Variant report

Variant	nsv1001926
Chromosome Location	chr3:89482918-89544929
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:109618581..109619323-chr3:89534199..89534756,2	MCF-7	breast:
2	chr3:89504768..89506340-chr3:89522107..89525061,2	MCF-7	breast:
3	chr3:89523628..89525803-chr3:89552585..89555851,3	MCF-7	breast:
4	chr3:89504768..89506340-chr3:89522107..89525061,2	MCF-7	breast:

Extended variants
information (count: 1840 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:1840 , 50 per page) page: 1 2 3 4 5 6 7 ... 37

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs147459863	chr3:89482935-89482936	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs530667705	chr3:89483067-89483068	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs112095078	chr3:89483090-89483091	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs567276560	chr3:89483148-89483149	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs191202173	chr3:89483198-89483199	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs540257169	chr3:89483286-89483287	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs544888667	chr3:89483351-89483352	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs550736069	chr3:89483353-89483354	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs184786970	chr3:89483370-89483371	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs189204557	chr3:89483379-89483380	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs35071595	chr3:89483385-89483386	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs139927302	chr3:89483409-89483410	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs376764249	chr3:89483417-89483418	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs369803165	chr3:89483421-89483422	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs557958272	chr3:89483436-89483437	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs576443601	chr3:89483486-89483487	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs543912127	chr3:89483488-89483489	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs192093782	chr3:89483524-89483525	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs573980306	chr3:89483541-89483542	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs575157084	chr3:89483604-89483605	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs184490270	chr3:89483666-89483667	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs564197195	chr3:89483681-89483682	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs559674382	chr3:89483695-89483696	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs564435235	chr3:89483705-89483706	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs190195708	chr3:89483746-89483747	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs533221979	chr3:89483766-89483767	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs545200095	chr3:89483790-89483791	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs114974989	chr3:89483879-89483880	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs531658096	chr3:89483880-89483881	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs546812803	chr3:89483904-89483905	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs530496172	chr3:89483971-89483972	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs549068036	chr3:89484002-89484003	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs181408483	chr3:89484029-89484030	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs186421130	chr3:89484034-89484035	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs546236810	chr3:89484062-89484063	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs566012688	chr3:89484090-89484091	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs572560178	chr3:89484109-89484110	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs189255347	chr3:89484111-89484112	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs180734003	chr3:89484113-89484114	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs186465603	chr3:89484123-89484124	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs539940493	chr3:89484152-89484153	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs111695037	chr3:89484165-89484166	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs570250606	chr3:89484205-89484206	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs373638614	chr3:89484228-89484229	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs190847587	chr3:89484239-89484240	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs1028013	chr3:89484268-89484269	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs574088460	chr3:89484333-89484334	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs112355332	chr3:89484369-89484370	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs535012681	chr3:89484377-89484378	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs369351475	chr3:89484464-89484465	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

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
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	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
Oligozoospermia	20877625	CNVD
Sertoli-cell only syndrome	20877625	CNVD
Obesity	21131291	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Autism	20531469	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89460800-89521200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:89469400-89483400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:89482400-89483000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:89482600-89483600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:89482800-89483600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:89483000-89484200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:89483000-89484400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:89483400-89484000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:89483400-89484200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:89483600-89483800	Enhancers	Brain Hippocampus Middle	brain
11	chr3:89483600-89484000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:89483600-89484000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:89483600-89484000	Active TSS	Brain Angular Gyrus	brain
14	chr3:89483600-89484200	Active TSS	Fetal Lung	lung
15	chr3:89483600-89484400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:89483800-89484200	Active TSS	Brain Anterior Caudate	brain
17	chr3:89483800-89484200	Active TSS	Brain Hippocampus Middle	brain
18	chr3:89483800-89484200	Enhancers	NH-A	brain
19	chr3:89484000-89484200	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr3:89484000-89484200	Enhancers	Brain Substantia Nigra	brain
21	chr3:89484200-89489400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:89484200-89491600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:89484600-89489600	Weak transcription	Fetal Brain Male	brain
24	chr3:89486600-89486800	Enhancers	Fetal Brain Female	brain
25	chr3:89486800-89489800	Weak transcription	Fetal Brain Female	brain
26	chr3:89488400-89488600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:89489200-89490000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:89489400-89490000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:89489600-89490400	Enhancers	Fetal Brain Male	brain
30	chr3:89489600-89491000	Enhancers	Fetal Lung	lung
31	chr3:89489800-89490600	Enhancers	Fetal Brain Female	brain
32	chr3:89489800-89491200	Enhancers	Fetal Stomach	stomach
33	chr3:89491600-89493000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:89493000-89498400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:89494200-89494400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:89494400-89499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:89498400-89501000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:89498800-89506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:89499400-89499600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:89500600-89500800	Enhancers	Fetal Brain Female	brain
41	chr3:89500800-89501600	Enhancers	Fetal Brain Male	brain
42	chr3:89500800-89532400	Weak transcription	Fetal Brain Female	brain
43	chr3:89501000-89503000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:89501400-89521600	Weak transcription	Brain Germinal Matrix	brain
45	chr3:89503000-89504000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:89504000-89519800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:89504200-89505000	Enhancers	Fetal Lung	lung
48	chr3:89506400-89506600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:89506600-89506800	ZNF genes & repeats	Fetal Stomach	stomach
50	chr3:89506600-89527800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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