Variant report

Variant	esv3344638
Chromosome Location	chr2:20588859-20589342
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20549816..20551964-chr2:20588277..20590176,3	MCF-7	breast:
2	chr2:20587063..20590081-chr2:20645437..20648292,3	MCF-7	breast:
3	chr2:20587207..20591991-chr2:20644052..20649862,9	MCF-7	breast:
4	chr2:20581393..20584603-chr2:20588898..20591026,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PUM2-4	chr2:20588794-20589712	l_1787_chr2:20588793-20591177_liver

Variant related genes	Relation type
ENSG00000055917	chromatin interactions
ENSG00000143878	chromatin interactions

Extended variants
information (count: 23 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs189056089	chr2:20588860-20588861	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs11887662	chr2:20588862-20588863	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs566995562	chr2:20588878-20588879	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs539117304	chr2:20588881-20588882	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs558972866	chr2:20588902-20588903	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs4666386	chr2:20588930-20588931	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs544746468	chr2:20588974-20588975	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs4666387	chr2:20589000-20589001	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs367782419	chr2:20589008-20589009	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs541554751	chr2:20589022-20589023	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs62124615	chr2:20589042-20589043	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs559698707	chr2:20589051-20589052	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs532111798	chr2:20589055-20589056	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
14	rs12623511	chr2:20589091-20589092	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs562555687	chr2:20589095-20589096	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs143985092	chr2:20589158-20589159	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs548356128	chr2:20589170-20589171	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs561878180	chr2:20589200-20589201	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs536071866	chr2:20589257-20589258	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs191813955	chr2:20589265-20589266	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
21	rs566885469	chr2:20589271-20589272	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs539008829	chr2:20589325-20589326	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs553189934	chr2:20589327-20589328	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:73)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	21508638	CNVD
Breast cancer	17603634	CNVD
Cancer	16751803	CNVD
Neuroblastoma	16790693	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Ependymoma	16718352	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Bladder cancer	21909424	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21785460	CNVD
Medulloblastoma	20607354	CNVD
Neuroblastoma	19638189	CNVD
Neuroblastoma	19435921	CNVD
Neuroblastoma	18574593	CNVD
Acute myeloid leukemia	18000384	CNVD
Medulloblastoma	16968546	CNVD
Medulloblastoma	22160402	CNVD
Schizophrenia	22118685	CNVD
Epilepsy	22118685	CNVD
Breast cancer	21509527	CNVD
Leukemia	18628472	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Ovarian cancer	17908972	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Neuroblastoma	18664255	CNVD
Neuroblastoma	18765546	CNVD
Neuroblastoma	18281664	CNVD
Neuroblastoma	17289879	CNVD
Neuroblastoma	19738985	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20581600-20601000	Weak transcription	Right Atrium	heart
2	chr2:20585800-20593800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:20586600-20589800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:20586600-20592000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:20587200-20591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:20587800-20591600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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