-94231049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs562756766	chr4:94231056-94231057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs115421637	chr4:94231090-94231091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs72876912	chr4:94231110-94231111	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs543651747	chr4:94231145-94231146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs77007867	chr4:94231154-94231155	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs79114040	chr4:94231244-94231245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs546799963	chr4:94231326-94231327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs566689215	chr4:94231374-94231375	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs12649061	chr4:94231375-94231376	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs150436888	chr4:94231393-94231394	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs562991781	chr4:94231465-94231466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs575526742	chr4:94231477-94231478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs188054616	chr4:94231492-94231493	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs557697399	chr4:94231537-94231538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs577572390	chr4:94231545-94231546	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs138026567	chr4:94231550-94231551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs142579646	chr4:94231577-94231578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs192147411	chr4:94231596-94231597	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs578139306	chr4:94231597-94231598	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

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
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
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Esophageal cancer	21851588	CNVD
Cancer	19907438	CNVD
early-passage human iPS cells	21368824	CNVD
Breast cancer	22522925	CNVD
Autism	20841430	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	20164919	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Epilepsy	20502679	CNVD

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:94230200-94241000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:94233400-94233600	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:94233600-94236800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:94233800-94234600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:94234000-94234400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:94234000-94234800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:94234200-94234600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:94234400-94234600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:94234400-94234800	Enhancers	A549	lung
10	chr4:94234400-94234800	Enhancers	NHEK	skin
11	chr4:94234400-94235000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:94234400-94235000	Enhancers	HMEC	breast
13	chr4:94234600-94235000	Enhancers	Hela-S3	cervix
14	chr4:94234600-94237200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:94234800-94238400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:94234800-94238400	Weak transcription	NHEK	skin
17	chr4:94235000-94237600	Weak transcription	Hela-S3	cervix
18	chr4:94235000-94237800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:94235000-94238200	Weak transcription	HMEC	breast
20	chr4:94236400-94237400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:94236800-94237000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr4:94237200-94237800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr4:94237600-94238600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:94237600-94239000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:94237600-94241400	Enhancers	Hela-S3	cervix
26	chr4:94237800-94238400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:94238200-94241000	Enhancers	HMEC	breast
28	chr4:94238200-94241000	Enhancers	HUVEC	blood vessel
29	chr4:94238400-94238600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:94238400-94238600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr4:94238400-94238800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:94238400-94240400	Enhancers	NHEK	skin
33	chr4:94238600-94239600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:94238600-94239600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:94238800-94239000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:94239400-94240400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:94239600-94240600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:94239600-94241000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:94239600-94241000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:94247000-94249600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:94248400-94249000	Enhancers	Brain Substantia Nigra	brain
42	chr4:94250600-94251400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:94251400-94252200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:94251400-94252800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:94252200-94254800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:94254200-94255600	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr4:94254800-94255200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:94255200-94255400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:94255200-94255600	Enhancers	Fetal Lung	lung
50	chr4:94255400-94258600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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