Variant report

Variant	esv2141246
Chromosome Location	chr12:42326869-42327313
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	ATF2	chr12:42327282-42327866	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr12:42327295-42327823	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr12:42326179-42326911	ECC-1	luminal epithelium:	n/a	n/a
4	EGR1	chr12:42326354-42326916	ECC-1	luminal epithelium:	n/a	chr12:42326723-42326732 chr12:42326721-42326736 chr12:42326721-42326735 chr12:42326722-42326735 chr12:42326723-42326734 chr12:42326722-42326735 chr12:42326723-42326733 chr12:42326723-42326733 chr12:42326722-42326735
5	EGR1	chr12:42326346-42326993	ECC-1	luminal epithelium:	n/a	chr12:42326723-42326732 chr12:42326721-42326736 chr12:42326721-42326735 chr12:42326722-42326735 chr12:42326723-42326734 chr12:42326722-42326735 chr12:42326723-42326733 chr12:42326723-42326733 chr12:42326722-42326735
6	EP300	chr12:42325920-42326980	ECC-1	luminal epithelium:	n/a	chr12:42326346-42326362 chr12:42326343-42326359 chr12:42326424-42326440
7	EP300	chr12:42326164-42326893	ECC-1	luminal epithelium:	n/a	chr12:42326346-42326362 chr12:42326343-42326359 chr12:42326424-42326440
8	HDAC2	chr12:42327218-42327786	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr12:42325973-42326975	ECC-1	luminal epithelium:	n/a	chr12:42326464-42326474
10	MAX	chr12:42326035-42326919	ECC-1	luminal epithelium:	n/a	chr12:42326464-42326474
11	MYC	chr12:42326182-42326899	NB4	blood:	n/a	chr12:42326464-42326474
12	NFIC	chr12:42326080-42326933	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr12:42325795-42327070	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr12:42326085-42326892	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr12:42326108-42326887	HL-60	blood:	n/a	n/a
16	RAD21	chr12:42326042-42326905	ECC-1	luminal epithelium:	n/a	n/a
17	SPI1	chr12:42326092-42326942	HL-60	blood:	n/a	chr12:42326886-42326899 chr12:42326538-42326551 chr12:42326583-42326596
18	TAF1	chr12:42326174-42326919	ECC-1	luminal epithelium:	n/a	n/a
19	TCF12	chr12:42325905-42326981	ECC-1	luminal epithelium:	n/a	chr12:42326288-42326297
20	TCF12	chr12:42326047-42327017	ECC-1	luminal epithelium:	n/a	chr12:42326288-42326297
21	TEAD4	chr12:42326160-42326959	ECC-1	luminal epithelium:	n/a	n/a
22	YY1	chr12:42326248-42326885	ECC-1	luminal epithelium:	n/a	chr12:42326428-42326442
23	ZBTB7A	chr12:42326076-42326950	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000257239	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570787068	chr12:42326887-42326888	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs1234016	chr12:42326911-42326912	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs550466345	chr12:42326925-42326926	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs74896341	chr12:42326942-42326943	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs536050279	chr12:42326993-42326994	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs376904987	chr12:42326997-42326998	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs202174088	chr12:42327013-42327014	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs74079321	chr12:42327019-42327020	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs201579237	chr12:42327026-42327027	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs201879656	chr12:42327027-42327028	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs566220140	chr12:42327094-42327095	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs539828482	chr12:42327095-42327096	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs150301066	chr12:42327210-42327211	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs137974044	chr12:42327252-42327253	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs4516032	chr12:42327254-42327255	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs1968132	chr12:42327261-42327262	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs544147084	chr12:42327264-42327265	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs11181256	chr12:42327267-42327268	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs556433382	chr12:42327296-42327297	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs12579248	chr12:42327311-42327312	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:57)

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
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	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
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Cancer	20164919	CNVD

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42323600-42327000	Active TSS	Right Atrium	heart
2	chr12:42324400-42327000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:42324600-42327000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:42324600-42327000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr12:42324800-42327000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:42325200-42327000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:42325200-42327000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:42325800-42327000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:42325800-42327000	Active TSS	Brain Anterior Caudate	brain
10	chr12:42325800-42327000	Active TSS	Brain Hippocampus Middle	brain
11	chr12:42325800-42327000	Active TSS	Brain Substantia Nigra	brain
12	chr12:42326000-42327000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr12:42326000-42327000	Active TSS	Primary T cells from cord blood	blood
14	chr12:42326000-42327000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr12:42326000-42327000	Active TSS	Muscle Satellite Cultured Cells	--
16	chr12:42326000-42327000	Active TSS	Brain Angular Gyrus	brain
17	chr12:42326000-42327000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr12:42326000-42327000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr12:42326000-42327000	Active TSS	Ovary	ovary
20	chr12:42326000-42327000	Active TSS	Psoas Muscle	Psoas
21	chr12:42326000-42327000	Flanking Active TSS	HUVEC	blood vessel
22	chr12:42326000-42327000	Active TSS	K562	blood
23	chr12:42326000-42327400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:42326000-42327800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr12:42326200-42327000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:42326200-42327000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
27	chr12:42326200-42327000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr12:42326200-42327000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:42326200-42327000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:42326200-42327000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:42326200-42327000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr12:42326200-42327000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:42326200-42327000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:42326200-42327000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:42326200-42327000	Active TSS	Fetal Kidney	kidney
36	chr12:42326200-42327000	Active TSS	Fetal Lung	lung
37	chr12:42326200-42327000	Active TSS	Fetal Muscle Trunk	muscle
38	chr12:42326200-42327000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:42326200-42327000	Active TSS	Osteobl	bone
40	chr12:42326200-42327600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr12:42326400-42327000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr12:42326400-42327000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:42326400-42327000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:42326400-42327000	Active TSS	Right Ventricle	heart
45	chr12:42326600-42327000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr12:42326600-42327000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:42326600-42327000	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr12:42326600-42327000	Flanking Active TSS	Fetal Brain Male	brain
49	chr12:42326600-42327000	Flanking Active TSS	Fetal Brain Female	brain
50	chr12:42326600-42327000	Flanking Active TSS	Fetal Muscle Leg	muscle

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