Variant report

Variant	esv3370825
Chromosome Location	chr12:49067251-49067700
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	CTCF	chr12:49067646-49067698	MCF-7	breast:	n/a	n/a
2	CTCF	chr12:49067663-49067680	MCF-7	breast:	n/a	n/a
3	CTCF	chr12:49067607-49067690	A549	lung:	n/a	n/a
4	POLR2A	chr12:49067543-49067705	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49066447..49069366-chr12:49075089..49076869,2	MCF-7	breast:
2	chr12:48933826..48935713-chr12:49066983..49069233,2	MCF-7	breast:

Variant related genes	Relation type
KANSL2	TF binding region
ENSG00000139620	chromatin interactions

Extended variants
information (count: 21 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs528423921	chr12:49067251-49067252	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs572961856	chr12:49067263-49067264	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs546609636	chr12:49067298-49067299	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs189918776	chr12:49067300-49067301	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs545249394	chr12:49067336-49067337	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs375933415	chr12:49067350-49067351	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs111737433	chr12:49067351-49067352	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs112739773	chr12:49067357-49067358	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs61496293	chr12:49067402-49067403	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs117825553	chr12:49067446-49067447	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs550662121	chr12:49067456-49067457	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs113393645	chr12:49067461-49067462	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs142766130	chr12:49067509-49067510	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs529681687	chr12:49067567-49067568	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs570942773	chr12:49067570-49067571	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs570118832	chr12:49067596-49067597	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs115876156	chr12:49067609-49067610	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs150609181	chr12:49067632-49067633	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs12231969	chr12:49067664-49067665	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs12230624	chr12:49067665-49067666	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs140023820	chr12:49067690-49067691	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
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
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	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
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	16616336	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD

Chromatin state (count:140 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49036800-49072000	Strong transcription	Liver	Liver
2	chr12:49037800-49072400	Strong transcription	Placenta	Placenta
3	chr12:49038200-49070800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:49038800-49071800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49039000-49072200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:49039400-49068800	Weak transcription	Right Atrium	heart
7	chr12:49039400-49071800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:49039800-49071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:49039800-49071000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:49040000-49072600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:49040400-49072800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:49041000-49071800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:49041200-49068200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr12:49041800-49070800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:49041800-49071000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:49041800-49072400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:49041800-49073800	Strong transcription	Fetal Intestine Large	intestine
18	chr12:49042400-49072800	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:49043800-49068800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:49044000-49068200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:49044200-49071000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:49044200-49072400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:49044200-49072800	Strong transcription	Fetal Thymus	thymus
24	chr12:49044400-49071000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:49044400-49071400	Strong transcription	Thymus	Thymus
26	chr12:49044400-49072400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:49044600-49072400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:49044800-49068000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:49044800-49071200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:49045000-49067600	Strong transcription	Left Ventricle	heart
31	chr12:49045000-49071600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:49045200-49068200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:49045200-49069400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:49045200-49070400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:49045400-49072600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:49045600-49071800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr12:49045600-49072400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:49045600-49073400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:49046200-49067400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:49046200-49072600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:49046400-49071000	Strong transcription	HUVEC	blood vessel
42	chr12:49046800-49069200	Strong transcription	Lung	lung
43	chr12:49047400-49069200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr12:49055800-49070400	Strong transcription	Fetal Stomach	stomach
45	chr12:49057200-49072400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:49057600-49068400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:49057600-49069400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:49057600-49069800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:49057800-49071400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:49057800-49072800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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