Variant report

Variant	nsv5328
Chromosome Location	chr6:65417895-65463156
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	BRCA1	chr6:65443446-65443561	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr6:65421458-65421712	IMR90	lung:	n/a	chr6:65421589-65421602 chr6:65421590-65421601 chr6:65421589-65421602
3	CEBPB	chr6:65436981-65437350	HepG2	liver:	n/a	chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437162-65437173 chr6:65437162-65437175
4	CEBPB	chr6:65436982-65437340	IMR90	lung:	n/a	chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437162-65437173 chr6:65437162-65437175
5	CEBPB	chr6:65448345-65448642	HepG2	liver:	n/a	chr6:65448503-65448514
6	CEBPB	chr6:65421473-65421750	HepG2	liver:	n/a	chr6:65421589-65421602 chr6:65421590-65421601 chr6:65421589-65421602
7	CEBPB	chr6:65446422-65446723	H1-hESC	embryonic stem cell:	n/a	chr6:65446561-65446570 chr6:65446561-65446570 chr6:65446559-65446570 chr6:65446561-65446570 chr6:65446559-65446572
8	CEBPB	chr6:65446447-65446715	A549	lung:	n/a	chr6:65446561-65446570 chr6:65446561-65446570 chr6:65446559-65446570 chr6:65446561-65446570 chr6:65446559-65446572
9	CEBPB	chr6:65446416-65446810	MCF-7	breast:	n/a	chr6:65446561-65446570 chr6:65446561-65446570 chr6:65446559-65446570 chr6:65446561-65446570 chr6:65446559-65446572
10	CEBPB	chr6:65437031-65437343	ECC-1	luminal epithelium:	n/a	chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437162-65437173 chr6:65437162-65437175
11	CEBPB	chr6:65446376-65446755	IMR90	lung:	n/a	chr6:65446561-65446570 chr6:65446561-65446570 chr6:65446559-65446570 chr6:65446561-65446570 chr6:65446559-65446572
12	CEBPB	chr6:65446290-65446790	MCF-7	breast:	n/a	chr6:65446561-65446570 chr6:65446561-65446570 chr6:65446559-65446570 chr6:65446561-65446570 chr6:65446559-65446572
13	CEBPB	chr6:65436997-65437335	H1-hESC	embryonic stem cell:	n/a	chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437162-65437173 chr6:65437162-65437175
14	CEBPB	chr6:65421566-65421761	A549	lung:	n/a	chr6:65421589-65421602 chr6:65421590-65421601 chr6:65421589-65421602
15	CEBPB	chr6:65446425-65446730	HepG2	liver:	n/a	chr6:65446561-65446570 chr6:65446561-65446570 chr6:65446559-65446570 chr6:65446561-65446570 chr6:65446559-65446572
16	CEBPB	chr6:65436982-65437316	A549	lung:	n/a	chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437162-65437173 chr6:65437162-65437175
17	CEBPB	chr6:65433198-65433512	IMR90	lung:	n/a	chr6:65433331-65433342
18	CEBPB	chr6:65442868-65443475	HepG2	liver:	n/a	chr6:65443299-65443310
19	CEBPB	chr6:65436989-65437316	K562	blood:	n/a	chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437164-65437173 chr6:65437162-65437173 chr6:65437162-65437175
