Variant report

Variant	esv2756986
Chromosome Location	chr3:42360106-42403380
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	chr3:42374093-42374366	IMR90	lung:	n/a	chr3:42374188-42374199
4	CEBPB	chr3:42393387-42393557	HepG2	liver:	n/a	chr3:42393519-42393530
5	CEBPB	chr3:42374064-42374341	H1-hESC	embryonic stem cell:	n/a	chr3:42374188-42374199
6	CEBPB	chr3:42377642-42377824	HepG2	liver:	n/a	chr3:42377731-42377742
7	CEBPB	chr3:42374037-42374350	HepG2	liver:	n/a	chr3:42374188-42374199
8	CEBPB	chr3:42388002-42388170	K562	blood:	n/a	n/a
9	CEBPB	chr3:42377656-42377881	K562	blood:	n/a	chr3:42377731-42377742
10	CEBPB	chr3:42377621-42377867	K562	blood:	n/a	chr3:42377731-42377742
11	CEBPB	chr3:42373982-42374289	K562	blood:	n/a	chr3:42374188-42374199
12	CEBPB	chr3:42387069-42387539	K562	blood:	n/a	chr3:42387217-42387230
13	CEBPB	chr3:42374038-42374369	A549	lung:	n/a	chr3:42374188-42374199
14	CEBPB	chr3:42374024-42374355	Hela-S3	cervix:	n/a	chr3:42374188-42374199
15	CEBPB	chr3:42374006-42374374	K562	blood:	n/a	chr3:42374188-42374199
16	CEBPD	chr3:42391166-42391729	K562	blood:	n/a	n/a
17	CEBPD	chr3:42391106-42391551	K562	blood:	n/a	n/a
18	CTCF	chr3:42383400-42383550	WERI-Rb-1	eye:	n/a	n/a
19	CTCF	chr3:42383400-42383550	HRPEpiC	eye:	n/a	n/a
20	CTCF	chr3:42379060-42379210	GM12867	blood:	n/a	n/a
21	CTCF	chr3:42383480-42383630	HEK293	kidney:	n/a	n/a
22	CTCF	chr3:42383486-42383594	HepG2	liver:	n/a	n/a
23	CTCF	chr3:42383500-42383650	RPTEC	kidney:	n/a	n/a
24	CTCF	chr3:42383380-42383530	GM12873	blood:	n/a	n/a
25	CTCF	chr3:42383580-42383730	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr3:42383480-42383630	MCF-7	breast:	n/a	n/a
27	CTCF	chr3:42383440-42383590	MCF-7	breast:	n/a	n/a
28	CTCF	chr3:42383720-42383870	GM12864	blood:	n/a	n/a
29	CTCF	chr3:42383420-42383570	HAc	cerebellar:	n/a	n/a
30	CTCF	chr3:42383440-42383590	HepG2	liver:	n/a	n/a
31	CTCF	chr3:42383500-42383650	HCT-116	colon:	n/a	n/a
32	CTCF	chr3:42383480-42383630	HCT-116	colon:	n/a	n/a
33	CTCF	chr3:42375356-42375410	K562	blood:	n/a	n/a
34	CTCF	chr3:42383460-42383610	WERI-Rb-1	eye:	n/a	n/a
35	CTCF	chr3:42383440-42383590	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr3:42383400-42383550	GM12864	blood:	n/a	n/a
37	CTCF	chr3:42383240-42383390	NHEK	skin:	n/a	n/a
38	CTCF	chr3:42395380-42395530	GM12866	blood:	n/a	n/a
39	CTCF	chr3:42383480-42383630	GM06990	blood:	n/a	n/a
40	CTCF	chr3:42378900-42379050	GM12867	blood:	n/a	n/a
41	CTCF	chr3:42383480-42383630	GM12872	blood:	n/a	n/a
42	CTCF	chr3:42375348-42375355	K562	blood:	n/a	n/a
43	CTCF	chr3:42383501-42383603	MCF-7	breast:	n/a	n/a
44	CTCF	chr3:42383480-42383630	K562	blood:	n/a	n/a
45	CTCF	chr3:42383480-42383630	A549	lung:	n/a	n/a
46	CTCF	chr3:42387800-42387841	GM10248	blood:	n/a	n/a
47	CTCF	chr3:42383400-42383550	GM12875	blood:	n/a	n/a
48	CTCF	chr3:42383500-42383650	GM12864	blood:	n/a	n/a
49	CTCF	chr3:42383480-42383630	Caco-2	colon:	n/a	n/a
50	CTCF	chr3:42383460-42383610	GM12867	blood:	n/a	n/a

