Variant report

Variant	nsv4417
Chromosome Location	chr4:90515836-90560439
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	chr4:90519647-90519847	H1-hESC	embryonic stem cell:	n/a	chr4:90519693-90519702
2	CEBPB	chr4:90516750-90516855	A549	lung:	n/a	chr4:90516840-90516853
3	CEBPB	chr4:90519585-90519863	HepG2	liver:	n/a	chr4:90519693-90519702
4	CHD1	chr4:90530266-90530311	GM12878	blood:	n/a	n/a
5	CTCF	chr4:90519599-90520180	SK-N-SH	brain:	n/a	chr4:90519922-90519929
6	CTCF	chr4:90519820-90519970	GM12871	blood:	n/a	chr4:90519922-90519929
7	CTCF	chr4:90519840-90519990	GM12873	blood:	n/a	chr4:90519922-90519929
8	CTCF	chr4:90519840-90519990	GM12872	blood:	n/a	chr4:90519922-90519929
9	CTCF	chr4:90519760-90519910	RPTEC	kidney:	n/a	n/a
10	CTCF	chr4:90519813-90519987	MCF-7	breast:	n/a	chr4:90519922-90519929
11	CTCF	chr4:90519840-90519990	AG04450	lung:	n/a	chr4:90519922-90519929
12	CTCF	chr4:90519825-90519992	HepG2	liver:	n/a	chr4:90519922-90519929
13	CTCF	chr4:90519860-90520010	Caco-2	colon:	n/a	chr4:90519922-90519929
14	CTCF	chr4:90519840-90519990	HMF	breast:	n/a	chr4:90519922-90519929
15	CTCF	chr4:90519800-90519950	HEEpiC	esophagus:	n/a	chr4:90519922-90519929
16	CTCF	chr4:90519814-90520012	LNCaP	prostate:	n/a	chr4:90519922-90519929
17	CTCF	chr4:90519860-90520010	HA-sp	spinal cord:	n/a	chr4:90519922-90519929
18	CTCF	chr4:90519880-90520030	GM12864	blood:	n/a	chr4:90519922-90519929
19	CTCF	chr4:90519820-90519970	GM12873	blood:	n/a	chr4:90519922-90519929
20	CTCF	chr4:90519800-90519950	HPAF	blood vessel:	n/a	chr4:90519922-90519929
21	CTCF	chr4:90519833-90519965	MCF-7	breast:	n/a	chr4:90519922-90519929
22	CTCF	chr4:90519816-90519984	Gliobla	brain:	n/a	chr4:90519922-90519929
23	CTCF	chr4:90531587-90531623	MCF-7	breast:	n/a	n/a
24	CTCF	chr4:90519765-90520007	H1-hESC	embryonic stem cell:	n/a	chr4:90519922-90519929
25	CTCF	chr4:90519820-90519970	GM12878	blood:	n/a	chr4:90519922-90519929
26	CTCF	chr4:90519820-90519970	BE2_C	brain:	n/a	chr4:90519922-90519929
27	CTCF	chr4:90519820-90519970	HRPEpiC	eye:	n/a	chr4:90519922-90519929
28	CTCF	chr4:90519840-90519990	GM12874	blood:	n/a	chr4:90519922-90519929
29	CTCF	chr4:90519800-90519950	GM12866	blood:	n/a	chr4:90519922-90519929
30	CTCF	chr4:90519846-90519982	Spleen_OC	spleen:	n/a	chr4:90519922-90519929
31	CTCF	chr4:90519760-90519910	HAc	cerebellar:	n/a	n/a
32	CTCF	chr4:90519760-90519910	GM12867	blood:	n/a	n/a
33	CTCF	chr4:90519799-90520034	Hela-S3	cervix:	n/a	chr4:90519922-90519929
34	CTCF	chr4:90519760-90519910	GM12871	blood:	n/a	n/a
35	CTCF	chr4:90531560-90531710	GM12878	blood:	n/a	n/a
36	CTCF	chr4:90519840-90519990	AG09319	gingival:	n/a	chr4:90519922-90519929
37	CTCF	chr4:90519826-90519931	NHEK	skin:	n/a	chr4:90519922-90519929
38	CTCF	chr4:90531484-90531679	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr4:90519820-90519970	HUVEC	blood vessel:	n/a	chr4:90519922-90519929
40	CTCF	chr4:90521285-90521311	GM20000	blood:	n/a	n/a
41	CTCF	chr4:90519842-90519998	Medullo	brain:	n/a	chr4:90519922-90519929
42	CTCF	chr4:90531605-90531619	GM20000	blood:	n/a	n/a
43	CTCF	chr4:90519840-90519990	SAEC	small airway:	n/a	chr4:90519922-90519929
44	CTCF	chr4:90519780-90519930	GM12875	blood:	n/a	chr4:90519922-90519929
45	CTCF	chr4:90531580-90531730	GM12864	blood:	n/a	n/a
46	CTCF	chr4:90519780-90519930	Hela-S3	cervix:	n/a	chr4:90519922-90519929
47	CTCF	chr4:90519840-90519990	AG04449	skin:	n/a	chr4:90519922-90519929
48	CTCF	chr4:90531946-90531999	LNCaP	prostate:	n/a	n/a
49	CTCF	chr4:90519820-90519970	Hela-S3	cervix:	n/a	chr4:90519922-90519929
50	CTCF	chr4:90519760-90519910	AG04450	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:90520190..90521796-chr4:90522744..90524416,2	K562	blood:
2	chr4:90520190..90521796-chr4:90522744..90524416,2	K562	blood:
3	chr4:90519485..90520442-chr4:90822646..90823686,5	MCF-7	breast:
4	chr4:90519778..90520510-chr4:90789267..90790448,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MMRN1-2	chr4:90548933-90549068	ENSG00000251095.1
2	lnc-TIGD2-1	chr4:90548935-90549068	ENSG00000251095.2
3	lnc-TIGD2-1	chr4:90548933-90549065	NONHSAT097397
4	lnc-MMRN1-2	chr4:90548933-90549068	ENSG00000251095.1
5	lnc-MMRN1-2	chr4:90548933-90549068	ENSG00000251095.1
6	lnc-MMRN1-2	chr4:90548935-90549068	ENSG00000251095.1
7	lnc-MMRN1-2	chr4:90548933-90549068	ENSG00000251095.1

