Variant report

Variant	esv3496349
Chromosome Location	chr4:90576823-90603051
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	ARID3A	chr4:90602260-90602839	HepG2	liver:	n/a	n/a
2	ARID3A	chr4:90596122-90596570	HepG2	liver:	n/a	n/a
3	BACH1	chr4:90602368-90602730	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr4:90582404-90582976	H1-hESC	embryonic stem cell:	n/a	n/a
5	BHLHE40	chr4:90602385-90602693	HepG2	liver:	n/a	n/a
6	BRCA1	chr4:90581499-90583099	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr4:90582143-90582305	A549	lung:	n/a	n/a
8	CEBPB	chr4:90581113-90581438	IMR90	lung:	n/a	chr4:90581275-90581288 chr4:90581277-90581286 chr4:90581277-90581286 chr4:90581277-90581286
9	CEBPB	chr4:90581122-90581402	H1-hESC	embryonic stem cell:	n/a	chr4:90581275-90581288 chr4:90581277-90581286 chr4:90581277-90581286 chr4:90581277-90581286
10	CEBPB	chr4:90581113-90581456	HepG2	liver:	n/a	chr4:90581275-90581288 chr4:90581277-90581286 chr4:90581277-90581286 chr4:90581277-90581286
11	CEBPB	chr4:90578903-90579031	K562	blood:	n/a	n/a
12	CEBPB	chr4:90578817-90579031	A549	lung:	n/a	n/a
13	CEBPB	chr4:90581749-90583044	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr4:90581119-90581470	Hela-S3	cervix:	n/a	chr4:90581275-90581288 chr4:90581277-90581286 chr4:90581277-90581286 chr4:90581277-90581286
15	CEBPB	chr4:90591479-90591574	HepG2	liver:	n/a	chr4:90591522-90591533
16	CEBPB	chr4:90581150-90581412	A549	lung:	n/a	chr4:90581275-90581288 chr4:90581277-90581286 chr4:90581277-90581286 chr4:90581277-90581286
17	CEBPB	chr4:90602405-90602566	H1-hESC	embryonic stem cell:	n/a	n/a
18	CEBPD	chr4:90602454-90602739	HepG2	liver:	n/a	n/a
19	CHD1	chr4:90602530-90604198	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD2	chr4:90582628-90583000	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr4:90579160-90579310	HCPEpiC	choroid plexus:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
22	CTCF	chr4:90579200-90579350	RPTEC	kidney:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
23	CTCF	chr4:90579240-90579390	GM12864	blood:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
24	CTCF	chr4:90579220-90579370	HCFaa	heart:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
25	CTCF	chr4:90578800-90578950	AG04450	lung:	n/a	n/a
26	CTCF	chr4:90579200-90579350	SK-N-SH_RA	brain:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
27	CTCF	chr4:90579220-90579370	HCT-116	colon:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
28	CTCF	chr4:90578660-90578810	BJ	skin:	n/a	n/a
29	CTCF	chr4:90579160-90579310	GM12878	blood:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
30	CTCF	chr4:90579160-90579310	HA-sp	spinal cord:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
31	CTCF	chr4:90578940-90579090	GM06990	blood:	n/a	n/a
32	CTCF	chr4:90579240-90579390	HCM	heart:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
33	CTCF	chr4:90579240-90579390	HCT-116	colon:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
34	CTCF	chr4:90579140-90579290	SAEC	small airway:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
35	CTCF	chr4:90579220-90579370	HCPEpiC	choroid plexus:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
36	CTCF	chr4:90579140-90579290	GM12865	blood:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
37	CTCF	chr4:90579180-90579330	NHEK	skin:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
38	CTCF	chr4:90579820-90579970	RPTEC	kidney:	n/a	n/a
39	CTCF	chr4:90579180-90579330	GM12873	blood:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
40	CTCF	chr4:90579060-90579210	GM12872	blood:	n/a	n/a
41	CTCF	chr4:90578964-90579568	HCT-116	colon:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
42	CTCF	chr4:90579077-90579487	IMR90	lung:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
43	CTCF	chr4:90579200-90579350	AG04449	skin:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
44	CTCF	chr4:90579180-90579330	NHDF-neo	bronchial:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
45	CTCF	chr4:90578989-90579598	A549	lung:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
46	CTCF	chr4:90579040-90579190	HAc	cerebellar:	n/a	n/a
47	CTCF	chr4:90579160-90579310	HEK293	kidney:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
48	CTCF	chr4:90579200-90579350	GM12864	blood:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
49	CTCF	chr4:90579193-90579360	GM13977	blood:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285
50	CTCF	chr4:90579220-90579370	GM12864	blood:	n/a	chr4:90579263-90579279 chr4:90579262-90579280 chr4:90579264-90579285

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MMRN1-2	chr4:90581365-90581506	ENSG00000251095.1
2	lnc-MMRN1-2	chr4:90602663-90602835	ENSG00000251095.1

