Variant report

Variant	nsv518873
Chromosome Location	chr3:143220697-143237419
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:143233845-143234126	GM12878	blood:	n/a	n/a
2	CTCF	chr3:143223078-143223097	Lung_OC	lung:	n/a	n/a
3	CTCF	chr3:143223099-143223134	Lung_OC	lung:	n/a	n/a
4	CTCF	chr3:143233880-143234030	GM06990	blood:	n/a	n/a
5	CTCF	chr3:143230060-143230210	HAc	cerebellar:	n/a	n/a
6	CTCF	chr3:143233964-143234052	GM12878	blood:	n/a	n/a
7	EP300	chr3:143236014-143236298	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOS	chr3:143226966-143227362	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:143229557-143229782	MCF10A-Er-Src	breast:	n/a	chr3:143229620-143229631 chr3:143229624-143229633
10	FOS	chr3:143227062-143227391	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr3:143229563-143229710	MCF10A-Er-Src	breast:	n/a	chr3:143229620-143229631 chr3:143229624-143229633
12	FOS	chr3:143231332-143231385	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr3:143229585-143229717	MCF10A-Er-Src	breast:	n/a	chr3:143229620-143229631 chr3:143229624-143229633
14	FOS	chr3:143227093-143227380	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr3:143228189-143228247	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr3:143229496-143229715	MCF10A-Er-Src	breast:	n/a	chr3:143229620-143229631 chr3:143229624-143229633
17	FOS	chr3:143231222-143231361	MCF10A-Er-Src	breast:	n/a	n/a
18	MAFK	chr3:143228705-143228872	HepG2	liver:	n/a	n/a
19	MAX	chr3:143226967-143227031	NB4	blood:	n/a	n/a
20	MYC	chr3:143227017-143227276	MCF10A-Er-Src	breast:	n/a	chr3:143227042-143227052 chr3:143227042-143227052
21	MYC	chr3:143222012-143222118	GM12878	blood:	n/a	n/a
22	MYC	chr3:143222218-143222550	H1-hESC	embryonic stem cell:	n/a	n/a
23	MYC	chr3:143222398-143222404	MCF-7	breast:	n/a	n/a
24	MYC	chr3:143222430-143222435	MCF-7	breast:	n/a	n/a
25	MYC	chr3:143226865-143227268	MCF10A-Er-Src	breast:	n/a	chr3:143227042-143227052 chr3:143227042-143227052
26	POLR2A	chr3:143222338-143222345	A549	lung:	n/a	n/a
27	POLR2A	chr3:143222346-143222433	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:143225582-143225782	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:143237008-143237140	ProgFib	skin:	n/a	n/a
30	POLR2A	chr3:143222285-143222318	A549	lung:	n/a	n/a
31	POLR2A	chr3:143224013-143224182	K562	blood:	n/a	n/a
32	POLR2A	chr3:143235917-143236533	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:143227235-143227363	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr3:143229376-143229460	K562	blood:	n/a	n/a
35	POLR2A	chr3:143227158-143227358	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr3:143222487-143222509	MCF-7	breast:	n/a	n/a
37	POLR2A	chr3:143222098-143222237	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:143222355-143222508	A549	lung:	n/a	n/a
39	REST	chr3:143235951-143236353	H1-hESC	embryonic stem cell:	n/a	n/a
40	REST	chr3:143235954-143236388	H1-hESC	embryonic stem cell:	n/a	n/a
41	SP1	chr3:143235921-143236339	H1-hESC	embryonic stem cell:	n/a	chr3:143236163-143236174
42	SP1	chr3:143235944-143236292	HepG2	liver:	n/a	chr3:143236163-143236174
43	SPI1	chr3:143225070-143225404	HL-60	blood:	n/a	n/a
44	SPI1	chr3:143225024-143225464	HL-60	blood:	n/a	n/a
45	STAT3	chr3:143225801-143225865	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT3	chr3:143227370-143227404	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr3:143229008-143229192	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr3:143226860-143227023	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr3:143227257-143227294	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr3:143233143-143233272	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143212932..143214521-chr3:143217945..143220851,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAQR9-6	chr3:143222117-143223115	NONHSAT092527

Variant related genes	Relation type
ST13P15	TF binding region
GAPDHP47	TF binding region

