Variant report

Variant	nsv1011402
Chromosome Location	chr3:89384121-89444995
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:89435683..89438107-chr3:89442264..89444057,2	MCF-7	breast:
2	chr3:89425184..89427715-chr3:89431081..89433096,2	MCF-7	breast:
3	chr3:89435683..89438107-chr3:89442264..89444057,2	MCF-7	breast:
4	chr3:89374528..89377645-chr3:89392593..89395332,3	MCF-7	breast:
5	chr3:89425184..89427715-chr3:89431081..89433096,2	MCF-7	breast:
6	chr3:89374362..89376361-chr3:89384187..89386718,2	MCF-7	breast:

Extended variants
information (count: 2456 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:2456 , 50 per page) page: 1 2 3 4 5 6 7 ... 50

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9868782	chr3:89384121-89384122	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs372186424	chr3:89384122-89384123	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs532990528	chr3:89384126-89384127	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs375934679	chr3:89384135-89384136	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs552665525	chr3:89384164-89384165	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs185783337	chr3:89384200-89384201	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs557557226	chr3:89384210-89384211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs539673366	chr3:89384216-89384217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs557916935	chr3:89384224-89384225	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs190656927	chr3:89384237-89384238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs527273000	chr3:89384270-89384271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs147221885	chr3:89384275-89384276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs114289501	chr3:89384405-89384406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs555263572	chr3:89384490-89384491	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs182333903	chr3:89384494-89384495	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs541029803	chr3:89384545-89384546	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs9817553	chr3:89384566-89384567	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs544603345	chr3:89384622-89384623	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs533441915	chr3:89384647-89384648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs140264932	chr3:89384706-89384707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs578217428	chr3:89384719-89384720	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs563471117	chr3:89384774-89384775	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs530575637	chr3:89384776-89384777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs556372893	chr3:89384800-89384801	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs2067847	chr3:89384884-89384885	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs117767814	chr3:89384888-89384889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs546168354	chr3:89384971-89384972	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs186230640	chr3:89384979-89384980	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs142711708	chr3:89384982-89384983	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs144458525	chr3:89384999-89385000	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs570234058	chr3:89385026-89385027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs111989587	chr3:89385083-89385084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs578084229	chr3:89385110-89385111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs556037958	chr3:89385137-89385138	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs148425167	chr3:89385196-89385197	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs541441685	chr3:89385238-89385239	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs369902557	chr3:89385265-89385266	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs36076074	chr3:89385283-89385284	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs182811689	chr3:89385302-89385303	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs553385424	chr3:89385303-89385304	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs116246238	chr3:89385343-89385344	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs75451665	chr3:89385364-89385365	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs185565605	chr3:89385376-89385377	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs530752474	chr3:89385397-89385398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs538581127	chr3:89385415-89385416	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs371349061	chr3:89385474-89385475	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs542429592	chr3:89385501-89385502	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs545597250	chr3:89385526-89385527	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs56132991	chr3:89385547-89385548	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs189977063	chr3:89385573-89385574	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

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
Acute lymphoblastic leukemia	20435627	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
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Lung cancer	19547694	CNVD
Cancer	20164919	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:150 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89382400-89391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:89382800-89391000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:89383000-89390200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:89383200-89384200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:89384200-89385200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:89385200-89386000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:89386000-89386600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:89386600-89386800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:89386800-89393200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:89389200-89390400	Enhancers	Fetal Lung	lung
11	chr3:89389400-89390400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:89389600-89390200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:89389600-89390400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:89389800-89390600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:89390200-89390400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:89390200-89391000	Enhancers	Fetal Brain Male	brain
17	chr3:89390200-89391000	Enhancers	Fetal Brain Female	brain
18	chr3:89390200-89391200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:89390400-89394000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:89391000-89392600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:89391000-89394400	Weak transcription	Fetal Brain Female	brain
22	chr3:89392000-89392200	Enhancers	Fetal Brain Male	brain
23	chr3:89392600-89417400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:89393200-89394400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:89394400-89394600	Enhancers	Fetal Brain Female	brain
26	chr3:89400200-89401000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:89400200-89401000	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr3:89400600-89401000	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:89401000-89401200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:89401000-89401200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:89402200-89403200	Enhancers	Hela-S3	cervix
32	chr3:89404400-89417600	Weak transcription	Brain Germinal Matrix	brain
33	chr3:89407400-89407600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:89407800-89409000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:89409000-89409800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:89409200-89409400	Enhancers	Fetal Lung	lung
37	chr3:89409200-89409600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:89409200-89409800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:89409200-89409800	Enhancers	Hela-S3	cervix
40	chr3:89409200-89410000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:89409400-89409800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:89409400-89410000	Enhancers	NHDF-Ad	bronchial
43	chr3:89409400-89410600	Weak transcription	Fetal Lung	lung
44	chr3:89409600-89410000	Enhancers	NH-A	brain
45	chr3:89410200-89410400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:89410200-89410400	Enhancers	Fetal Brain Female	brain
47	chr3:89410400-89412600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:89410400-89421200	Weak transcription	Fetal Brain Female	brain
49	chr3:89410600-89414000	Enhancers	Fetal Lung	lung
50	chr3:89411600-89411800	Enhancers	Fetal Muscle Leg	muscle

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