Variant report

Variant	esv3465898
Chromosome Location	chr4:106940339-106943358
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106933880..106935775-chr4:106939732..106941383,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBCK-1	chr4:106940966-106943635	XLOC_004040

Extended variants
information (count: 82 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:82 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17259106	chr4:106940351-106940352	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs17259148	chr4:106940408-106940409	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs377429583	chr4:106940411-106940412	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs62320068	chr4:106940487-106940488	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs140455876	chr4:106940502-106940503	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs572460413	chr4:106940509-106940510	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs114409852	chr4:106940523-106940524	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs78207585	chr4:106940574-106940575	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs398083369	chr4:106940575-106940576	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs116482501	chr4:106940622-106940623	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs185307921	chr4:106940637-106940638	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs372753823	chr4:106940638-106940639	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs114734319	chr4:106940654-106940655	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs531827394	chr4:106940722-106940723	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs556822433	chr4:106940763-106940764	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs150000178	chr4:106940811-106940812	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs574959551	chr4:106940820-106940821	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs189726945	chr4:106940821-106940822	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs11721938	chr4:106940855-106940856	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs373196118	chr4:106940898-106940899	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs566600535	chr4:106941003-106941004	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs538917987	chr4:106941045-106941046	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs180777006	chr4:106941059-106941060	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs569059886	chr4:106941061-106941062	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs538069580	chr4:106941111-106941112	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs187273491	chr4:106941296-106941297	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs192193795	chr4:106941332-106941333	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs533515032	chr4:106941339-106941340	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs542363819	chr4:106941380-106941381	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs553733443	chr4:106941504-106941505	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs116617051	chr4:106941540-106941541	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs575286910	chr4:106941673-106941674	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs183620929	chr4:106941676-106941677	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs188612712	chr4:106941677-106941678	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs528862324	chr4:106941778-106941779	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs145251059	chr4:106941779-106941780	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs76675136	chr4:106941784-106941785	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs190466428	chr4:106941791-106941792	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs545860302	chr4:106941798-106941799	Enhancers Bivalent Enhancer Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs541212241	chr4:106941846-106941847	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs564493952	chr4:106941874-106941875	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs149178483	chr4:106941921-106941922	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs528426322	chr4:106941979-106941980	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs182688352	chr4:106941980-106941981	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs145135406	chr4:106942021-106942022	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs559440813	chr4:106942027-106942028	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs531501000	chr4:106942107-106942108	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs548416042	chr4:106942110-106942111	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs568117308	chr4:106942118-106942119	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs533885436	chr4:106942133-106942134	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

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
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
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
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	16573809	CNVD
Multiple myeloma	16616336	CNVD
Melanoma	20688739	CNVD
Breast cancer	16397240	CNVD
Acute myeloid leukemia	18000384	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Myelofibrosis	22110671	CNVD
myeloid cancer	21057493	CNVD
Cognitive impairment	21505072	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	22522925	CNVD
Chronic lymphocytic leukemia	21546498	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106935000-106948400	Weak transcription	Aorta	Aorta
2	chr4:106939800-106942400	Enhancers	NHDF-Ad	bronchial
3	chr4:106940400-106941600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:106940400-106941600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:106940400-106942000	Enhancers	HSMM	muscle
6	chr4:106940400-106943000	Enhancers	HSMMtube	muscle
7	chr4:106940600-106941600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr4:106940800-106941600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:106940800-106941800	Enhancers	Osteobl	bone
10	chr4:106941000-106941400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:106941000-106941800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:106941000-106943200	Enhancers	Fetal Heart	heart
13	chr4:106941000-106944000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:106941200-106941400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:106941200-106941400	Enhancers	Left Ventricle	heart
16	chr4:106941200-106944400	Enhancers	Primary hematopoietic stem cells	blood
17	chr4:106941400-106943800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:106941800-106942000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:106942000-106942400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:106942000-106942600	Weak transcription	HSMM	muscle
21	chr4:106942400-106942800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:106942600-106942800	Enhancers	HSMM	muscle
23	chr4:106942800-106943400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:106943000-106943800	Enhancers	Left Ventricle	heart
25	chr4:106943000-106945400	Weak transcription	Fetal Intestine Small	intestine
26	chr4:106943200-106943600	Flanking Active TSS	Fetal Heart	heart

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