Variant report

Variant	esv3523317
Chromosome Location	chr3:142172020-142176793
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	GATA3	chr3:142176594-142176899	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr3:142176667-142176993	MCF-7	breast:	n/a	n/a
3	MAFK	chr3:142172116-142172200	HepG2	liver:	n/a	chr3:142172124-142172140 chr3:142172124-142172135
4	MAFK	chr3:142172033-142172238	HepG2	liver:	n/a	chr3:142172124-142172140 chr3:142172124-142172135
5	MAZ	chr3:142173780-142173870	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:142175317-142175330	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:142174888-142175086	A549	lung:	n/a	n/a
8	POLR2A	chr3:142175254-142175446	K562	blood:	n/a	n/a
9	POLR2A	chr3:142172821-142173251	K562	blood:	n/a	n/a
10	POLR2A	chr3:142176336-142176423	K562	blood:	n/a	n/a
11	POLR2A	chr3:142174996-142175050	MCF-7	breast:	n/a	n/a
12	POLR2A	chr3:142175075-142175076	MCF-7	breast:	n/a	n/a
13	SPI1	chr3:142176649-142176851	GM12891	blood:	n/a	n/a
14	STAT3	chr3:142174597-142174623	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142165266..142167494-chr3:142176108..142178776,2	K562	blood:
2	chr3:142166774..142168881-chr3:142175818..142179023,4	MCF-7	breast:
3	chr3:142166755..142169411-chr3:142174583..142176894,2	K562	blood:
4	chr3:142165537..142167981-chr3:142173026..142174613,2	K562	blood:
5	chr3:142164997..142168564-chr3:142170242..142173896,7	MCF-7	breast:
6	chr3:142173107..142175736-chr3:142179768..142182228,2	K562	blood:

Variant related genes	Relation type
ATR	TF binding region
ENSG00000114127	chromatin interactions
ENSG00000242479	chromatin interactions

Extended variants
information (count: 140 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:140 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200490116	chr3:142172064-142172065	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs377119120	chr3:142172122-142172123	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs531239444	chr3:142172132-142172133	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs113408073	chr3:142172143-142172144	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs191926315	chr3:142172156-142172157	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs528973840	chr3:142172225-142172226	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs7634495	chr3:142172410-142172411	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs558788889	chr3:142172451-142172452	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs566265616	chr3:142172518-142172519	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs114346887	chr3:142172537-142172538	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs374871085	chr3:142172578-142172579	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs111936453	chr3:142172715-142172716	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs570349821	chr3:142172728-142172729	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs9816736	chr3:142172780-142172781	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs116199234	chr3:142172781-142172782	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs574094517	chr3:142172804-142172805	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs541527439	chr3:142172888-142172889	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs370847066	chr3:142172896-142172897	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs151073988	chr3:142172972-142172973	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs571933129	chr3:142173007-142173008	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs545576283	chr3:142173031-142173032	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs564065731	chr3:142173129-142173130	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs531495889	chr3:142173141-142173142	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs543052293	chr3:142173142-142173143	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs561732711	chr3:142173150-142173151	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs528835539	chr3:142173172-142173173	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs547489696	chr3:142173207-142173208	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs565603304	chr3:142173240-142173241	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs533602120	chr3:142173276-142173277	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs372141339	chr3:142173280-142173281	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs551982870	chr3:142173315-142173316	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs570410230	chr3:142173398-142173399	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs537731746	chr3:142173461-142173462	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs13073093	chr3:142173504-142173505	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs200162754	chr3:142173515-142173516	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs201506412	chr3:142173518-142173519	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs534682958	chr3:142173525-142173526	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs368653419	chr3:142173530-142173531	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs577692059	chr3:142173562-142173563	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs539292910	chr3:142173563-142173564	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs542141006	chr3:142173578-142173579	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs147115242	chr3:142173579-142173580	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs371239077	chr3:142173583-142173584	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs575790895	chr3:142173584-142173585	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs543703505	chr3:142173685-142173686	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs147770864	chr3:142173686-142173687	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs573596806	chr3:142173741-142173742	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs540655051	chr3:142173766-142173767	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs559428389	chr3:142173810-142173811	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs75000545	chr3:142173869-142173870	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:52)

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
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:216 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167200-142174800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:142167200-142174800	Weak transcription	Lung	lung
3	chr3:142167200-142176800	Weak transcription	Gastric	stomach
4	chr3:142167200-142178800	Weak transcription	Small Intestine	intestine
5	chr3:142167200-142187600	Weak transcription	Esophagus	oesophagus
6	chr3:142167200-142192400	Weak transcription	Pancreas	Pancrea
7	chr3:142167400-142175600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:142167400-142176400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:142167400-142176800	Weak transcription	Placenta	Placenta
10	chr3:142167400-142179600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:142167400-142199400	Weak transcription	Colonic Mucosa	Colon
12	chr3:142167400-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
14	chr3:142167600-142176400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:142167600-142177000	Weak transcription	Right Ventricle	heart
16	chr3:142167600-142177000	Weak transcription	NH-A	brain
17	chr3:142167600-142177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:142167600-142177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:142167600-142177600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:142167600-142180000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:142167600-142180000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:142167600-142187200	Weak transcription	Fetal Brain Male	brain
23	chr3:142167600-142191800	Weak transcription	Fetal Brain Female	brain
24	chr3:142167600-142199600	Weak transcription	Ovary	ovary
25	chr3:142167600-142200000	Weak transcription	HSMMtube	muscle
26	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
27	chr3:142167800-142175800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:142167800-142176000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:142167800-142176200	Weak transcription	HUVEC	blood vessel
30	chr3:142167800-142177000	Weak transcription	Brain Anterior Caudate	brain
31	chr3:142167800-142177000	Weak transcription	NHDF-Ad	bronchial
32	chr3:142167800-142177400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:142167800-142177600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:142167800-142177600	Weak transcription	NHEK	skin
35	chr3:142167800-142179000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:142167800-142179800	Weak transcription	Brain Substantia Nigra	brain
37	chr3:142167800-142180000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:142167800-142180200	Weak transcription	HepG2	liver
39	chr3:142167800-142184800	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:142167800-142186400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:142167800-142188800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:142167800-142190400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:142167800-142199400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:142167800-142200000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:142167800-142200000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:142168000-142172400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:142168000-142176400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:142168000-142182600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:142168000-142192000	Weak transcription	Fetal Lung	lung
50	chr3:142168000-142200000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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