Variant report

Variant	esv3444667
Chromosome Location	chr12:56667436-56668657
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	chr12:56668573-56668714	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:56668587-56668721	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:56667444-56667494	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56667286-56667492	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:56667773-56668453	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:56667376-56667564	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:56668526-56668823	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:56667048-56667460	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr12:56668070-56668359	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56660814..56663303-chr12:56668023..56670170,2	MCF-7	breast:
2	chr12:56659385..56662814-chr12:56663155..56667840,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258260	TF binding region
CS	TF binding region
ENSG00000135469	chromatin interactions

Extended variants
information (count: 46 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:46 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372108588	chr12:56667461-56667462	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs149476836	chr12:56667493-56667494	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs201683368	chr12:56667527-56667528	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs78871887	chr12:56667528-56667529	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs541154361	chr12:56667536-56667537	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs143961151	chr12:56667572-56667573	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs375865192	chr12:56667578-56667579	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs17118439	chr12:56667604-56667605	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs574886203	chr12:56667693-56667694	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs542448680	chr12:56667761-56667762	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs150218636	chr12:56667779-56667780	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs35366727	chr12:56667782-56667783	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs538167657	chr12:56667820-56667821	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs201041042	chr12:56667840-56667841	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs563935532	chr12:56667845-56667846	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs531252003	chr12:56667879-56667880	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs544748789	chr12:56667885-56667886	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs112931321	chr12:56667894-56667895	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	mRNA abundance
19	rs528129975	chr12:56667927-56667928	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs571707258	chr12:56667974-56667975	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs568151213	chr12:56667995-56667996	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs534190802	chr12:56667997-56667998	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs554258585	chr12:56668015-56668016	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs146449836	chr12:56668037-56668038	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs535256133	chr12:56668055-56668056	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs59911757	chr12:56668104-56668105	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs397785050	chr12:56668124-56668125	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs573748928	chr12:56668129-56668130	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs561310014	chr12:56668130-56668131	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs113245305	chr12:56668170-56668171	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs872103	chr12:56668174-56668175	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs372769794	chr12:56668198-56668199	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs376140919	chr12:56668217-56668218	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs370558788	chr12:56668226-56668227	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs557667514	chr12:56668251-56668252	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs577162251	chr12:56668268-56668269	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs536432316	chr12:56668364-56668365	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs117863049	chr12:56668380-56668381	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs184085414	chr12:56668424-56668425	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs542411832	chr12:56668461-56668462	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs371772089	chr12:56668541-56668542	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs375369120	chr12:56668542-56668543	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs563849597	chr12:56668550-56668551	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs575942993	chr12:56668562-56668563	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs112704313	chr12:56668569-56668570	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs139897823	chr12:56668609-56668610	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Bladder cancer	21909424	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	20531469	CNVD
Rhabdomyosarcoma	16790082	CNVD
Renal cell carcinoma	18765545	CNVD
Urothelial cell carcinoma	18451213	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21138945	CNVD
Glioblastoma multiforme	21569311	CNVD
Glioblastoma multiforme	19115005	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	21509527	CNVD
Leukemia	18628472	CNVD
Glioblastoma multiforme	22291905	CNVD
Glioblastoma multiforme	19435819	CNVD
Myelofibrosis	22110671	CNVD
Phyllodes tumor	17334353	CNVD
Glaucoma	21310917	CNVD
Breast cancer	16272173	CNVD
Mental retardation	19951919	CNVD
Glaucoma	21447600	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Developmental delay	21267005	CNVD
12q14 microdeletion syndrome	21267005	CNVD
Developmental delay	19277063	CNVD
Dwarfism	19277063	CNVD
Fibroblasts	20926602	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Glycogen storage disease	18421352	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Glioblastoma multiforme	20080666	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	17133270	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD

Chromatin state (count:131 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56661400-56684400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:56661600-56669600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56661600-56671600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:56661800-56668200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:56662000-56690000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:56662200-56678200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:56662400-56670600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:56662400-56673200	Strong transcription	HSMM	muscle
9	chr12:56662400-56677200	Strong transcription	Primary T cells from cord blood	blood
10	chr12:56662400-56680800	Strong transcription	Brain Hippocampus Middle	brain
11	chr12:56662400-56692400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:56662600-56673400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:56662600-56680800	Strong transcription	Placenta	Placenta
14	chr12:56662600-56681000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:56662600-56681000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:56662600-56681400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:56662600-56682800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:56662600-56685400	Strong transcription	Fetal Thymus	thymus
19	chr12:56662600-56686000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:56662600-56690000	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:56662800-56667800	Genic enhancers	Liver	Liver
22	chr12:56662800-56670200	Strong transcription	Brain Anterior Caudate	brain
23	chr12:56662800-56670600	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr12:56662800-56679600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:56662800-56680000	Strong transcription	Lung	lung
26	chr12:56662800-56680600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:56662800-56680800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:56662800-56680800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:56662800-56680800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:56662800-56680800	Strong transcription	Thymus	Thymus
31	chr12:56662800-56681000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:56662800-56681000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr12:56662800-56682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:56662800-56682200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:56662800-56682800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:56662800-56683200	Strong transcription	Dnd41	blood
37	chr12:56662800-56686400	Strong transcription	Fetal Stomach	stomach
38	chr12:56663000-56670200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:56663000-56680600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:56663000-56680600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:56663000-56692600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:56663200-56668800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:56663200-56678000	Strong transcription	NHLF	lung
44	chr12:56663200-56680400	Strong transcription	Osteobl	bone
45	chr12:56663200-56680800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:56663200-56685600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:56663400-56668200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:56663400-56671800	Strong transcription	Pancreas	Pancrea
49	chr12:56663400-56682200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:56663400-56687000	Strong transcription	Fetal Intestine Small	intestine

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