Variant report

Variant	esv3528586
Chromosome Location	chr3:17719048-17726146
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	ATF2	chr3:17719869-17720228	GM12878	blood:	n/a	n/a
2	ATF2	chr3:17719752-17720261	GM12878	blood:	n/a	n/a
3	BATF	chr3:17719836-17720148	GM12878	blood:	n/a	chr3:17720079-17720089
4	BATF	chr3:17719740-17720156	GM12878	blood:	n/a	chr3:17720079-17720089
5	BCL11A	chr3:17719823-17720178	GM12878	blood:	n/a	n/a
6	CEBPB	chr3:17722726-17722935	A549	lung:	n/a	chr3:17722891-17722900 chr3:17722889-17722900 chr3:17722891-17722900 chr3:17722889-17722902 chr3:17722891-17722900 chr3:17722889-17722902 chr3:17722891-17722900 chr3:17722771-17722782 chr3:17722889-17722900 chr3:17722889-17722902
7	CEBPB	chr3:17722654-17722976	IMR90	lung:	n/a	chr3:17722891-17722900 chr3:17722889-17722900 chr3:17722891-17722900 chr3:17722889-17722902 chr3:17722891-17722900 chr3:17722889-17722902 chr3:17722891-17722900 chr3:17722771-17722782 chr3:17722889-17722900 chr3:17722889-17722902
8	CEBPB	chr3:17726138-17726159	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPB	chr3:17722693-17722950	HepG2	liver:	n/a	chr3:17722891-17722900 chr3:17722889-17722900 chr3:17722891-17722900 chr3:17722889-17722902 chr3:17722891-17722900 chr3:17722889-17722902 chr3:17722891-17722900 chr3:17722771-17722782 chr3:17722889-17722900 chr3:17722889-17722902
10	E2F4	chr3:17725446-17725874	MCF10A-Er-Src	breast:	n/a	n/a
11	EBF1	chr3:17720042-17720065	GM12878	blood:	n/a	n/a
12	EP300	chr3:17719891-17720203	GM12878	blood:	n/a	n/a
13	EP300	chr3:17719981-17720163	SK-N-SH_RA	brain:	n/a	n/a
14	FOS	chr3:17719835-17720286	HUVEC	blood vessel:	n/a	chr3:17720080-17720091 chr3:17720082-17720089 chr3:17720083-17720094 chr3:17720082-17720090
15	FOS	chr3:17719926-17720219	MCF10A-Er-Src	breast:	n/a	chr3:17720080-17720091 chr3:17720082-17720089 chr3:17720083-17720094 chr3:17720082-17720090
16	FOS	chr3:17720032-17720160	MCF10A-Er-Src	breast:	n/a	chr3:17720080-17720091 chr3:17720082-17720089 chr3:17720083-17720094 chr3:17720082-17720090
17	FOS	chr3:17719909-17720253	MCF10A-Er-Src	breast:	n/a	chr3:17720080-17720091 chr3:17720082-17720089 chr3:17720083-17720094 chr3:17720082-17720090
18	FOS	chr3:17719873-17720276	MCF10A-Er-Src	breast:	n/a	chr3:17720080-17720091 chr3:17720082-17720089 chr3:17720083-17720094 chr3:17720082-17720090
19	FOSL2	chr3:17719816-17720368	SK-N-SH	brain:	n/a	chr3:17720082-17720089 chr3:17720083-17720094 chr3:17720082-17720090
20	FOXM1	chr3:17719751-17720178	GM12878	blood:	n/a	n/a
21	GATA2	chr3:17721695-17722018	SH-SY5Y	brain:	n/a	n/a
22	GATA3	chr3:17725335-17725485	SH-SY5Y	brain:	n/a	n/a
23	GATA3	chr3:17722944-17723067	SH-SY5Y	brain:	n/a	n/a
24	GATA3	chr3:17721919-17722066	SH-SY5Y	brain:	n/a	n/a
25	GATA3	chr3:17724803-17725001	SH-SY5Y	brain:	n/a	n/a
26	GATA3	chr3:17724028-17724167	SH-SY5Y	brain:	n/a	n/a
27	IKZF1	chr3:17719785-17720215	GM12878	blood:	n/a	n/a
28	IRF1	chr3:17722592-17722598	K562	blood:	n/a	n/a
29	JUN	chr3:17725280-17725435	K562	blood:	n/a	n/a
30	JUND	chr3:17719818-17720366	SK-N-SH	brain:	n/a	chr3:17720082-17720089 chr3:17720083-17720094 chr3:17720082-17720090
31	MAFF	chr3:17722864-17722951	HepG2	liver:	n/a	n/a
32	MAFK	chr3:17722792-17723084	HepG2	liver:	n/a	n/a
33	MAFK	chr3:17722884-17722934	HepG2	liver:	n/a	n/a
34	MEF2A	chr3:17719835-17720159	GM12878	blood:	n/a	n/a
35	MEF2A	chr3:17719772-17720251	GM12878	blood:	n/a	n/a
36	MYC	chr3:17723355-17723358	MCF-7	breast:	n/a	n/a
37	MYC	chr3:17723370-17723378	MCF-7	breast:	n/a	n/a
38	NFIC	chr3:17719684-17720315	GM12878	blood:	n/a	n/a
39	NFIC	chr3:17719626-17720296	GM12878	blood:	n/a	n/a
40	PBX3	chr3:17719798-17720234	SK-N-SH	brain:	n/a	n/a
41	PBX3	chr3:17719880-17720288	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr3:17721339-17721460	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:17725195-17725224	ProgFib	skin:	n/a	n/a
44	POLR2A	chr3:17723272-17723475	ProgFib	skin:	n/a	n/a
45	POLR2A	chr3:17724802-17724815	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr3:17721336-17721443	ProgFib	skin:	n/a	n/a
47	POLR2A	chr3:17724675-17724810	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr3:17720704-17720845	MCF10A-Er-Src	breast:	n/a	n/a
49	RCOR1	chr3:17719794-17720288	IMR90	lung:	n/a	n/a
50	RUNX3	chr3:17719649-17720274	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:17725117..17727704-chr3:17732645..17734795,3	MCF-7	breast:
2	chr3:17721696..17724606-chr3:17732689..17735501,2	K562	blood:
3	chr3:17712967..17714833-chr3:17718759..17720430,2	K562	blood:
4	chr3:17703859..17706608-chr3:17724124..17726176,2	K562	blood:
5	chr3:17710199..17712453-chr3:17724629..17727105,2	MCF-7	breast:
6	chr3:17709687..17712550-chr3:17720068..17722568,2	K562	blood:
7	chr3:17712945..17715676-chr3:17721430..17724365,2	K562	blood:

