Variant report

Variant	esv3396842
Chromosome Location	chr3:142054803-142083800
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	chr3:142082266-142082975	HepG2	liver:	n/a	n/a
2	BATF	chr3:142074556-142074897	GM12878	blood:	n/a	n/a
3	BHLHE40	chr3:142066400-142066735	K562	blood:	n/a	n/a
4	CEBPB	chr3:142082835-142083473	HepG2	liver:	n/a	chr3:142083349-142083360
5	CEBPB	chr3:142082697-142083090	MCF-7	breast:	n/a	n/a
6	CEBPB	chr3:142083216-142083476	IMR90	lung:	n/a	chr3:142083349-142083360
7	CEBPB	chr3:142083225-142083451	K562	blood:	n/a	chr3:142083349-142083360
8	CEBPB	chr3:142055027-142055231	HepG2	liver:	n/a	chr3:142055127-142055140 chr3:142055129-142055140 chr3:142055041-142055052 chr3:142055127-142055138 chr3:142055127-142055140
9	CEBPB	chr3:142054990-142055271	K562	blood:	n/a	chr3:142055127-142055140 chr3:142055129-142055140 chr3:142055041-142055052 chr3:142055127-142055138 chr3:142055127-142055140
10	CTCF	chr3:142080892-142080911	Spleen_OC	spleen:	n/a	n/a
11	CUX1	chr3:142075778-142075903	GM12878	blood:	n/a	n/a
12	E2F4	chr3:142071085-142071089	MCF10A-Er-Src	breast:	n/a	n/a
13	E2F4	chr3:142070429-142070493	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr3:142066453-142066613	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F6	chr3:142066435-142066579	K562	blood:	n/a	n/a
16	EBF1	chr3:142075709-142076034	GM12878	blood:	n/a	chr3:142075899-142075910
17	EBF1	chr3:142075695-142075979	GM12878	blood:	n/a	chr3:142075899-142075910
18	EP300	chr3:142082341-142082694	HepG2	liver:	n/a	n/a
19	EP300	chr3:142078171-142078415	GM12878	blood:	n/a	n/a
20	EP300	chr3:142074746-142074800	GM12878	blood:	n/a	chr3:142074786-142074800
21	EP300	chr3:142066434-142066616	K562	blood:	n/a	n/a
22	EP300	chr3:142074555-142074859	GM12878	blood:	n/a	chr3:142074786-142074800
23	FOS	chr3:142066377-142066737	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr3:142066388-142066713	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr3:142083328-142083369	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr3:142066386-142066665	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr3:142066392-142066677	MCF10A-Er-Src	breast:	n/a	n/a
28	FOXA1	chr3:142082109-142083206	HepG2	liver:	n/a	chr3:142082761-142082773
29	FOXA1	chr3:142082195-142083113	HepG2	liver:	n/a	chr3:142082761-142082773
30	FOXA1	chr3:142082228-142083061	T-47D	breast:	n/a	chr3:142082761-142082773
31	FOXA1	chr3:142082018-142083211	HepG2	liver:	n/a	chr3:142082761-142082773
32	FOXA1	chr3:142079989-142080330	T-47D	breast:	n/a	n/a
33	FOXA1	chr3:142082178-142082498	HepG2	liver:	n/a	n/a
34	FOXA1	chr3:142082667-142083178	HepG2	liver:	n/a	chr3:142082761-142082773
35	FOXA2	chr3:142082185-142083105	HepG2	liver:	n/a	chr3:142082761-142082773
36	FOXA2	chr3:142082306-142082682	A549	lung:	n/a	n/a
37	FOXA2	chr3:142081573-142083510	HepG2	liver:	n/a	chr3:142082761-142082773
38	GATA3	chr3:142082079-142082993	MCF-7	breast:	n/a	n/a
39	GATA3	chr3:142054769-142054869	SH-SY5Y	brain:	n/a	n/a
40	GATA3	chr3:142079961-142080265	T-47D	breast:	n/a	n/a
41	GATA3	chr3:142076046-142076095	SH-SY5Y	brain:	n/a	n/a
42	GATA3	chr3:142082221-142082540	T-47D	breast:	n/a	n/a
43	GATA3	chr3:142074534-142074734	SH-SY5Y	brain:	n/a	n/a
44	HDAC2	chr3:142082632-142083128	HepG2	liver:	n/a	chr3:142082761-142082770
45	HDAC2	chr3:142082710-142083109	HepG2	liver:	n/a	chr3:142082761-142082770
46	HDAC2	chr3:142082382-142082656	HepG2	liver:	n/a	n/a
47	JUND	chr3:142082342-142082610	HepG2	liver:	n/a	n/a
48	JUND	chr3:142066400-142066697	K562	blood:	n/a	n/a
49	MAFK	chr3:142066475-142066557	K562	blood:	n/a	n/a
50	MAX	chr3:142056775-142057364	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142066835..142068380-chr3:142068524..142070586,2	K562	blood:
2	chr3:142061779..142063304-chr3:142065930..142068810,2	K562	blood:
3	chr3:142066835..142068380-chr3:142068524..142070586,2	K562	blood:
4	chr3:142064702..142067188-chr3:142070699..142072268,2	K562	blood:
5	chr3:142077588..142080075-chr3:142081701..142083765,2	K562	blood:
6	chr3:142061779..142063304-chr3:142065930..142068810,2	K562	blood:
7	chr3:142064702..142067188-chr3:142070699..142072268,2	K562	blood:
8	chr3:142071094..142074933-chr3:142076608..142079513,3	MCF-7	breast:
9	chr3:142071094..142074933-chr3:142076608..142079513,3	MCF-7	breast:
10	chr3:142077588..142080075-chr3:142081701..142083765,2	K562	blood:

