Variant report

Variant	esv1824492
Chromosome Location	chr3:98899125-98919134
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	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:
2	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST3GAL6-6	chr3:98899387-98899480	NONHSAT090838
2	lnc-ST3GAL6-6	chr3:98904502-98904611	NONHSAT090838

Extended variants
information (count: 573 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:573 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs376736785	chr3:98899155-98899156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs141784591	chr3:98899159-98899160	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs369790843	chr3:98899226-98899227	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs374207310	chr3:98899236-98899237	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs377628782	chr3:98899245-98899246	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs369329566	chr3:98899246-98899247	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs373692609	chr3:98899248-98899249	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs376324850	chr3:98899255-98899256	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs370400878	chr3:98899260-98899261	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs373570092	chr3:98899267-98899268	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs377527190	chr3:98899268-98899269	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs370954040	chr3:98899269-98899270	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs374370047	chr3:98899270-98899271	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs368303108	chr3:98899274-98899275	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs371753375	chr3:98899275-98899276	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs374746903	chr3:98899278-98899279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs367910107	chr3:98899283-98899284	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs371827302	chr3:98899287-98899288	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs374842338	chr3:98899290-98899291	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs370025812	chr3:98899292-98899293	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs372684989	chr3:98899303-98899304	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs150455860	chr3:98899347-98899348	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs138241072	chr3:98899434-98899435	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs547621330	chr3:98899683-98899684	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs536893669	chr3:98900014-98900015	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs552338073	chr3:98900143-98900144	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs570611760	chr3:98900165-98900166	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs111706229	chr3:98900188-98900189	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs547684921	chr3:98902330-98902331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs371249884	chr3:98902389-98902390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs7641092	chr3:98902395-98902396	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs774973	chr3:98902416-98902417	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs76157764	chr3:98902432-98902433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs398091671	chr3:98902437-98902438	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs200556058	chr3:98902438-98902439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs116192946	chr3:98902456-98902457	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs188148368	chr3:98902505-98902506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs201886641	chr3:98902519-98902520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs9857240	chr3:98902532-98902533	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs535526680	chr3:98902540-98902541	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs555078196	chr3:98902578-98902579	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs7629965	chr3:98902589-98902590	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs139406779	chr3:98902620-98902621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs184276535	chr3:98902631-98902632	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs577098774	chr3:98902636-98902637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs142637360	chr3:98902657-98902658	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs112881503	chr3:98902667-98902668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs189479857	chr3:98902693-98902694	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs150550873	chr3:98902703-98902704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs192472979	chr3:98902725-98902726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98879200-98899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:98899200-98899600	Enhancers	NHEK	skin
4	chr3:98899200-98900200	Enhancers	HMEC	breast
5	chr3:98901800-98912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:98904600-98906000	Weak transcription	Aorta	Aorta
7	chr3:98906000-98906200	ZNF genes & repeats	Aorta	Aorta
8	chr3:98910000-98910200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:98910000-98910200	Enhancers	HSMMtube	muscle
10	chr3:98910000-98910800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:98911000-98911400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:98915200-98918000	Active TSS	Fetal Thymus	thymus
13	chr3:98918000-98918400	Enhancers	Fetal Thymus	thymus

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