Extended variants
information (count: 665 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:665 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs838602	chr3:143220697-143220698	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs530322176	chr3:143220722-143220723	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs188596994	chr3:143220729-143220730	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs544408245	chr3:143220754-143220755	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs556324118	chr3:143220762-143220763	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs192295302	chr3:143220782-143220783	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs542092094	chr3:143220813-143220814	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs560418986	chr3:143220835-143220836	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs527253502	chr3:143220840-143220841	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs545777786	chr3:143220869-143220870	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs563950500	chr3:143220934-143220935	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs185134311	chr3:143220946-143220947	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs190834546	chr3:143220951-143220952	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs544744120	chr3:143220961-143220962	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs568232882	chr3:143220968-143220969	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs78351754	chr3:143220982-143220983	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs139688199	chr3:143221003-143221004	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs534584804	chr3:143221077-143221078	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs547673633	chr3:143221093-143221094	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs565970240	chr3:143221113-143221114	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs553021855	chr3:143221163-143221164	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs376991921	chr3:143221261-143221262	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs565259899	chr3:143221315-143221316	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs532805519	chr3:143221316-143221317	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs398052327	chr3:143221323-143221324	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs538767604	chr3:143221353-143221354	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs539398602	chr3:143221426-143221427	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs557189870	chr3:143221509-143221510	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs558890265	chr3:143221550-143221551	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs570792476	chr3:143221570-143221571	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs538303439	chr3:143221589-143221590	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs556262704	chr3:143221636-143221637	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs143709577	chr3:143221662-143221663	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs369102302	chr3:143221666-143221667	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs542030930	chr3:143221670-143221671	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs553988568	chr3:143221700-143221701	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs572674782	chr3:143221721-143221722	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs144187293	chr3:143221741-143221742	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs940637	chr3:143221777-143221778	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs148716303	chr3:143221805-143221806	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs543495135	chr3:143221810-143221811	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs182151499	chr3:143221830-143221831	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs529039251	chr3:143221864-143221865	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs187225459	chr3:143221892-143221893	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs76336852	chr3:143221919-143221920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs533241632	chr3:143221924-143221925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs940636	chr3:143221925-143221926	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs111692276	chr3:143221945-143221946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs112421984	chr3:143221975-143221976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs371049663	chr3:143222004-143222005	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	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
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	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
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Adrenocortical carcinoma	18281524	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:144 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143186000-143223000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:143201800-143226400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:143209000-143226800	Weak transcription	Adipose Nuclei	Adipose
5	chr3:143212600-143224800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:143212600-143247400	Weak transcription	Primary T cells from cord blood	blood
7	chr3:143215600-143226800	Weak transcription	Fetal Stomach	stomach
8	chr3:143219800-143222200	Weak transcription	Esophagus	oesophagus
9	chr3:143220200-143220800	Enhancers	Brain Angular Gyrus	brain
10	chr3:143220200-143220800	Enhancers	Brain Germinal Matrix	brain
11	chr3:143220200-143221200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:143220200-143221200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:143220200-143221200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:143220200-143221200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:143220400-143220800	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:143220400-143220800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:143220400-143221000	Enhancers	Brain Substantia Nigra	brain
18	chr3:143220400-143221200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:143220400-143221200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:143220400-143221200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr3:143220400-143221200	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:143220400-143221200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:143220400-143221200	Enhancers	Brain Hippocampus Middle	brain
24	chr3:143220400-143221400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:143220400-143221800	Enhancers	Fetal Lung	lung
26	chr3:143220400-143226400	Weak transcription	HSMMtube	muscle
27	chr3:143220600-143220800	Enhancers	Brain Anterior Caudate	brain
28	chr3:143220600-143221200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:143220600-143221200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:143220800-143221200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr3:143220800-143221200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
32	chr3:143220800-143226600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:143221000-143222400	Weak transcription	Spleen	Spleen
34	chr3:143221000-143227200	Weak transcription	Brain Substantia Nigra	brain
35	chr3:143221200-143224000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:143221200-143226800	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:143221200-143228200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:143221400-143223800	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:143221400-143224600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:143221800-143222200	Weak transcription	Fetal Lung	lung
41	chr3:143222200-143222400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:143222200-143222600	Enhancers	Gastric	stomach
43	chr3:143222200-143222800	Strong transcription	Fetal Lung	lung
44	chr3:143222200-143223000	ZNF genes & repeats	Esophagus	oesophagus
45	chr3:143222400-143222800	Enhancers	Spleen	Spleen
46	chr3:143222600-143226600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:143222800-143224400	Weak transcription	Fetal Lung	lung
48	chr3:143223000-143256200	Weak transcription	Esophagus	oesophagus
49	chr3:143224000-143227400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:143224400-143225600	Enhancers	Fetal Lung	lung

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