Variant related genes	Relation type
ENSG00000251095	TF binding region

Extended variants
information (count: 1080 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:1080 , 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	rs28673968	chr4:90576890-90576891	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs142701895	chr4:90576892-90576893	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs549995913	chr4:90576921-90576922	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs182047218	chr4:90576928-90576929	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs538695676	chr4:90576953-90576954	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs534009821	chr4:90576971-90576972	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs185604899	chr4:90576986-90576987	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs565650893	chr4:90577002-90577003	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs534239881	chr4:90577013-90577014	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs370695511	chr4:90577026-90577027	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs574229708	chr4:90577039-90577040	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs189263238	chr4:90577041-90577042	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs77169992	chr4:90577044-90577045	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs544432438	chr4:90577097-90577098	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs186381783	chr4:90577099-90577100	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs111644023	chr4:90577150-90577151	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs552243819	chr4:90577169-90577170	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs138104136	chr4:90577210-90577211	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs561280403	chr4:90577226-90577227	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs34679330	chr4:90577228-90577229	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs531495271	chr4:90577272-90577273	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs550008355	chr4:90577306-90577307	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs571419952	chr4:90577310-90577311	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs568898549	chr4:90577328-90577329	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs577875194	chr4:90577377-90577378	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs547481534	chr4:90577406-90577407	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs565623779	chr4:90577467-90577468	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs536273531	chr4:90577479-90577480	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs554265436	chr4:90577554-90577555	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs567991236	chr4:90577562-90577563	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs149506766	chr4:90577563-90577564	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs563897615	chr4:90577568-90577569	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs556344438	chr4:90577586-90577587	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs554756032	chr4:90577645-90577646	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs577790626	chr4:90577666-90577667	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs538766574	chr4:90577709-90577710	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs189934164	chr4:90577719-90577720	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs181198173	chr4:90577727-90577728	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs73833508	chr4:90577745-90577746	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs186032292	chr4:90577746-90577747	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs568282175	chr4:90577843-90577844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs543712080	chr4:90577852-90577853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs565091378	chr4:90577879-90577880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs368354237	chr4:90577886-90577887	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs532383064	chr4:90577914-90577915	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs547593617	chr4:90577969-90577970	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs559446803	chr4:90578020-90578021	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs529748916	chr4:90578033-90578034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs190443387	chr4:90578109-90578110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs576628535	chr4:90578122-90578123	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:83)

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
Multiple myeloma	17550852	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	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
Olfactory neuroblastoma	18408657	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
Acute monocytic leukemia	16498392	CNVD
Multiple myeloma	16616336	CNVD
Esophageal adenocarcinoma	18820669	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myelofibrosis	22110671	CNVD
Parkinson disease	20877625	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Obesity	20622171	CNVD
Hodgkin''s lymphoma	17606441	CNVD

Chromatin state (count:142 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90576800-90577800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:90577800-90602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:90578800-90579000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:90579000-90581600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:90579200-90579600	Enhancers	Dnd41	blood
6	chr4:90579200-90580000	Enhancers	NHEK	skin
7	chr4:90579600-90580000	Enhancers	HMEC	breast
8	chr4:90579600-90580200	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:90579600-90580200	Enhancers	GM12878-XiMat	blood
10	chr4:90579800-90580000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:90579800-90580000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:90579800-90580000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:90580000-90581400	Weak transcription	HMEC	breast
14	chr4:90580000-90581400	Weak transcription	NHEK	skin
15	chr4:90581000-90583400	Enhancers	Hela-S3	cervix
16	chr4:90581400-90582200	Enhancers	NHEK	skin
17	chr4:90581400-90587200	Enhancers	HMEC	breast
18	chr4:90581600-90583200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:90581600-90583200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:90581600-90583400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr4:90581600-90583800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:90581600-90587200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:90581800-90582200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:90581800-90583000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:90581800-90583200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:90581800-90585800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:90581800-90587400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:90582200-90582400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:90582200-90582600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr4:90582200-90582800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:90582200-90583000	Enhancers	HUVEC	blood vessel
32	chr4:90582200-90583000	Flanking Active TSS	NHEK	skin
33	chr4:90582200-90583000	Enhancers	Osteobl	bone
34	chr4:90582200-90583200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr4:90582200-90583200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr4:90582200-90583200	Enhancers	NH-A	brain
37	chr4:90582400-90582800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr4:90582400-90582800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:90582400-90582800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:90582400-90582800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr4:90582400-90582800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr4:90582400-90582800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr4:90582400-90583000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:90582400-90583000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr4:90582400-90583000	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr4:90582400-90583000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:90582400-90583000	Enhancers	HSMMtube	muscle
48	chr4:90582400-90583000	Enhancers	NHLF	lung
49	chr4:90582400-90583200	Enhancers	HSMM	muscle
50	chr4:90582600-90602600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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