Variant report

Variant	nsv1008543
Chromosome Location	chr3:42372639-42401033
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	chr3:42391318-42391484	K562	blood:	n/a	n/a
2	CCNT2	chr3:42391260-42391638	K562	blood:	n/a	chr3:42391381-42391401
3	CEBPB	chr3:42387069-42387539	K562	blood:	n/a	chr3:42387217-42387230
4	CEBPB	chr3:42374037-42374350	HepG2	liver:	n/a	chr3:42374188-42374199
5	CEBPB	chr3:42374024-42374355	Hela-S3	cervix:	n/a	chr3:42374188-42374199
6	CEBPB	chr3:42388002-42388170	K562	blood:	n/a	n/a
7	CEBPB	chr3:42374006-42374374	K562	blood:	n/a	chr3:42374188-42374199
8	CEBPB	chr3:42377642-42377824	HepG2	liver:	n/a	chr3:42377731-42377742
9	CEBPB	chr3:42373982-42374289	K562	blood:	n/a	chr3:42374188-42374199
10	CEBPB	chr3:42377656-42377881	K562	blood:	n/a	chr3:42377731-42377742
11	CEBPB	chr3:42374093-42374366	IMR90	lung:	n/a	chr3:42374188-42374199
12	CEBPB	chr3:42374064-42374341	H1-hESC	embryonic stem cell:	n/a	chr3:42374188-42374199
13	CEBPB	chr3:42393387-42393557	HepG2	liver:	n/a	chr3:42393519-42393530
14	CEBPB	chr3:42374038-42374369	A549	lung:	n/a	chr3:42374188-42374199
15	CEBPB	chr3:42377621-42377867	K562	blood:	n/a	chr3:42377731-42377742
16	CEBPD	chr3:42391166-42391729	K562	blood:	n/a	n/a
17	CEBPD	chr3:42391106-42391551	K562	blood:	n/a	n/a
18	CTCF	chr3:42383500-42383650	HCT-116	colon:	n/a	n/a
19	CTCF	chr3:42383500-42383650	RPTEC	kidney:	n/a	n/a
20	CTCF	chr3:42383460-42383610	WERI-Rb-1	eye:	n/a	n/a
21	CTCF	chr3:42383400-42383550	HRPEpiC	eye:	n/a	n/a
22	CTCF	chr3:42379060-42379210	GM12867	blood:	n/a	n/a
23	CTCF	chr3:42383480-42383630	A549	lung:	n/a	n/a
24	CTCF	chr3:42383486-42383594	HepG2	liver:	n/a	n/a
25	CTCF	chr3:42387800-42387841	GM10248	blood:	n/a	n/a
26	CTCF	chr3:42383720-42383870	GM12864	blood:	n/a	n/a
27	CTCF	chr3:42375356-42375410	K562	blood:	n/a	n/a
28	CTCF	chr3:42378900-42379050	GM12867	blood:	n/a	n/a
29	CTCF	chr3:42383501-42383603	MCF-7	breast:	n/a	n/a
30	CTCF	chr3:42383480-42383630	MCF-7	breast:	n/a	n/a
31	CTCF	chr3:42383440-42383590	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr3:42383380-42383530	GM12873	blood:	n/a	n/a
33	CTCF	chr3:42383480-42383630	Caco-2	colon:	n/a	n/a
34	CTCF	chr3:42383580-42383730	SK-N-SH_RA	brain:	n/a	n/a
35	CTCF	chr3:42375348-42375355	K562	blood:	n/a	n/a
36	CTCF	chr3:42383480-42383630	K562	blood:	n/a	n/a
37	CTCF	chr3:42383500-42383650	GM12864	blood:	n/a	n/a
38	CTCF	chr3:42383480-42383630	HEK293	kidney:	n/a	n/a
39	CTCF	chr3:42383240-42383390	NHEK	skin:	n/a	n/a
40	CTCF	chr3:42383400-42383550	GM12864	blood:	n/a	n/a
41	CTCF	chr3:42383480-42383630	HCT-116	colon:	n/a	n/a
42	CTCF	chr3:42383440-42383590	GM12865	blood:	n/a	n/a
43	CTCF	chr3:42383440-42383590	MCF-7	breast:	n/a	n/a
44	CTCF	chr3:42383400-42383550	GM12875	blood:	n/a	n/a
45	CTCF	chr3:42395380-42395530	GM12866	blood:	n/a	n/a
46	CTCF	chr3:42383400-42383550	WERI-Rb-1	eye:	n/a	n/a
47	CTCF	chr3:42375260-42375410	GM06990	blood:	n/a	n/a
48	CTCF	chr3:42383480-42383630	NHEK	skin:	n/a	n/a
49	CTCF	chr3:42383460-42383610	GM12867	blood:	n/a	n/a
50	CTCF	chr3:42383480-42383630	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42387656..42389611-chr3:42394968..42396498,2	K562	blood:
2	chr3:42380106..42383647-chr3:42383812..42387475,4	K562	blood:
3	chr3:42387656..42389611-chr3:42394968..42396498,2	K562	blood:
4	chr3:42355817..42358731-chr3:42372025..42373776,2	MCF-7	breast:
5	chr3:42399764..42401290-chr3:42403071..42405403,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAK1-8	chr3:42382080-42383859	NONHSAT089217