Variant related genes	Relation type
XRN1	TF binding region

Extended variants
information (count: 984 )
Associated
traits (count: 51 )

Variant overlapped rSNPs/rCNVs (count:984 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs535228996	chr3:142054831-142054832	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs553244164	chr3:142054874-142054875	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs578228871	chr3:142054877-142054878	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs141779113	chr3:142054934-142054935	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs73238143	chr3:142054935-142054936	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs186870075	chr3:142054949-142054950	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs542582207	chr3:142054970-142054971	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs192118185	chr3:142055006-142055007	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs561064090	chr3:142055095-142055096	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs201295930	chr3:142055141-142055142	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs185280262	chr3:142055177-142055178	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs190554209	chr3:142055180-142055181	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs370880510	chr3:142055199-142055200	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs559283221	chr3:142055232-142055233	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs533298562	chr3:142055245-142055246	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs111774789	chr3:142055274-142055275	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs372080167	chr3:142055275-142055276	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs116943979	chr3:142055282-142055283	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs34907623	chr3:142055295-142055296	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs112538204	chr3:142055330-142055331	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs76357951	chr3:142055443-142055444	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs557579330	chr3:142055455-142055456	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs558532064	chr3:142055460-142055461	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs370442716	chr3:142055518-142055519	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs567371422	chr3:142055519-142055520	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs193239227	chr3:142055569-142055570	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs536926232	chr3:142055575-142055576	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs547209051	chr3:142055598-142055599	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs73238144	chr3:142055624-142055625	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs369346038	chr3:142055626-142055627	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs539346990	chr3:142055669-142055670	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs557252645	chr3:142055705-142055706	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs569171885	chr3:142055744-142055745	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs149400254	chr3:142055799-142055800	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs139691010	chr3:142055824-142055825	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs34657909	chr3:142055841-142055842	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs144622329	chr3:142055844-142055845	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs147473202	chr3:142055864-142055865	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs540362365	chr3:142055986-142055987	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs139998694	chr3:142055999-142056000	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs577742911	chr3:142056053-142056054	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs184466573	chr3:142056059-142056060	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs563591746	chr3:142056200-142056201	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs114703162	chr3:142056283-142056284	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs542689943	chr3:142056361-142056362	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs188372522	chr3:142056380-142056381	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs370753913	chr3:142056386-142056387	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs528223752	chr3:142056412-142056413	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs74338136	chr3:142056487-142056488	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs571291535	chr3:142056492-142056493	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:51)

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
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	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
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:987 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142024000-142057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:142026600-142056800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:142026800-142057600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:142026800-142057800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:142028800-142056800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:142030200-142061400	Weak transcription	Fetal Brain Male	brain
7	chr3:142030600-142091400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:142030800-142067800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:142030800-142073200	Weak transcription	Stomach Mucosa	stomach
10	chr3:142031000-142057000	Weak transcription	Brain Angular Gyrus	brain
11	chr3:142031200-142056800	Weak transcription	Gastric	stomach
12	chr3:142034200-142057400	Weak transcription	Esophagus	oesophagus
13	chr3:142038600-142056800	Weak transcription	NHEK	skin
14	chr3:142038600-142073600	Weak transcription	NHLF	lung
15	chr3:142043400-142058600	Strong transcription	Liver	Liver
16	chr3:142045000-142055800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:142045400-142055000	Strong transcription	Primary B cells from cord blood	blood
18	chr3:142045400-142055000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:142045400-142055000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:142045400-142070400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:142045600-142055000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:142045600-142055000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:142045600-142055000	Strong transcription	Dnd41	blood
24	chr3:142045600-142055200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:142045800-142055000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:142045800-142055200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:142045800-142062400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:142046400-142112400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:142047000-142057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:142047000-142058800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:142048800-142056800	Weak transcription	Lung	lung
32	chr3:142048800-142057600	Weak transcription	Pancreas	Pancrea
33	chr3:142050000-142055400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:142050600-142073400	Weak transcription	HMEC	breast
35	chr3:142050800-142057400	Weak transcription	Right Ventricle	heart
36	chr3:142051000-142056800	Weak transcription	Spleen	Spleen
37	chr3:142051000-142057200	Weak transcription	Aorta	Aorta
38	chr3:142051200-142056800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:142051200-142056800	Weak transcription	Fetal Intestine Small	intestine
40	chr3:142051800-142057000	Weak transcription	Brain Substantia Nigra	brain
41	chr3:142051800-142058400	Weak transcription	Brain Germinal Matrix	brain
42	chr3:142051800-142073400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:142051800-142073400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:142051800-142075200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:142051800-142093000	Weak transcription	Hela-S3	cervix
46	chr3:142052000-142056200	Weak transcription	Brain Anterior Caudate	brain
47	chr3:142052000-142056600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:142052000-142057600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:142052000-142058000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:142052000-142059400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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