Variant report

Variant	nsv1040076
Chromosome Location	chr15:54012505-54037424
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	chr15:54025360-54025395	Lung_OC	lung:	n/a	n/a
2	ESR1	chr15:54031761-54032202	T-47D	breast:	n/a	chr15:54032015-54032032 chr15:54032016-54032031
3	ESR1	chr15:54031813-54032192	T-47D	breast:	n/a	chr15:54032015-54032032 chr15:54032016-54032031
4	ESR1	chr15:54031893-54032184	T-47D	breast:	n/a	chr15:54032015-54032032 chr15:54032016-54032031
5	ESR1	chr15:54031835-54032175	T-47D	breast:	n/a	chr15:54032015-54032032 chr15:54032016-54032031
6	ESR1	chr15:54031804-54032196	T-47D	breast:	n/a	chr15:54032015-54032032 chr15:54032016-54032031
7	GATA3	chr15:54030227-54030617	MCF-7	breast:	n/a	n/a
8	JUND	chr15:54021494-54021682	HepG2	liver:	n/a	n/a
9	KAP1	chr15:54034824-54035042	K562	blood:	n/a	n/a
10	POLR2A	chr15:54015351-54015425	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr15:54026992-54027067	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr15:54016845-54017008	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr15:54036697-54036840	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr15:54028478-54028824	A549	lung:	n/a	n/a
15	POLR2A	chr15:54019555-54019642	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:54014795-54014980	MCF10A-Er-Src	breast:	n/a	n/a
17	SMC3	chr15:54019728-54019773	HepG2	liver:	n/a	n/a
18	SPI1	chr15:54036300-54036485	GM12878	blood:	n/a	chr15:54036413-54036422
19	SPI1	chr15:54036293-54036508	GM12891	blood:	n/a	chr15:54036413-54036422
20	STAT3	chr15:54023384-54023772	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:54023576..54026750-chr15:54026892..54029549,4	MCF-7	breast:
2	chr15:54025883..54029184-chr15:54031386..54034833,4	MCF-7	breast:
3	chr15:54031475..54033401-chr15:54036496..54038741,2	MCF-7	breast:
4	chr12:2392202..2393702-chr15:54036267..54038499,2	MCF-7	breast:
5	chr15:54031475..54033401-chr15:54036496..54038741,2	MCF-7	breast:
6	chr15:54035259..54036883-chr15:54037384..54039611,2	MCF-7	breast:
7	chr15:54035259..54036883-chr15:54037384..54039611,2	MCF-7	breast:
8	chr15:54034974..54037119-chr15:54039892..54041894,2	MCF-7	breast:
9	chr15:54025883..54029184-chr15:54031386..54034833,4	MCF-7	breast:

Variant related genes	Relation type
WDR72	TF binding region
ENSG00000166415	chromatin interactions

Extended variants
information (count: 609 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:609 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1381194	chr15:54012505-54012506	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs548488117	chr15:54012525-54012526	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs10518736	chr15:54012542-54012543	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs185756344	chr15:54012575-54012576	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs189890125	chr15:54012586-54012587	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs2470078	chr15:54012616-54012617	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs115325786	chr15:54012618-54012619	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs193158282	chr15:54012662-54012663	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs543742173	chr15:54012666-54012667	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs564036726	chr15:54012697-54012698	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs184587406	chr15:54012705-54012706	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs188646515	chr15:54012713-54012714	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs564597881	chr15:54012746-54012747	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs370521526	chr15:54012785-54012786	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs578909	chr15:54012805-54012806	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs148933312	chr15:54012864-54012865	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs181430191	chr15:54012912-54012913	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs373770587	chr15:54012943-54012944	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs529729836	chr15:54012953-54012954	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs75813488	chr15:54012986-54012987	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs569946228	chr15:54012989-54012990	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs538411734	chr15:54013035-54013036	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs113032525	chr15:54013063-54013064	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs565926986	chr15:54013080-54013081	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs535112259	chr15:54013083-54013084	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs143641459	chr15:54013107-54013108	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs575983146	chr15:54013165-54013166	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs148081648	chr15:54013179-54013180	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs10518737	chr15:54013216-54013217	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs376092604	chr15:54013359-54013360	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs185224144	chr15:54013370-54013371	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs76564573	chr15:54013483-54013484	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs142308826	chr15:54013491-54013492	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs956553	chr15:54013493-54013494	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs560437059	chr15:54013504-54013505	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs58563467	chr15:54013564-54013565	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs146139919	chr15:54013565-54013566	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs540711256	chr15:54013568-54013569	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs561069671	chr15:54013611-54013612	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs138877588	chr15:54013624-54013625	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs956552	chr15:54013638-54013639	Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs188413959	chr15:54013651-54013652	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs532431789	chr15:54013797-54013798	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs77609290	chr15:54013854-54013855	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs181967143	chr15:54013864-54013865	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs142779048	chr15:54013870-54013871	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs75254789	chr15:54013882-54013883	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs568556009	chr15:54013885-54013886	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs16966558	chr15:54013905-54013906	Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs150746961	chr15:54013946-54013947	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16774939	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Prostate cancer	16573809	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17053054	CNVD
Breast cancer	22032731	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Cancer	21129771	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Abnormal phenotypes	18644119	CNVD
Cancer	16751803	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Myelofibrosis	22110671	CNVD
Acute monocytic leukemia	16498392	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54009200-54014600	Weak transcription	HepG2	liver
2	chr15:54012000-54012600	Weak transcription	Liver	Liver
3	chr15:54012600-54013000	Enhancers	Liver	Liver
4	chr15:54013000-54013600	Flanking Active TSS	Liver	Liver
5	chr15:54013000-54013600	Enhancers	Fetal Intestine Small	intestine
6	chr15:54013600-54014400	Active TSS	Liver	Liver
7	chr15:54014400-54014600	Flanking Active TSS	Liver	Liver
8	chr15:54014600-54015200	Enhancers	Liver	Liver
9	chr15:54014600-54015200	Enhancers	HepG2	liver
10	chr15:54015200-54015400	Weak transcription	HepG2	liver
11	chr15:54023600-54028600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:54026400-54028400	Weak transcription	Right Atrium	heart
13	chr15:54027200-54027600	Enhancers	Pancreas	Pancrea
14	chr15:54027600-54028600	Weak transcription	Pancreas	Pancrea
15	chr15:54028400-54028800	ZNF genes & repeats	Right Atrium	heart
16	chr15:54028600-54028800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:54028600-54028800	Enhancers	Pancreas	Pancrea
18	chr15:54028800-54031400	Weak transcription	Pancreas	Pancrea
19	chr15:54028800-54032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:54031200-54033800	Enhancers	Liver	Liver
21	chr15:54031400-54031600	Enhancers	Pancreas	Pancrea
22	chr15:54031400-54032400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr15:54031600-54032000	Enhancers	Fetal Lung	lung
24	chr15:54032600-54032800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:54035400-54039800	Weak transcription	Fetal Kidney	kidney
26	chr15:54037400-54038000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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