Variant related genes	Relation type
EIF4BP4	TF binding region
ENSG00000229572	chromatin interactions

Extended variants
information (count: 901 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:901 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541037047	chr3:42377411-42377412	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs6802259	chr3:42377413-42377414	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs11714921	chr3:42377442-42377443	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs367703663	chr3:42377485-42377486	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs150906636	chr3:42377504-42377505	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs544680836	chr3:42377536-42377537	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs531809617	chr3:42377545-42377546	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs184010602	chr3:42377558-42377559	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs187767536	chr3:42377560-42377561	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs533895602	chr3:42377631-42377632	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs80059903	chr3:42377644-42377645	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs140244181	chr3:42377713-42377714	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs539775122	chr3:42377744-42377745	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs556693279	chr3:42377752-42377753	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs116610893	chr3:42377797-42377798	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs377500074	chr3:42377823-42377824	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs581175	chr3:42377856-42377857	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs191335224	chr3:42377862-42377863	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs560493095	chr3:42377879-42377880	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs540998155	chr3:42377883-42377884	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs13322333	chr3:42377940-42377941	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs577987623	chr3:42377961-42377962	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs182798926	chr3:42377989-42377990	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs74934197	chr3:42377999-42378000	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs529117181	chr3:42378002-42378003	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs549173961	chr3:42378015-42378016	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs561995781	chr3:42378023-42378024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs527803821	chr3:42378049-42378050	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs115368591	chr3:42378069-42378070	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs6781092	chr3:42378073-42378074	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs79541859	chr3:42378080-42378081	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs17073603	chr3:42378103-42378104	Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance
33	rs76246369	chr3:42378113-42378114	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs666391	chr3:42378133-42378134	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs555947971	chr3:42378150-42378151	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs572135208	chr3:42378178-42378179	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs1019188	chr3:42378179-42378180	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs557765380	chr3:42378188-42378189	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs566382844	chr3:42378240-42378241	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs577759157	chr3:42378249-42378250	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs543732392	chr3:42378255-42378256	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs373089962	chr3:42378308-42378309	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs534087700	chr3:42378324-42378325	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs552744510	chr3:42378939-42378940	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs367804178	chr3:42378966-42378967	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs548920870	chr3:42378975-42378976	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs572738159	chr3:42378978-42378979	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs73828817	chr3:42379012-42379013	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs368737486	chr3:42379013-42379014	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs564193926	chr3:42379097-42379098	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42377400-42378400	Enhancers	HMEC	breast
2	chr3:42381000-42381800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:42381600-42382400	Enhancers	Brain Germinal Matrix	brain
4	chr3:42381800-42382000	Enhancers	HSMM	muscle
5	chr3:42382000-42384200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr3:42383600-42384000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:42384000-42387000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:42384200-42385800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:42385800-42389800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr3:42386400-42388200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:42386600-42391600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:42386800-42387000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:42386800-42387200	Enhancers	Primary T cells from cord blood	blood
14	chr3:42386800-42387400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr3:42386800-42388000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:42386800-42388000	Enhancers	Thymus	Thymus
17	chr3:42386800-42390400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:42387000-42387400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr3:42387000-42387800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:42387000-42387800	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:42387200-42387600	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr3:42387200-42387600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr3:42387200-42388000	Enhancers	K562	blood
24	chr3:42387200-42388200	Enhancers	Fetal Thymus	thymus
25	chr3:42387400-42387600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:42387400-42387600	Enhancers	Brain Germinal Matrix	brain
27	chr3:42387400-42387800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr3:42387400-42389800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr3:42387400-42390400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr3:42387400-42390600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:42387600-42389400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:42387600-42390000	Enhancers	Primary T cells from cord blood	blood
33	chr3:42387800-42388400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:42387800-42388800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:42387800-42390200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:42388000-42389600	Weak transcription	Thymus	Thymus
37	chr3:42388000-42391000	Weak transcription	K562	blood
38	chr3:42388200-42388600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:42388200-42388600	Weak transcription	Fetal Thymus	thymus
40	chr3:42388400-42388800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:42388600-42390000	Enhancers	Fetal Thymus	thymus
42	chr3:42388600-42390600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:42388800-42391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:42389000-42389200	Enhancers	Primary hematopoietic stem cells	blood
45	chr3:42389400-42390200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:42389400-42390600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr3:42389400-42391200	Weak transcription	Right Atrium	heart
48	chr3:42389800-42390000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:42389800-42390000	Enhancers	Thymus	Thymus
50	chr3:42389800-42390200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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