Variant report

Variant	nsv1009629
Chromosome Location	chr3:98846458-98903887
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:98839672..98842383-chr3:98845089..98846835,2	K562	blood:
2	chr3:98742225..98743062-chr3:98891577..98892142,2	MCF-7	breast:
3	chr3:98742090..98742958-chr3:98891307..98892432,5	MCF-7	breast:
4	chr3:98833031..98833794-chr3:98891585..98892473,5	MCF-7	breast:
5	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:
6	chr3:98898412..98900467-chr3:98901353..98902956,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST3GAL6-6	chr3:98899387-98899480	NONHSAT090838
2	lnc-ST3GAL6-6	chr3:98896222-98896357	NONHSAT090838

No data

Extended variants
information (count: 2432 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:2432 , 50 per page) page: 1 2 3 4 5 6 7 ... 49

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4928204	chr3:98846458-98846459	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs190821600	chr3:98846470-98846471	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs537241308	chr3:98846475-98846476	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs149059627	chr3:98846478-98846479	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs556824963	chr3:98846495-98846496	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs534603874	chr3:98846496-98846497	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs536268623	chr3:98846508-98846509	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs182289006	chr3:98846525-98846526	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs185061767	chr3:98846550-98846551	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs541323882	chr3:98846594-98846595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs190264952	chr3:98846600-98846601	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs564793905	chr3:98846634-98846635	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs578146555	chr3:98846667-98846668	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs75067627	chr3:98846668-98846669	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs72932771	chr3:98846697-98846698	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs138890281	chr3:98846741-98846742	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs377374257	chr3:98846783-98846784	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs548985289	chr3:98847005-98847006	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs369688589	chr3:98847015-98847016	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs374145516	chr3:98847053-98847054	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs142821949	chr3:98847054-98847055	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs571515055	chr3:98847067-98847068	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs536883716	chr3:98847086-98847087	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs550760592	chr3:98847099-98847100	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs183041868	chr3:98847154-98847155	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs11294684	chr3:98847166-98847167	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs397770334	chr3:98847167-98847168	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs200001642	chr3:98847168-98847169	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs536307188	chr3:98847195-98847196	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs373312975	chr3:98847202-98847203	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs188078425	chr3:98847216-98847217	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs572792764	chr3:98847217-98847218	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs370510816	chr3:98847336-98847337	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs558197930	chr3:98847348-98847349	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs147404513	chr3:98847377-98847378	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs192946432	chr3:98847380-98847381	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs541257806	chr3:98847412-98847413	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs559585562	chr3:98847418-98847419	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs573797637	chr3:98847419-98847420	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs183541793	chr3:98847453-98847454	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs530055977	chr3:98847455-98847456	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs75465974	chr3:98847456-98847457	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs559410510	chr3:98847497-98847498	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs563137521	chr3:98847562-98847563	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs1082505	chr3:98847601-98847602	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs374345287	chr3:98847658-98847659	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs375266952	chr3:98847659-98847660	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs140382115	chr3:98847662-98847663	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs200023618	chr3:98847664-98847665	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs55804173	chr3:98847665-98847666	Weak transcription Enhancers Flanking Active TSS	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
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:146 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98834400-98848200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:98838400-98846800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:98838800-98847000	Weak transcription	NH-A	brain
4	chr3:98839400-98846800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:98839400-98846800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:98844600-98851200	Enhancers	HSMM	muscle
7	chr3:98845400-98846800	Weak transcription	HMEC	breast
8	chr3:98845400-98847000	Weak transcription	NHLF	lung
9	chr3:98845600-98847000	Weak transcription	Osteobl	bone
10	chr3:98845600-98847600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:98845800-98846800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:98846000-98847000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:98846000-98847200	Weak transcription	HSMMtube	muscle
14	chr3:98846800-98847600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:98846800-98848000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:98846800-98848400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:98846800-98849000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:98846800-98849000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:98846800-98849000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:98846800-98849000	Enhancers	HMEC	breast
21	chr3:98846800-98849400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:98847000-98847200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:98847000-98847200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:98847000-98847200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:98847000-98848200	Enhancers	NHLF	lung
26	chr3:98847000-98848400	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:98847000-98848800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:98847000-98848800	Enhancers	HUVEC	blood vessel
29	chr3:98847000-98849200	Enhancers	Osteobl	bone
30	chr3:98847000-98849400	Enhancers	NH-A	brain
31	chr3:98847000-98849400	Enhancers	NHDF-Ad	bronchial
32	chr3:98847200-98847800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:98847200-98847800	Enhancers	Brain Hippocampus Middle	brain
34	chr3:98847200-98848200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:98847200-98848600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:98847200-98848800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:98847200-98848800	Enhancers	NHEK	skin
38	chr3:98847200-98849400	Enhancers	HSMMtube	muscle
39	chr3:98847600-98848000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:98847600-98848000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:98847600-98848000	Enhancers	Adipose Nuclei	Adipose
42	chr3:98847600-98848400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:98847600-98848400	Enhancers	Brain Anterior Caudate	brain
44	chr3:98847600-98848400	Enhancers	Stomach Smooth Muscle	stomach
45	chr3:98847800-98848400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:98848000-98848200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:98848000-98848200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:98848000-98848400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:98848000-98849000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:98848200-98848400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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