Variant report

Variant	esv3356671
Chromosome Location	chr3:195975455-195979753
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	BATF	chr3:195977742-195977985	GM12878	blood:	n/a	n/a
2	BATF	chr3:195976826-195977663	GM12878	blood:	n/a	n/a
3	BATF	chr3:195977172-195977384	GM12878	blood:	n/a	n/a
4	BCL11A	chr3:195977748-195978193	GM12878	blood:	n/a	n/a
5	BCL11A	chr3:195977692-195978090	GM12878	blood:	n/a	n/a
6	EBF1	chr3:195976616-195976902	GM12878	blood:	n/a	n/a
7	EP300	chr3:195977641-195978208	GM12878	blood:	n/a	n/a
8	EP300	chr3:195976557-195976848	GM12878	blood:	n/a	n/a
9	EP300	chr3:195977117-195977367	GM12878	blood:	n/a	n/a
10	EP300	chr3:195977303-195977553	GM12878	blood:	n/a	n/a
11	EP300	chr3:195977801-195978062	GM12878	blood:	n/a	n/a
12	EP300	chr3:195976627-195976898	GM12878	blood:	n/a	n/a
13	FOSL2	chr3:195977138-195977729	HepG2	liver:	n/a	n/a
14	FOSL2	chr3:195976600-195977049	HepG2	liver:	n/a	n/a
15	FOSL2	chr3:195977083-195977648	HepG2	liver:	n/a	n/a
16	FOSL2	chr3:195977719-195978203	HepG2	liver:	n/a	n/a
17	GABPA	chr3:195977828-195978196	Hela-S3	cervix:	n/a	n/a
18	GABPA	chr3:195977166-195977390	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr3:195976534-195976846	Hela-S3	cervix:	n/a	n/a
20	GABPA	chr3:195977092-195978290	Hela-S3	cervix:	n/a	n/a
21	HEY1	chr3:195977113-195977598	HepG2	liver:	n/a	n/a
22	IRF4	chr3:195977700-195978314	GM12878	blood:	n/a	n/a
23	IRF4	chr3:195976902-195977678	GM12878	blood:	n/a	n/a
24	JUND	chr3:195977778-195978070	HepG2	liver:	n/a	n/a
25	JUND	chr3:195976630-195976806	HepG2	liver:	n/a	n/a
26	JUND	chr3:195977170-195977391	HepG2	liver:	n/a	n/a
27	NR3C1	chr3:195977716-195978233	A549	lung:	n/a	n/a
28	NR3C1	chr3:195977669-195978290	A549	lung:	n/a	n/a
29	PAX5	chr3:195978034-195978205	GM12878	blood:	n/a	n/a
30	PAX5	chr3:195976536-195978346	GM12878	blood:	n/a	n/a
31	PAX5	chr3:195977990-195978246	GM12878	blood:	n/a	n/a
32	PAX5	chr3:195977146-195977413	GM12878	blood:	n/a	n/a
33	PAX5	chr3:195977772-195978174	GM12878	blood:	n/a	n/a
34	PAX5	chr3:195978842-195979019	GM12878	blood:	n/a	chr3:195978931-195978950 chr3:195978960-195978979 chr3:195978989-195979008
35	PAX5	chr3:195978756-195979170	GM12878	blood:	n/a	chr3:195978931-195978950 chr3:195978960-195978979 chr3:195978989-195979008
36	PAX5	chr3:195976599-195977358	GM12878	blood:	n/a	n/a
37	PAX5	chr3:195975658-195975961	GM12878	blood:	n/a	n/a
38	PAX5	chr3:195978749-195979084	GM12878	blood:	n/a	chr3:195978931-195978950 chr3:195978960-195978979 chr3:195978989-195979008
39	PAX5	chr3:195978742-195979090	GM12892	blood:	n/a	chr3:195978931-195978950 chr3:195978960-195978979 chr3:195978989-195979008
40	PAX5	chr3:195978702-195979180	GM12878	blood:	n/a	chr3:195978931-195978950 chr3:195978960-195978979 chr3:195978989-195979008
41	PAX5	chr3:195978846-195979099	GM12892	blood:	n/a	chr3:195978931-195978950 chr3:195978960-195978979 chr3:195978989-195979008
42	PBX3	chr3:195976620-195976764	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:195976881-195977587	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr3:195976919-195977129	A549	lung:	n/a	n/a
45	POLR2A	chr3:195976621-195977663	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:195976631-195977642	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:195976564-195976881	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr3:195975337-195975503	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:195977826-195978160	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:195977638-195978297	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:195971582..195973149-chr3:195978489..195981811,3	MCF-7	breast:
2	chr3:195976340..195978485-chr3:196049925..196051821,2	K562	blood:
3	chr3:195952863..195955052-chr3:195973498..195975966,2	K562	blood:
4	chr3:195979094..195980840-chr3:195981274..195983857,2	K562	blood:
5	chr3:195977668..195980618-chr3:195990006..195991667,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228028	TF binding region
PCYT1A	TF binding region
ENSG00000145107	chromatin interactions
ENSG00000163959	chromatin interactions