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

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

Variant related genes	Relation type
SALL4P6	TF binding region
EIF4BP4	TF binding region
ENSG00000229572	chromatin interactions

Extended variants
information (count: 1165 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:1165 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs552881238	chr3:42360573-42360574	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs7634057	chr3:42360590-42360591	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs578148570	chr3:42360631-42360632	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs543127716	chr3:42360645-42360646	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs562234529	chr3:42360731-42360732	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs375374071	chr3:42360749-42360750	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs141526572	chr3:42360803-42360804	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs528872975	chr3:42360834-42360835	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs548958180	chr3:42360864-42360865	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs474470	chr3:42360871-42360872	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs142877475	chr3:42360935-42360936	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs550308703	chr3:42360944-42360945	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs571334100	chr3:42361020-42361021	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs186825608	chr3:42361042-42361043	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs549999529	chr3:42361056-42361057	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs151051418	chr3:42361076-42361077	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs191554348	chr3:42361132-42361133	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs555311207	chr3:42361199-42361200	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs678574	chr3:42362817-42362818	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs550255404	chr3:42362860-42362861	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs559919175	chr3:42362866-42362867	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs528538261	chr3:42362885-42362886	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs551617352	chr3:42362919-42362920	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs192858094	chr3:42362938-42362939	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs677695	chr3:42362969-42362970	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs184823215	chr3:42363001-42363002	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs114198767	chr3:42363058-42363059	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs79210575	chr3:42363098-42363099	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs76302012	chr3:42363099-42363100	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs538714580	chr3:42363102-42363103	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs74405898	chr3:42363108-42363109	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs17081666	chr3:42363126-42363127	ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs189193913	chr3:42363186-42363187	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs574346950	chr3:42363192-42363193	ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs540159970	chr3:42363243-42363244	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs191374561	chr3:42363277-42363278	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs576991669	chr3:42363292-42363293	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs545481002	chr3:42363316-42363317	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs147416888	chr3:42363330-42363331	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs375141795	chr3:42363344-42363345	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs17223780	chr3:42363369-42363370	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs55881614	chr3:42363370-42363371	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs550945784	chr3:42363375-42363376	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs561287283	chr3:42363380-42363381	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs530380575	chr3:42363408-42363409	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs563366207	chr3:42363424-42363425	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs547349709	chr3:42363445-42363446	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs567052365	chr3:42363484-42363485	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs533648456	chr3:42363499-42363500	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs80089405	chr3:42363540-42363541	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	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:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42360600-42361200	Enhancers	Brain Germinal Matrix	brain
2	chr3:42362800-42363600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:42362800-42363600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:42363200-42366600	Weak transcription	Right Atrium	heart
5	chr3:42369400-42369600	Bivalent Enhancer	HSMMtube	muscle
6	chr3:42369400-42369800	Enhancers	Colon Smooth Muscle	Colon
7	chr3:42377400-42378400	Enhancers	HMEC	breast
8	chr3:42381000-42381800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:42381600-42382400	Enhancers	Brain Germinal Matrix	brain
10	chr3:42381800-42382000	Enhancers	HSMM	muscle
11	chr3:42382000-42384200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr3:42383600-42384000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:42384000-42387000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:42384200-42385800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:42385800-42389800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr3:42386400-42388200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:42386600-42391600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:42386800-42387000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr3:42386800-42387200	Enhancers	Primary T cells from cord blood	blood
20	chr3:42386800-42387400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr3:42386800-42388000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:42386800-42388000	Enhancers	Thymus	Thymus
23	chr3:42386800-42390400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr3:42387000-42387400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr3:42387000-42387800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:42387000-42387800	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:42387200-42387600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr3:42387200-42387600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr3:42387200-42388000	Enhancers	K562	blood
30	chr3:42387200-42388200	Enhancers	Fetal Thymus	thymus
31	chr3:42387400-42387600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:42387400-42387600	Enhancers	Brain Germinal Matrix	brain
33	chr3:42387400-42387800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr3:42387400-42389800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:42387400-42390400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr3:42387400-42390600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr3:42387600-42389400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:42387600-42390000	Enhancers	Primary T cells from cord blood	blood
39	chr3:42387800-42388400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:42387800-42388800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:42387800-42390200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr3:42388000-42389600	Weak transcription	Thymus	Thymus
43	chr3:42388000-42391000	Weak transcription	K562	blood
44	chr3:42388200-42388600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:42388200-42388600	Weak transcription	Fetal Thymus	thymus
46	chr3:42388400-42388800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:42388600-42390000	Enhancers	Fetal Thymus	thymus
48	chr3:42388600-42390600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:42388800-42391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:42389000-42389200	Enhancers	Primary hematopoietic stem cells	blood

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