20	CEBPB	chr6:65421500-65421697	K562	blood:	n/a	chr6:65421589-65421602 chr6:65421590-65421601 chr6:65421589-65421602
21	CEBPB	chr6:65433201-65433520	A549	lung:	n/a	chr6:65433331-65433342
22	CEBPB	chr6:65446394-65446706	Hela-S3	cervix:	n/a	chr6:65446561-65446570 chr6:65446561-65446570 chr6:65446559-65446570 chr6:65446561-65446570 chr6:65446559-65446572
23	CEBPB	chr6:65442685-65443109	MCF-7	breast:	n/a	n/a
24	CEBPB	chr6:65433198-65433524	HepG2	liver:	n/a	chr6:65433331-65433342
25	CTCF	chr6:65442820-65442970	WERI-Rb-1	eye:	n/a	n/a
26	CTCF	chr6:65442860-65443010	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr6:65442780-65442930	MCF-7	breast:	n/a	n/a
28	CTCF	chr6:65442760-65442910	RPTEC	kidney:	n/a	n/a
29	CTCF	chr6:65442800-65442950	HCFaa	heart:	n/a	n/a
30	CTCF	chr6:65442897-65442944	K562	blood:	n/a	n/a
31	CTCF	chr6:65442820-65442970	HAc	cerebellar:	n/a	n/a
32	CTCF	chr6:65446580-65446730	HPAF	blood vessel:	n/a	n/a
33	CTCF	chr6:65442860-65443010	HVMF	connective:	n/a	n/a
34	CTCF	chr6:65442829-65443050	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr6:65442840-65442990	RPTEC	kidney:	n/a	n/a
36	CTCF	chr6:65442820-65442970	HCPEpiC	choroid plexus:	n/a	n/a
37	CTCF	chr6:65442652-65443206	MCF-7	breast:	n/a	n/a
38	CTCF	chr6:65442840-65443016	ProgFib	skin:	n/a	n/a
39	CTCF	chr6:65442880-65443030	HVMF	connective:	n/a	n/a
40	CTCF	chr6:65446560-65446710	HPF	lung:	n/a	n/a
41	CTCF	chr6:65446580-65446730	HCPEpiC	choroid plexus:	n/a	n/a
42	CTCF	chr6:65461500-65461650	HMEC	breast:	n/a	n/a
43	CTCF	chr6:65442940-65443090	A549	lung:	n/a	n/a
44	CTCF	chr6:65446480-65446630	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr6:65442920-65443070	HEEpiC	esophagus:	n/a	n/a
46	CTCF	chr6:65442840-65442990	NB4	blood:	n/a	n/a
47	CTCF	chr6:65446486-65446765	MCF-7	breast:	n/a	n/a
48	CTCF	chr6:65442725-65443084	GM12878	blood:	n/a	n/a
49	CTCF	chr6:65442840-65442990	HPAF	blood vessel:	n/a	n/a
50	CTCF	chr6:65442840-65442990	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:65429271..65430989-chr6:65432501..65434234,2	K562	blood:
2	chr6:64523219..64524103-chr6:65442776..65443345,2	MCF-7	breast:
3	chr6:65423336..65423981-chr6:160399331..160400281,2	MCF-7	breast:
4	chr6:65429271..65430989-chr6:65432501..65434234,2	K562	blood:
5	chr6:64990450..64991143-chr6:65442394..65443437,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LGSN-1	chr6:65440706-65440885	ENSG00000243828.1
2	lnc-LGSN-1	chr6:65438730-65438951	ENSG00000243828.1
3	lnc-LGSN-1	chr6:65443266-65443460	ENSG00000243828.1
4	lnc-LGSN-1	chr6:65443266-65443438	ENSG00000243828.1
5	lnc-LGSN-5	chr6:65423165-65423228	NONHSAT113363