Variant related genes	Relation type
ENSG00000251095	TF binding region
ENSG00000138722	chromatin interactions

Extended variants
information (count: 897 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:897 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541242711	chr4:90515888-90515889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs542109841	chr4:90515889-90515890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs373746089	chr4:90515894-90515895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs11932543	chr4:90515903-90515904	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs367920827	chr4:90515931-90515932	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs372512158	chr4:90515988-90515989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs75870625	chr4:90516045-90516046	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs189717135	chr4:90516057-90516058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs563297146	chr4:90516104-90516105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs34812564	chr4:90516129-90516130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs10516841	chr4:90516159-90516160	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs546122536	chr4:90516194-90516195	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs564222676	chr4:90516247-90516248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs528318825	chr4:90516254-90516255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs546464749	chr4:90516266-90516267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs56997103	chr4:90516267-90516268	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs139620814	chr4:90516276-90516277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs550602766	chr4:90516288-90516289	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs577380803	chr4:90516295-90516296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs568909874	chr4:90516299-90516300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs181755583	chr4:90516304-90516305	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs11097227	chr4:90516308-90516309	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs571039531	chr4:90516318-90516319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs535235050	chr4:90516391-90516392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs553125041	chr4:90516462-90516463	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs574596882	chr4:90516577-90516578	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs113929335	chr4:90516636-90516637	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs541881538	chr4:90516644-90516645	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs1473533	chr4:90516679-90516680	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs186780142	chr4:90516732-90516733	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs572039040	chr4:90516733-90516734	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs564442216	chr4:90516758-90516759	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs1473532	chr4:90516766-90516767	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs540423778	chr4:90516811-90516812	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs111945040	chr4:90516857-90516858	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs190627457	chr4:90516858-90516859	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs182050630	chr4:90516861-90516862	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs73830657	chr4:90516865-90516866	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs568951065	chr4:90516903-90516904	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs532977823	chr4:90516936-90516937	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs189954712	chr4:90516948-90516949	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs571147124	chr4:90516985-90516986	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs147853385	chr4:90516997-90516998	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs554239259	chr4:90519553-90519554	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs58739806	chr4:90519571-90519572	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs78764154	chr4:90519630-90519631	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs565009776	chr4:90519644-90519645	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs527664340	chr4:90519667-90519668	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs563054564	chr4:90519707-90519708	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs533647716	chr4:90519708-90519709	Inactive region	Chromatin interactive region	1 gene(s)	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:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90512400-90516400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:90516400-90516800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:90516600-90517000	Enhancers	Fetal Kidney	kidney
4	chr4:90520000-90520600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:90530000-90530400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:90530400-90535200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:90531400-90531800	Enhancers	Dnd41	blood
8	chr4:90531600-90532000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:90531800-90537200	Weak transcription	Dnd41	blood
10	chr4:90535200-90535800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:90535200-90535800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr4:90535600-90535800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:90535800-90536000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:90535800-90536000	Enhancers	Fetal Kidney	kidney
15	chr4:90535800-90537600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:90535800-90537800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:90536000-90537400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:90536200-90537400	Weak transcription	Fetal Kidney	kidney
19	chr4:90537200-90538200	Enhancers	Dnd41	blood
20	chr4:90537400-90538800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:90537400-90538800	Enhancers	Fetal Kidney	kidney
22	chr4:90537600-90538000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:90537600-90538000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr4:90537600-90541400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:90537800-90538000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr4:90537800-90538200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:90537800-90538400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr4:90537800-90538800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:90538000-90540200	Enhancers	Primary T cells from cord blood	blood
30	chr4:90538200-90538800	Enhancers	Stomach Mucosa	stomach
31	chr4:90538200-90539400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:90538200-90539400	Weak transcription	Dnd41	blood
33	chr4:90538200-90545200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:90538800-90539200	Weak transcription	Fetal Kidney	kidney
35	chr4:90538800-90539600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:90538800-90540200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:90539200-90540600	Enhancers	Fetal Kidney	kidney
38	chr4:90539200-90541200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:90539400-90539600	Enhancers	Fetal Thymus	thymus
40	chr4:90539400-90540200	Enhancers	Dnd41	blood
41	chr4:90539400-90541000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr4:90539400-90541000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:90539400-90541400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:90539600-90540200	Weak transcription	Fetal Thymus	thymus
45	chr4:90539600-90540400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:90539600-90541400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr4:90539800-90540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:90539800-90541000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr4:90540000-90540800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:90540000-90541200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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