Variant report

Variant	nsv963574
Chromosome Location	chr3:90136994-90143491
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:89996596..89997810-chr3:90140377..90141392,6	MCF-7	breast:
2	chr3:89996325..89997175-chr3:90140367..90141418,4	MCF-7	breast:
3	chr3:89611242..89611987-chr3:90140381..90141293,2	MCF-7	breast:
4	chr3:89900833..89901811-chr3:90140473..90141334,4	MCF-7	breast:
5	chr3:89996606..89997218-chr3:90142348..90142978,2	MCF-7	breast:

Extended variants
information (count: 251 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:251 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs192797799	chr3:90137011-90137012	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs539390253	chr3:90137046-90137047	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs549708650	chr3:90137064-90137065	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs559318516	chr3:90137107-90137108	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs547557698	chr3:90137146-90137147	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs57823373	chr3:90137160-90137161	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs571557771	chr3:90137211-90137212	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs141341647	chr3:90137232-90137233	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs544858654	chr3:90137265-90137266	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs182565244	chr3:90137288-90137289	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs145125986	chr3:90137289-90137290	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs541971029	chr3:90137292-90137293	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs538472014	chr3:90137305-90137306	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs560602383	chr3:90137323-90137324	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs551973725	chr3:90137405-90137406	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs572370739	chr3:90137427-90137428	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs545770488	chr3:90137433-90137434	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs564075834	chr3:90137451-90137452	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs554139549	chr3:90137461-90137462	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs189074226	chr3:90137495-90137496	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs549616437	chr3:90137515-90137516	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs561742048	chr3:90137521-90137522	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs529049728	chr3:90137527-90137528	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs193024084	chr3:90137530-90137531	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs565743841	chr3:90137531-90137532	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs184603813	chr3:90137551-90137552	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs188971484	chr3:90137562-90137563	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs571206176	chr3:90137571-90137572	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs538542971	chr3:90137593-90137594	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs192082209	chr3:90137594-90137595	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs150381924	chr3:90137626-90137627	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs184286145	chr3:90137627-90137628	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs188631519	chr3:90137633-90137634	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs536022196	chr3:90137648-90137649	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs112334526	chr3:90137691-90137692	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs12638078	chr3:90137705-90137706	Weak transcription Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs181067605	chr3:90137707-90137708	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs12107978	chr3:90137713-90137714	Weak transcription Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs200594954	chr3:90137749-90137750	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs575986974	chr3:90137751-90137752	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs148074037	chr3:90137765-90137766	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs561988841	chr3:90137815-90137816	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs529104638	chr3:90137846-90137847	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs547550962	chr3:90137852-90137853	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs559220211	chr3:90137853-90137854	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs533054757	chr3:90137894-90137895	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs577472529	chr3:90137964-90137965	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs551451176	chr3:90137972-90137973	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs12106840	chr3:90138024-90138025	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs537012373	chr3:90138117-90138118	Weak transcription Transcr. at gene 5' and 3' Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
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
Acute myeloid leukemia	20729466	CNVD
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
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Soft tissue tumor	16732325	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Lung cancer	19547694	CNVD
Cancer	20164919	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:90133800-90138600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:90136200-90137200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:90136200-90138800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:90136400-90138800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:90136600-90138600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:90136600-90138800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:90136600-90139000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:90136600-90156400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:90137200-90137800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:90137800-90139800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:90138600-90139000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:90138600-90139200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:90138600-90141000	Enhancers	Fetal Lung	lung
14	chr3:90138800-90139200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:90138800-90139400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr3:90138800-90139400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:90139000-90140000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:90139200-90146000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:90139400-90139600	Enhancers	Ovary	ovary
20	chr3:90139400-90140400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:90139400-90140800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:90139600-90140600	Weak transcription	Ovary	ovary
23	chr3:90139800-90140400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:90139800-90140800	Enhancers	NHDF-Ad	bronchial
25	chr3:90139800-90142800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:90140000-90145000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:90140000-90151800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:90140200-90140600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:90140200-90140800	Enhancers	Fetal Heart	heart
30	chr3:90140200-90141000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:90140200-90141000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:90140400-90140600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:90140400-90140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:90140400-90140800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:90140600-90140800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:90140600-90140800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:90140600-90140800	Enhancers	Brain Angular Gyrus	brain
38	chr3:90140600-90141000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:90140600-90141000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:90140600-90141000	Enhancers	Brain Substantia Nigra	brain
41	chr3:90140600-90141000	Enhancers	Ovary	ovary
42	chr3:90140600-90141000	Enhancers	HSMMtube	muscle
43	chr3:90140600-90141000	Active TSS	Osteobl	bone
44	chr3:90140800-90141000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr3:90140800-90141000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:90141000-90144400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:90142800-90146600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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