Variant related genes	Relation type
ENSG00000243828	TF binding region
EYS	TF binding region

Extended variants
information (count: 467 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:467 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs147807339	chr6:65419807-65419808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs16895682	chr6:65419819-65419820	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs6915156	chr6:65419889-65419890	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs6914002	chr6:65419968-65419969	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs6914016	chr6:65419997-65419998	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs532666668	chr6:65420010-65420011	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs530117564	chr6:65420031-65420032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs552454429	chr6:65420063-65420064	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs141245844	chr6:65420077-65420078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs376165515	chr6:65420088-65420089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs570867812	chr6:65420098-65420099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs186701370	chr6:65420104-65420105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs547034379	chr6:65420130-65420131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs567225646	chr6:65420146-65420147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs6914376	chr6:65420160-65420161	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs542116798	chr6:65420179-65420180	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs556059827	chr6:65420200-65420201	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs146923828	chr6:65420207-65420208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs569839074	chr6:65420259-65420260	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs560418713	chr6:65420286-65420287	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs55931380	chr6:65420298-65420299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs552755491	chr6:65420314-65420315	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs116259040	chr6:65420315-65420316	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs190075271	chr6:65420323-65420324	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs73442626	chr6:65420331-65420332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs543917213	chr6:65420337-65420338	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs564801134	chr6:65420359-65420360	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs532749056	chr6:65420394-65420395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs140584374	chr6:65420407-65420408	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs559613015	chr6:65420440-65420441	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs115071751	chr6:65420454-65420455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs546970284	chr6:65420460-65420461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs567266316	chr6:65420469-65420470	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs527628993	chr6:65420525-65420526	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs60496485	chr6:65420580-65420581	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs567486844	chr6:65420625-65420626	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs549860816	chr6:65420633-65420634	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs569692128	chr6:65420710-65420711	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs114352750	chr6:65420714-65420715	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs59418456	chr6:65420727-65420728	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs367887418	chr6:65420758-65420759	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs181023780	chr6:65420827-65420828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs534932213	chr6:65420849-65420850	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs554975094	chr6:65420857-65420858	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs76362101	chr6:65420893-65420894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs36118226	chr6:65420913-65420914	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs557417421	chr6:65420927-65420928	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs75644396	chr6:65420963-65420964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs545963687	chr6:65420993-65420994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs559551801	chr6:65421013-65421014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Systemic lupus erythematosus	17503323	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Melanoma	18172304	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Cancer	21637783	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
T-cell lymphomas	19863542	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	19010834	CNVD
Non-small cell lung cancer	21044232	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21385341	CNVD
Prostate cancer	16705090	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Ependymoma	16718352	CNVD
High-proliferative meningiomas	17937814	CNVD
Intracranial tumor	16823260	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	16573809	CNVD
Ovarian cancer	19835627	CNVD
Myelofibrosis	22110671	CNVD
Cancer	21183584	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	16272173	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	20016488	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Epilepsy	20502679	CNVD
Dyslexia	22102821	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Urothelial carcinoma	18382360	CNVD
Ovarian neoplasms	16753589	CNVD
Hepatocellular carcinoma	16750200	CNVD

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:65419800-65422000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:65420600-65420800	Enhancers	HUVEC	blood vessel
3	chr6:65420800-65421800	Weak transcription	HUVEC	blood vessel
4	chr6:65421800-65423400	Enhancers	HUVEC	blood vessel
5	chr6:65422000-65423200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:65422200-65422800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:65422200-65423600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:65422200-65423600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:65422400-65422800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:65422600-65423000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr6:65422800-65423400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:65422800-65423600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:65423400-65423800	Weak transcription	HUVEC	blood vessel
14	chr6:65423800-65424200	Enhancers	HUVEC	blood vessel
15	chr6:65427400-65427600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:65430800-65431000	Enhancers	Fetal Brain Male	brain
17	chr6:65431000-65431400	Enhancers	Fetal Brain Female	brain
18	chr6:65431000-65432400	Weak transcription	Fetal Brain Male	brain
19	chr6:65431400-65431800	Weak transcription	Fetal Brain Female	brain
20	chr6:65431800-65432000	Enhancers	Fetal Brain Female	brain
21	chr6:65432000-65433000	Weak transcription	Fetal Brain Female	brain
22	chr6:65432400-65434400	Enhancers	Fetal Brain Male	brain
23	chr6:65433000-65434400	Enhancers	Fetal Brain Female	brain
24	chr6:65436800-65437000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:65460600-65461200	Enhancers	NHEK	skin
26	chr6:65460600-65461400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr6:65460600-65461600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:65460600-65461800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:65460600-65461800	Enhancers	Esophagus	oesophagus
30	chr6:65460600-65461800	Enhancers	HMEC	breast

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