Variant report

Variant	esv3363446
Chromosome Location	chr1:239887329-239890727
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	EP300	chr1:239888710-239888962	SK-N-SH_RA	brain:	n/a	n/a
2	GATA2	chr1:239888174-239888505	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr1:239890654-239890659	SH-SY5Y	brain:	n/a	n/a
4	GATA3	chr1:239888297-239888608	SH-SY5Y	brain:	n/a	n/a
5	POLR2A	chr1:239889816-239889987	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:239888726-239889087	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr1:239889705-239889905	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:239888372-239888681	MCF10A-Er-Src	breast:	n/a	n/a
9	SRF	chr1:239887280-239887547	ECC-1	luminal epithelium:	n/a	chr1:239887406-239887423 chr1:239887405-239887419 chr1:239887405-239887423 chr1:239887403-239887420 chr1:239887409-239887423
10	STAT3	chr1:239888262-239888391	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF7L2	chr1:239888651-239888972	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
CHRM3-AS2	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:118 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553116102	chr1:239887361-239887362	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs116012568	chr1:239887375-239887376	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs113031952	chr1:239887387-239887388	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs568611227	chr1:239887390-239887391	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs577767796	chr1:239887410-239887411	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs563574158	chr1:239887419-239887420	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs544775999	chr1:239887428-239887429	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs369032727	chr1:239887452-239887453	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs553844509	chr1:239887482-239887483	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs572429581	chr1:239887483-239887484	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs185085263	chr1:239887490-239887491	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs557867662	chr1:239887504-239887505	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs373398395	chr1:239887514-239887515	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs556958832	chr1:239887551-239887552	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs1030591	chr1:239887562-239887563	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs78386100	chr1:239887700-239887701	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs368512462	chr1:239887733-239887734	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs149835316	chr1:239887746-239887747	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs573813601	chr1:239887759-239887760	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs541334723	chr1:239887823-239887824	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs559064467	chr1:239887865-239887866	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs532977916	chr1:239887900-239887901	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs74667778	chr1:239887961-239887962	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs528670260	chr1:239888007-239888008	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs563418544	chr1:239888043-239888044	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs114027425	chr1:239888078-239888079	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs566162840	chr1:239888112-239888113	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs565134035	chr1:239888133-239888134	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs535743456	chr1:239888189-239888190	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs548100289	chr1:239888227-239888228	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs565923099	chr1:239888240-239888241	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs539491190	chr1:239888241-239888242	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs201320390	chr1:239888259-239888260	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs557828987	chr1:239888280-239888281	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs12743042	chr1:239888304-239888305	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs550779365	chr1:239888318-239888319	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs114264453	chr1:239888361-239888362	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs61834839	chr1:239888384-239888385	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs6695600	chr1:239888387-239888388	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs370705070	chr1:239888463-239888464	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs540952092	chr1:239888486-239888487	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs553271992	chr1:239888488-239888489	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs12066872	chr1:239888533-239888534	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs544972350	chr1:239888571-239888572	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs115209173	chr1:239888589-239888590	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs530584833	chr1:239888607-239888608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs535069636	chr1:239888624-239888625	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs113765520	chr1:239888633-239888634	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs61834840	chr1:239888663-239888664	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs114732771	chr1:239888740-239888741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Hepatocellular carcinoma	16750200	CNVD
Arrhythmogenic right ventricular cardiomyopathy	17576883	CNVD
Multiple myeloma	16616336	CNVD
Developmental delay	21147756	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239875400-239890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:239878200-239891000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:239883400-239888200	Weak transcription	Pancreas	Pancrea
4	chr1:239884800-239887400	Weak transcription	Thymus	Thymus
5	chr1:239885000-239894000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:239885400-239888000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:239885400-239888600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:239885600-239887600	Enhancers	Dnd41	blood
9	chr1:239885600-239905600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:239885800-239888600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:239885800-239888600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:239886000-239888200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:239886000-239888200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:239886000-239888400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:239886200-239887400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:239886200-239888800	Enhancers	Primary T cells from cord blood	blood
17	chr1:239886800-239908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:239887000-239887400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr1:239887000-239887600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr1:239887000-239888400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:239887200-239887400	Enhancers	Fetal Thymus	thymus
22	chr1:239887200-239887600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:239887200-239888000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:239887200-239888600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:239887400-239887600	Enhancers	Thymus	Thymus
26	chr1:239887400-239887800	Weak transcription	Fetal Thymus	thymus
27	chr1:239887400-239888600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr1:239887400-239888800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:239887600-239888200	Weak transcription	Thymus	Thymus
30	chr1:239887600-239888800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:239887800-239888400	Enhancers	Fetal Thymus	thymus
32	chr1:239888200-239888400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:239888200-239888400	Enhancers	Thymus	Thymus
34	chr1:239888200-239889000	Enhancers	Fetal Kidney	kidney
35	chr1:239888200-239889000	Enhancers	Pancreas	Pancrea
36	chr1:239888600-239890200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:239888600-239891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:239888800-239889600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:239888800-239889600	Enhancers	Fetal Lung	lung
40	chr1:239888800-239891000	Weak transcription	Primary T cells from cord blood	blood
41	chr1:239888800-239891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:239889000-239890200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr1:239889000-239949800	Weak transcription	Pancreas	Pancrea
44	chr1:239890200-239890400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:239890400-239890800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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