Variant report

Variant	esv3333229
Chromosome Location	chr1:239894129-239897327
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	chr1:239896980-239899701	SK-N-SH	brain:	n/a	chr1:239898325-239898339 chr1:239897082-239897091 chr1:239897070-239897084
2	EP300	chr1:239897276-239897681	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr1:239897202-239897879	SK-N-SH	brain:	n/a	n/a
4	EP300	chr1:239897252-239897735	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr1:239897144-239897925	SK-N-SH	brain:	n/a	n/a
6	FOSL2	chr1:239897230-239897827	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr1:239897126-239897899	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr1:239897128-239897895	SK-N-SH	brain:	n/a	n/a
9	JUND	chr1:239897262-239897742	SK-N-SH	brain:	n/a	n/a
10	JUND	chr1:239897201-239897767	SK-N-SH	brain:	n/a	n/a
11	MEF2A	chr1:239897145-239897657	SK-N-SH	brain:	n/a	chr1:239897342-239897357 chr1:239897242-239897258 chr1:239897342-239897353 chr1:239897341-239897355 chr1:239897343-239897354
12	NFIC	chr1:239897262-239897856	SK-N-SH	brain:	n/a	n/a
13	PBX3	chr1:239897271-239897830	SK-N-SH	brain:	n/a	n/a
14	PBX3	chr1:239897134-239897928	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:239897248-239897695	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr1:239897256-239897685	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr1:239897225-239897644	H1-neurons	neurons:	n/a	n/a
18	REST	chr1:239896421-239896632	PFSK-1	brain:	n/a	n/a
19	REST	chr1:239896409-239896769	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr1:239897163-239897671	H1-neurons	neurons:	n/a	n/a
21	REST	chr1:239896413-239896654	SK-N-SH	brain:	n/a	n/a
22	REST	chr1:239896431-239896716	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr1:239896380-239896785	HL-60	blood:	n/a	n/a
24	REST	chr1:239896464-239896702	Hela-S3	cervix:	n/a	n/a
25	RXRA	chr1:239897316-239897784	SK-N-SH	brain:	n/a	n/a
26	STAT3	chr1:239896378-239896403	MCF10A-Er-Src	breast:	n/a	n/a
27	TCF12	chr1:239897094-239897951	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr1:239897178-239897848	SK-N-SH	brain:	n/a	n/a
29	TEAD4	chr1:239897221-239897867	SK-N-SH	brain:	n/a	n/a
30	TEAD4	chr1:239897167-239897801	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
CHRM3-AS2	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:126 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs145367533	chr1:239894141-239894142	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs192894481	chr1:239894206-239894207	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs150056260	chr1:239894300-239894301	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs528956005	chr1:239894337-239894338	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs185043785	chr1:239894391-239894392	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs547499467	chr1:239894465-239894466	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs75749765	chr1:239894494-239894495	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs534435419	chr1:239894501-239894502	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs61834841	chr1:239894536-239894537	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs559742599	chr1:239894555-239894556	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs543286466	chr1:239894634-239894635	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs144212120	chr1:239894646-239894647	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs556254311	chr1:239894660-239894661	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs574804301	chr1:239894666-239894667	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs140785036	chr1:239894702-239894703	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs374174320	chr1:239894714-239894715	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs535560559	chr1:239894715-239894716	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs147786111	chr1:239894814-239894815	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs565164210	chr1:239894878-239894879	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs545545348	chr1:239894927-239894928	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs563950975	chr1:239895031-239895032	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs17597501	chr1:239895046-239895047	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs373659620	chr1:239895054-239895055	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs561508541	chr1:239895073-239895074	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs377599056	chr1:239895100-239895101	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs532494666	chr1:239895213-239895214	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs16838841	chr1:239895239-239895240	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs189585687	chr1:239895257-239895258	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs148030650	chr1:239895263-239895264	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs559538309	chr1:239895333-239895334	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs533064746	chr1:239895398-239895399	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs552768642	chr1:239895437-239895438	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs860928	chr1:239895496-239895497	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs531889120	chr1:239895509-239895510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs844531	chr1:239895548-239895549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs12143756	chr1:239895561-239895562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs12144568	chr1:239895567-239895568	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs10925957	chr1:239895574-239895575	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs556281158	chr1:239895584-239895585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs12029745	chr1:239895600-239895601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs568112333	chr1:239895610-239895611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs12047381	chr1:239895613-239895614	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs12048136	chr1:239895619-239895620	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs12125105	chr1:239895626-239895627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs71166889	chr1:239895635-239895636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs34092911	chr1:239895636-239895637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs111590075	chr1:239895639-239895640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs112187675	chr1:239895645-239895646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs369025754	chr1:239895662-239895663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs10925959	chr1:239895678-239895679	Weak transcription	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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239885600-239905600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:239886800-239908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:239889000-239949800	Weak transcription	Pancreas	Pancrea
4	chr1:239891200-239918400	Weak transcription	Fetal Intestine Small	intestine
5	chr1:239891600-239898000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:239892000-239894200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:239893600-239895200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:239893600-239895400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:239894000-239895200	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:239894000-239895200	Enhancers	Colon Smooth Muscle	Colon
11	chr1:239894200-239895000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:239894200-239895400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:239894600-239895000	Enhancers	Fetal Heart	heart
14	chr1:239894600-239895000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:239895000-239896800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:239895200-239897200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:239895200-239898400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:239895200-239901400	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:239895400-239897200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:239895800-239898200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:239896400-239896800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:239896600-239896800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:239896800-239898400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:239896800-239898800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:239897200-239897600	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:239897200-239898800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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