Variant report

Variant	nsv966992
Chromosome Location	chr3:17504895-17508174
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	ARID3A	chr3:17506407-17506512	K562	blood:	n/a	n/a
2	CEBPB	chr3:17507591-17507882	IMR90	lung:	n/a	n/a
3	CTCF	chr3:17506331-17506571	K562	blood:	n/a	chr3:17506468-17506477 chr3:17506428-17506449 chr3:17506426-17506444
4	CTCF	chr3:17506340-17506490	MCF-7	breast:	n/a	chr3:17506468-17506477 chr3:17506428-17506449 chr3:17506426-17506444
5	CTCF	chr3:17506520-17506670	A549	lung:	n/a	n/a
6	CTCF	chr3:17506300-17506450	A549	lung:	n/a	chr3:17506428-17506449 chr3:17506426-17506444
7	CTCF	chr3:17506313-17506566	K562	blood:	n/a	chr3:17506468-17506477 chr3:17506428-17506449 chr3:17506426-17506444
8	E2F4	chr3:17507584-17507876	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chr3:17507649-17507652	Hela-S3	cervix:	n/a	n/a
10	FOS	chr3:17507589-17507868	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr3:17507543-17507991	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr3:17507554-17507896	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr3:17507552-17507965	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr3:17507610-17507913	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr3:17507511-17507698	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr3:17506676-17506734	A549	lung:	n/a	n/a
17	RAD21	chr3:17506353-17506506	SK-N-SH_RA	brain:	n/a	n/a
18	RAD21	chr3:17506322-17506562	SK-N-SH_RA	brain:	n/a	n/a
19	STAT3	chr3:17507621-17507885	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr3:17507548-17507897	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr3:17507444-17507888	MCF10A-Er-Src	breast:	n/a	n/a
22	TBP	chr3:17507420-17507428	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:17497521..17499126-chr3:17503539..17506247,2	MCF-7	breast:
2	chr3:17497865..17499392-chr3:17503466..17506313,2	K562	blood:
3	chr3:17507187..17509434-chr3:17516355..17517975,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLCL2-8	chr3:17506642-17507002	NONHSAT088548

Variant related genes	Relation type
ENSG00000227309	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:112 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs188290192	chr3:17504933-17504934	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs368188759	chr3:17504936-17504937	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs191398414	chr3:17504979-17504980	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs566062374	chr3:17504996-17504997	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs185056215	chr3:17505038-17505039	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs557814638	chr3:17505091-17505092	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs190309722	chr3:17505097-17505098	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs182282064	chr3:17505140-17505141	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs556700951	chr3:17505165-17505166	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs573762346	chr3:17505194-17505195	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs569080640	chr3:17505235-17505236	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs542856884	chr3:17505246-17505247	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs111268287	chr3:17505314-17505315	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs559433317	chr3:17505337-17505338	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs531383173	chr3:17505370-17505371	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs572784384	chr3:17505405-17505406	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs545052053	chr3:17505419-17505420	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs564897773	chr3:17505433-17505434	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs74996328	chr3:17505461-17505462	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs530587272	chr3:17505466-17505467	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs3892499	chr3:17505468-17505469	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs529892765	chr3:17505469-17505470	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs550705337	chr3:17505501-17505502	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs563859202	chr3:17505502-17505503	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs149757234	chr3:17505505-17505506	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs377341463	chr3:17505577-17505578	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs549642232	chr3:17505583-17505584	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs566278022	chr3:17505605-17505606	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs145559087	chr3:17505606-17505607	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs577909988	chr3:17505619-17505620	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs551686150	chr3:17505632-17505633	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs571220333	chr3:17505687-17505688	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs141289701	chr3:17505699-17505700	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs186817638	chr3:17505714-17505715	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs557175829	chr3:17505741-17505742	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs573774236	chr3:17505743-17505744	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs190080029	chr3:17505744-17505745	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs181217075	chr3:17505784-17505785	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs113670813	chr3:17505830-17505831	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs146984253	chr3:17505835-17505836	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs573148767	chr3:17505857-17505858	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs137982933	chr3:17505881-17505882	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs368636506	chr3:17505885-17505886	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs185461618	chr3:17505979-17505980	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs575315667	chr3:17505990-17505991	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs7432241	chr3:17506024-17506025	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs189870345	chr3:17506040-17506041	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs73161502	chr3:17506064-17506065	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs549339404	chr3:17506071-17506072	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs559916662	chr3:17506089-17506090	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:76)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
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
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	21364760	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Ovarian cancer	21781307	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Schizophrenia	23813976	CNVD
Bipolar disorder	19114987	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17448000-17506600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:17462400-17521400	Weak transcription	Pancreas	Pancrea
3	chr3:17472400-17522000	Weak transcription	Fetal Lung	lung
4	chr3:17473800-17509600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:17476200-17530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:17477600-17521600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:17480400-17521200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:17491600-17521200	Weak transcription	Fetal Stomach	stomach
9	chr3:17495400-17521800	Weak transcription	Ovary	ovary
10	chr3:17497400-17510000	Weak transcription	Left Ventricle	heart
11	chr3:17497600-17513000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:17497600-17522000	Weak transcription	Dnd41	blood
13	chr3:17498200-17511000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:17498400-17521800	Weak transcription	GM12878-XiMat	blood
15	chr3:17498800-17522600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:17499800-17521800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr3:17501000-17521800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:17501200-17512000	Weak transcription	Liver	Liver
19	chr3:17502000-17506600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:17502000-17521400	Weak transcription	Fetal Intestine Small	intestine
21	chr3:17503400-17511000	Weak transcription	Primary B cells from cord blood	blood
22	chr3:17504200-17505000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:17504200-17507200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:17504200-17514000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:17505000-17521200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:17505800-17508600	Weak transcription	Esophagus	oesophagus
27	chr3:17506400-17507000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:17506600-17506800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:17506600-17507800	Strong transcription	Primary hematopoietic stem cells	blood
30	chr3:17506800-17522200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:17507000-17508800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:17507200-17508200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:17507200-17511000	Weak transcription	Fetal Kidney	kidney
34	chr3:17507200-17521600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:17507800-17508200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:17507800-17522000	Weak transcription	Primary hematopoietic stem cells	blood

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