Variant report

Variant	nsv461199
Chromosome Location	chr4:7253260-7270126
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7261309..7263686-chr4:7264453..7266541,2	MCF-7	breast:
2	chr4:7248341..7250372-chr4:7253151..7255642,2	MCF-7	breast:
3	chr4:7261309..7263686-chr4:7264453..7266541,2	MCF-7	breast:
4	chr4:7213661..7215472-chr4:7265582..7267704,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TADA2B-4	chr4:7259241-7259517	NONHSAT095054
2	lnc-TADA2B-4	chr4:7264564-7264801	NONHSAT095054

Extended variants
information (count: 889 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:889 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs905010	chr4:7253260-7253261	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs573607721	chr4:7253333-7253334	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs544055500	chr4:7253334-7253335	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs59138913	chr4:7253406-7253407	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs537531434	chr4:7253411-7253412	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs533205040	chr4:7253445-7253446	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
7	rs555966711	chr4:7253477-7253478	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs534956937	chr4:7253480-7253481	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs187757744	chr4:7253523-7253524	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs577435666	chr4:7253526-7253527	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs148550850	chr4:7253565-7253566	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs142914795	chr4:7253578-7253579	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs567810742	chr4:7253601-7253602	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs7659846	chr4:7253603-7253604	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs572304188	chr4:7253608-7253609	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs550537743	chr4:7253649-7253650	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs4234799	chr4:7253656-7253657	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs539092231	chr4:7253692-7253693	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs905011	chr4:7253718-7253719	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs572868395	chr4:7253727-7253728	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs111666722	chr4:7253738-7253739	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs61015938	chr4:7253791-7253792	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs905012	chr4:7253808-7253809	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs543987152	chr4:7253820-7253821	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs78246398	chr4:7253825-7253826	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs577840598	chr4:7253862-7253863	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs189792524	chr4:7253869-7253870	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs905013	chr4:7253915-7253916	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs553584557	chr4:7253924-7253925	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
30	rs543187959	chr4:7253926-7253927	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs561360762	chr4:7253953-7253954	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs571858332	chr4:7253958-7253959	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
33	rs550377167	chr4:7254005-7254006	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
34	rs555250562	chr4:7254016-7254017	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs571870821	chr4:7254035-7254036	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs74702605	chr4:7254055-7254056	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs551100271	chr4:7254072-7254073	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs562937130	chr4:7254096-7254097	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs71601832	chr4:7254100-7254101	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs4689669	chr4:7254118-7254119	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs533542045	chr4:7254123-7254124	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs555077604	chr4:7254131-7254132	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs370498003	chr4:7254165-7254166	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs537670523	chr4:7254217-7254218	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs556288403	chr4:7254224-7254225	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs577866518	chr4:7254238-7254239	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs545240046	chr4:7254254-7254255	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs553777083	chr4:7254256-7254257	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs182787045	chr4:7254285-7254286	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs187254425	chr4:7254312-7254313	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Schizophrenia	22241247	CNVD
Autosomal-dominant microtia	18179897	CNVD
Glioma	17123091	CNVD
Colorectal cancer	20459617	CNVD
Breast cancer	17133270	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Cancer	20164919	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:288 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7252000-7254200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr4:7252400-7253400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr4:7252400-7253600	Enhancers	Rectal Smooth Muscle	rectum
4	chr4:7252600-7253600	Enhancers	Brain Cingulate Gyrus	brain
5	chr4:7252600-7254000	Enhancers	Fetal Stomach	stomach
6	chr4:7252600-7261800	Weak transcription	Fetal Brain Female	brain
7	chr4:7252600-7262400	Weak transcription	Fetal Brain Male	brain
8	chr4:7252800-7253400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:7252800-7253400	Enhancers	Brain Anterior Caudate	brain
10	chr4:7252800-7253400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr4:7252800-7253400	Enhancers	Colon Smooth Muscle	Colon
12	chr4:7252800-7253600	Enhancers	Brain Hippocampus Middle	brain
13	chr4:7252800-7254000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr4:7252800-7254400	Weak transcription	Brain Germinal Matrix	brain
15	chr4:7252800-7255400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr4:7252800-7255400	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr4:7252800-7255400	Weak transcription	HSMM	muscle
18	chr4:7252800-7256800	Weak transcription	HSMMtube	muscle
19	chr4:7252800-7257800	Weak transcription	Ovary	ovary
20	chr4:7253000-7253400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:7253000-7253600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:7253000-7253600	Weak transcription	Brain Angular Gyrus	brain
23	chr4:7253000-7253600	Enhancers	Stomach Smooth Muscle	stomach
24	chr4:7253000-7253800	Weak transcription	Fetal Thymus	thymus
25	chr4:7253000-7254200	Weak transcription	Fetal Lung	lung
26	chr4:7253000-7257200	Weak transcription	Psoas Muscle	Psoas
27	chr4:7253000-7265400	Weak transcription	Brain Substantia Nigra	brain
28	chr4:7253200-7253400	Enhancers	Left Ventricle	heart
29	chr4:7253200-7253600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:7253200-7253800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:7253200-7254000	Enhancers	Esophagus	oesophagus
32	chr4:7253400-7253800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr4:7253400-7254600	Weak transcription	Left Ventricle	heart
34	chr4:7253400-7256400	Weak transcription	Brain Anterior Caudate	brain
35	chr4:7253400-7256600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:7253400-7258000	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:7253600-7253800	Enhancers	Brain Angular Gyrus	brain
38	chr4:7253600-7254200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:7253600-7256200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:7253600-7256600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:7253600-7256600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:7253600-7258000	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:7253600-7258200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:7253600-7258400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:7253800-7254000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:7253800-7254000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:7253800-7254000	Enhancers	Spleen	Spleen
48	chr4:7253800-7254800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr4:7253800-7255200	Enhancers	Fetal Thymus	thymus
50	chr4:7253800-7256600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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