Extended variants
information (count: 186 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:186 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs376235974	chr3:195975474-195975475	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs150279772	chr3:195975491-195975492	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs369919251	chr3:195975544-195975545	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs550252860	chr3:195975573-195975574	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs200812322	chr3:195975625-195975626	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs139963712	chr3:195975634-195975635	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs371638887	chr3:195975651-195975652	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs185434610	chr3:195975690-195975691	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs529409799	chr3:195975721-195975722	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs138938051	chr3:195975733-195975734	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs565970744	chr3:195975742-195975743	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs376292370	chr3:195975754-195975755	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs534069000	chr3:195975778-195975779	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs552065981	chr3:195975780-195975781	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs538939066	chr3:195975782-195975783	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs149362595	chr3:195975804-195975805	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs188994889	chr3:195975817-195975818	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs568136840	chr3:195975867-195975868	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs554482738	chr3:195975877-195975878	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs369274269	chr3:195975901-195975902	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs371900497	chr3:195975913-195975914	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs76885646	chr3:195976035-195976036	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs147036245	chr3:195976067-195976068	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs546478832	chr3:195976079-195976080	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs558493635	chr3:195976093-195976094	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs572536331	chr3:195976094-195976095	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs576856476	chr3:195976105-195976106	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs80243486	chr3:195976183-195976184	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs10668425	chr3:195976201-195976202	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs397955370	chr3:195976202-195976203	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs544022498	chr3:195976257-195976258	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs112937413	chr3:195976287-195976288	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs529364387	chr3:195976418-195976419	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs541185366	chr3:195976518-195976519	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs386670152	chr3:195976566-195976567	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs201474710	chr3:195976643-195976644	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs73084695	chr3:195976646-195976647	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs201616907	chr3:195976648-195976649	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs533184525	chr3:195976655-195976656	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs552008778	chr3:195976665-195976666	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs570413325	chr3:195976693-195976694	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs200603721	chr3:195976707-195976708	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs151176766	chr3:195976709-195976710	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs138475422	chr3:195976729-195976730	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs531543002	chr3:195976800-195976801	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs369731581	chr3:195976803-195976804	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs147265854	chr3:195976826-195976827	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs115044549	chr3:195976834-195976835	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs72611187	chr3:195976845-195976846	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs538624831	chr3:195976865-195976866	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:83)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:215 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195959600-195978200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:195962400-195977000	Strong transcription	Fetal Stomach	stomach
3	chr3:195962400-195979400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:195965200-195994200	Weak transcription	A549	lung
5	chr3:195965600-195975800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:195965800-195976600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:195967200-195988600	Strong transcription	Fetal Intestine Small	intestine
9	chr3:195967400-195975600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:195968400-195976400	Strong transcription	Spleen	Spleen
11	chr3:195968800-195993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:195969200-195978200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:195969600-195982400	Weak transcription	Fetal Heart	heart
14	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
15	chr3:195971200-195979600	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:195971600-195978400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:195971800-195976000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:195972200-195976400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:195972200-195978600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:195972200-195979000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:195972200-195979200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:195972400-195975800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr3:195972400-195976400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:195972400-195977200	Strong transcription	Fetal Intestine Large	intestine
25	chr3:195972400-195977800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:195972800-195976600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:195973000-195975600	Strong transcription	HMEC	breast
28	chr3:195973000-195976800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:195973400-195997200	Weak transcription	Small Intestine	intestine
30	chr3:195974400-195988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:195974400-195999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:195974600-195975800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:195974600-195976600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:195974600-195981600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:195974600-195981800	Weak transcription	Brain Germinal Matrix	brain
36	chr3:195974600-195981800	Weak transcription	Psoas Muscle	Psoas
37	chr3:195974600-195981800	Weak transcription	NHDF-Ad	bronchial
38	chr3:195974600-195982400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:195974600-195983600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:195974600-195987800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:195974600-195999800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:195974800-195976200	Weak transcription	Primary B cells from cord blood	blood
43	chr3:195974800-195977600	Weak transcription	Fetal Lung	lung
44	chr3:195974800-195999600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:195974800-195999600	Weak transcription	Pancreas	Pancrea
46	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
47	chr3:195975000-195976600	Weak transcription	GM12878-XiMat	blood
48	chr3:195975000-195977600	Weak transcription	Brain Angular Gyrus	brain
49	chr3:195975000-195978200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:195975000-195980200	Weak transcription	Muscle Satellite Cultured Cells	--

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