Variant report

Variant	esv3339861
Chromosome Location	chr3:42952973-42955196
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	chr3:42946486..42948443-chr3:42951858..42953439,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCBP2-2	chr3:42953509-42953561	NONHSAT089272
2	lnc-CCBP2-2	chr3:42954693-42954795	NONHSAT089272

Variant related genes	Relation type
ENSG00000182983	chromatin interactions

Extended variants
information (count: 94 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:94 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539343541	chr3:42953035-42953036	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs561788420	chr3:42953047-42953048	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs116359963	chr3:42953049-42953050	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs188067461	chr3:42953063-42953064	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs541882698	chr3:42953076-42953077	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs555469677	chr3:42953146-42953147	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs74429788	chr3:42953161-42953162	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs145603432	chr3:42953190-42953191	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs199814871	chr3:42953210-42953211	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs150805941	chr3:42953211-42953212	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs75901092	chr3:42953212-42953213	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs181311876	chr3:42953218-42953219	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs532778721	chr3:42953262-42953263	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs185438735	chr3:42953328-42953329	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs9311330	chr3:42953329-42953330	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs531580107	chr3:42953333-42953334	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs548192438	chr3:42953338-42953339	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs192082993	chr3:42953353-42953354	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs527783104	chr3:42953394-42953395	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs181487003	chr3:42953472-42953473	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs547528881	chr3:42953504-42953505	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs570552164	chr3:42953527-42953528	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs539648106	chr3:42953541-42953542	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs549793064	chr3:42953549-42953550	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs187437982	chr3:42953554-42953555	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs148721539	chr3:42953584-42953585	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs200011780	chr3:42953643-42953644	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs144656342	chr3:42953656-42953657	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs376307422	chr3:42953664-42953665	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs555408293	chr3:42953669-42953670	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs572133148	chr3:42953687-42953688	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs577398028	chr3:42953746-42953747	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs369647450	chr3:42953771-42953772	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs530220692	chr3:42953813-42953814	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs528366301	chr3:42953904-42953905	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs375197583	chr3:42953940-42953941	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs534406542	chr3:42953942-42953943	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs7621267	chr3:42953952-42953953	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs36176787	chr3:42953987-42953988	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs150809642	chr3:42953993-42953994	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs55888800	chr3:42953994-42953995	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs3045048	chr3:42953995-42953996	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs13079704	chr3:42953996-42953997	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs13079888	chr3:42954033-42954034	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs13060120	chr3:42954049-42954050	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs139754134	chr3:42954050-42954051	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs145376202	chr3:42954051-42954052	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs3045049	chr3:42954053-42954054	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs373358803	chr3:42954054-42954055	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs28818785	chr3:42954056-42954057	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:88)

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
Prostate cancer	18632612	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:189 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42948400-42954600	Weak transcription	NH-A	brain
2	chr3:42948600-42954200	Weak transcription	Small Intestine	intestine
3	chr3:42948600-42955200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:42948600-42955600	Weak transcription	NHDF-Ad	bronchial
5	chr3:42948800-42954600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:42948800-42954600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:42949000-42954400	Weak transcription	Stomach Mucosa	stomach
8	chr3:42949000-42954600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:42949200-42955000	Weak transcription	Brain Substantia Nigra	brain
10	chr3:42949400-42953000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr3:42949400-42953000	ZNF genes & repeats	Lung	lung
12	chr3:42949600-42953400	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr3:42949600-42953400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr3:42949600-42953600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:42949600-42954000	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:42949800-42953600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:42949800-42957000	ZNF genes & repeats	Ovary	ovary
18	chr3:42950000-42953400	Strong transcription	Brain Hippocampus Middle	brain
19	chr3:42950000-42953600	ZNF genes & repeats	Fetal Brain Female	brain
20	chr3:42950000-42954000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:42950400-42954400	Weak transcription	Thymus	Thymus
22	chr3:42950800-42953600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr3:42950800-42954400	Weak transcription	Colonic Mucosa	Colon
24	chr3:42951000-42953200	ZNF genes & repeats	Spleen	Spleen
25	chr3:42951200-42953000	ZNF genes & repeats	Brain Germinal Matrix	brain
26	chr3:42951200-42953400	Strong transcription	Right Ventricle	heart
27	chr3:42951200-42954600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:42951400-42953400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:42951400-42953400	Strong transcription	Brain Anterior Caudate	brain
30	chr3:42951400-42953400	Strong transcription	Placenta	Placenta
31	chr3:42951400-42953600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr3:42951400-42953600	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr3:42951600-42953400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
34	chr3:42951600-42953600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr3:42951600-42954400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:42951800-42953400	Strong transcription	Left Ventricle	heart
37	chr3:42951800-42953600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:42951800-42953600	ZNF genes & repeats	Colon Smooth Muscle	Colon
39	chr3:42951800-42953600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr3:42951800-42953800	ZNF genes & repeats	Fetal Kidney	kidney
41	chr3:42951800-42954200	Weak transcription	Fetal Thymus	thymus
42	chr3:42951800-42959000	ZNF genes & repeats	Fetal Lung	lung
43	chr3:42952000-42953400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:42952000-42953400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:42952000-42953600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:42952000-42953600	ZNF genes & repeats	Adipose Nuclei	Adipose
47	chr3:42952000-42953600	Strong transcription	Brain Angular Gyrus	brain
48	chr3:42952000-42953600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:42952000-42953600	Strong transcription	Fetal Heart	heart
50	chr3:42952000-42953600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet

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