Variant related genes	Relation type
TBC1D5	TF binding region
ENSG00000131374	chromatin interactions
ENSG00000271841	chromatin interactions

Extended variants
information (count: 253 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:253 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200884186	chr3:17719075-17719076	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs538978799	chr3:17719103-17719104	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs552532437	chr3:17719119-17719120	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs569201327	chr3:17719161-17719162	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs369471433	chr3:17719189-17719190	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs538240079	chr3:17719201-17719202	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs372701448	chr3:17719202-17719203	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs376326397	chr3:17719226-17719227	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs150854404	chr3:17719228-17719229	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs201133991	chr3:17719231-17719232	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs533946936	chr3:17719236-17719237	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs370727165	chr3:17719299-17719300	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs374611359	chr3:17719310-17719311	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs558855983	chr3:17719336-17719337	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs546161704	chr3:17719363-17719364	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs562503567	chr3:17719397-17719398	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs572384861	chr3:17719431-17719432	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs139480765	chr3:17719474-17719475	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs36172181	chr3:17719478-17719479	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs146024681	chr3:17719524-17719525	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs139990288	chr3:17719529-17719530	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs539951773	chr3:17719576-17719577	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs560353309	chr3:17719593-17719594	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs532662304	chr3:17719602-17719603	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs552547588	chr3:17719609-17719610	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs183195496	chr3:17719651-17719652	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs13097908	chr3:17719764-17719765	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs116485564	chr3:17719823-17719824	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs556196112	chr3:17719825-17719826	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs568545994	chr3:17719899-17719900	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs112046832	chr3:17719939-17719940	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs187680102	chr3:17719944-17719945	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs117354245	chr3:17719949-17719950	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs200314626	chr3:17719967-17719968	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs368169039	chr3:17719971-17719972	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs570708143	chr3:17719978-17719979	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs539625265	chr3:17719992-17719993	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs556145876	chr3:17720020-17720021	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs551107834	chr3:17720044-17720045	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs576304291	chr3:17720052-17720053	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs192758355	chr3:17720084-17720085	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs4909009	chr3:17720104-17720105	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs13434111	chr3:17720108-17720109	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs551223487	chr3:17720157-17720158	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs369845688	chr3:17720159-17720160	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs76218630	chr3:17720174-17720175	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs535580521	chr3:17720175-17720176	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs149716786	chr3:17720206-17720207	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs540680401	chr3:17720219-17720220	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs547534478	chr3:17720242-17720243	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

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

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17694400-17721800	Weak transcription	A549	lung
2	chr3:17707000-17734800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:17709200-17723200	Weak transcription	Aorta	Aorta
4	chr3:17709200-17732000	Weak transcription	Psoas Muscle	Psoas
5	chr3:17709600-17725800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:17710800-17719800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:17711400-17755000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:17712600-17732600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:17712800-17719600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:17712800-17719800	Weak transcription	HUVEC	blood vessel
11	chr3:17713400-17723200	Weak transcription	Primary B cells from cord blood	blood
12	chr3:17714400-17719600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:17714400-17719600	Weak transcription	NHDF-Ad	bronchial
14	chr3:17714400-17719800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:17714400-17725200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:17714600-17724800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:17715000-17719800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:17719000-17720600	Enhancers	Dnd41	blood
19	chr3:17719600-17719800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:17719600-17720000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:17719600-17720000	Enhancers	NHEK	skin
22	chr3:17719600-17720200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:17719600-17720200	Enhancers	NHDF-Ad	bronchial
24	chr3:17719600-17720400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:17719600-17720600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:17719600-17720800	Enhancers	Osteobl	bone
27	chr3:17719800-17720000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:17719800-17720000	Enhancers	Brain Substantia Nigra	brain
29	chr3:17719800-17720000	Enhancers	HUVEC	blood vessel
30	chr3:17719800-17720000	Enhancers	NH-A	brain
31	chr3:17719800-17720200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:17719800-17720200	Enhancers	HMEC	breast
33	chr3:17719800-17720200	Enhancers	HSMM	muscle
34	chr3:17719800-17720600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:17719800-17720800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:17719800-17723400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:17720000-17722200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:17720000-17727600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:17720000-17747400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:17720200-17734200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:17720600-17722800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:17720600-17723600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:17720600-17734400	Weak transcription	Dnd41	blood
44	chr3:17720800-17723800	Weak transcription	Osteobl	bone
45	chr3:17721800-17723400	Enhancers	A549	lung
46	chr3:17722200-17723000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:17722400-17722600	Enhancers	Brain Anterior Caudate	brain
48	chr3:17722400-17723600	Enhancers	Colon Smooth Muscle	Colon
49	chr3:17722400-17723600	Enhancers	Ovary	ovary
50	chr3:17722600-17725600	Weak transcription	Brain Anterior Caudate	brain

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