Variant report

Variant	esv1829946
Chromosome Location	chr3:98894246-98930445
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
3	lnc-ST3GAL6-6	chr3:98896222-98896357	NONHSAT090838

Extended variants
information (count: 939 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:939 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2687670	chr3:98894246-98894247	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs139218173	chr3:98894279-98894280	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs541815437	chr3:98894285-98894286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs572555483	chr3:98894395-98894396	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs375046276	chr3:98894442-98894443	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs548368344	chr3:98894449-98894450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs183455113	chr3:98894471-98894472	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs143127851	chr3:98894495-98894496	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs368802925	chr3:98894564-98894565	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs111927671	chr3:98894590-98894591	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs563663936	chr3:98894594-98894595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs61031480	chr3:98894624-98894625	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs570277407	chr3:98894647-98894648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs542858963	chr3:98894660-98894661	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs148108512	chr3:98894667-98894668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs9830015	chr3:98894721-98894722	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs187795259	chr3:98894741-98894742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs141864994	chr3:98894747-98894748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs191545748	chr3:98894761-98894762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs535137127	chr3:98894782-98894783	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs372543819	chr3:98894803-98894804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs3914875	chr3:98894806-98894807	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs376362216	chr3:98894862-98894863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs6807227	chr3:98894863-98894864	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs374011966	chr3:98894908-98894909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs115966049	chr3:98894911-98894912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs566159680	chr3:98894915-98894916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs183732299	chr3:98894954-98894955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs188431130	chr3:98894985-98894986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs34291508	chr3:98895021-98895022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs578177989	chr3:98895023-98895024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs1851066	chr3:98895124-98895125	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs150612675	chr3:98895129-98895130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs573949794	chr3:98895141-98895142	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs78645911	chr3:98895155-98895156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs576407222	chr3:98895173-98895174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs559630973	chr3:98895190-98895191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs573028953	chr3:98895249-98895250	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs117912354	chr3:98895321-98895322	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs192702803	chr3:98895334-98895335	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs12636065	chr3:98895386-98895387	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs558538773	chr3:98895397-98895398	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs11720946	chr3:98895407-98895408	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs560746102	chr3:98895428-98895429	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs184696926	chr3:98895512-98895513	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs73859819	chr3:98895537-98895538	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs75060193	chr3:98895573-98895574	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs79810267	chr3:98895575-98895576	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs566391747	chr3:98895603-98895604	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs190027589	chr3:98895619-98895620	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:20 , 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	chr3:98892400-98895200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:98894200-98894600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:98894200-98894600	Enhancers	HUVEC	blood vessel
5	chr3:98895200-98895400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:98895200-98895600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:98899200-98899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:98899200-98899600	Enhancers	NHEK	skin
9	chr3:98899200-98900200	Enhancers	HMEC	breast
10	chr3:98901800-98912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:98904600-98906000	Weak transcription	Aorta	Aorta
12	chr3:98906000-98906200	ZNF genes & repeats	Aorta	Aorta
13	chr3:98910000-98910200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:98910000-98910200	Enhancers	HSMMtube	muscle
15	chr3:98910000-98910800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:98911000-98911400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:98915200-98918000	Active TSS	Fetal Thymus	thymus
18	chr3:98918000-98918400	Enhancers	Fetal Thymus	thymus
19	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:98928400-98928800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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