Variant report

Variant	esv3369831
Chromosome Location	chr2:188313304-188313703
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr2:188312809-188313314	H1-hESC	embryonic stem cell:	n/a	n/a
2	BCLAF1	chr2:188312732-188313340	GM12878	blood:	n/a	n/a
3	BCLAF1	chr2:188312648-188313438	GM12878	blood:	n/a	n/a
4	BHLHE40	chr2:188312812-188313323	GM12878	blood:	n/a	n/a
5	CBX3	chr2:188312818-188313395	HCT-116	colon:	n/a	n/a
6	CHD1	chr2:188312848-188313460	GM12878	blood:	n/a	n/a
7	CHD2	chr2:188312761-188313306	GM12878	blood:	n/a	n/a
8	CREB1	chr2:188312758-188313327	GM12878	blood:	n/a	n/a
9	CREB1	chr2:188312721-188313388	GM12878	blood:	n/a	n/a
10	EBF1	chr2:188312833-188313306	GM12878	blood:	n/a	n/a
11	EP300	chr2:188312851-188313310	GM12878	blood:	n/a	n/a
12	FOS	chr2:188312874-188313332	MCF10A-Er-Src	breast:	n/a	chr2:188313050-188313061 chr2:188313221-188313233
13	GATA2	chr2:188312781-188313557	HUVEC	blood vessel:	n/a	n/a
14	KAP1	chr2:188312743-188313466	HEK293	kidney:	n/a	n/a
15	KAP1	chr2:188312817-188313426	U2OS	brain:	n/a	n/a
16	MAZ	chr2:188312746-188313338	GM12878	blood:	n/a	n/a
17	MXI1	chr2:188312771-188313475	GM12878	blood:	n/a	n/a
18	NFIC	chr2:188312857-188313436	ECC-1	luminal epithelium:	n/a	n/a
19	NFIC	chr2:188312715-188313309	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:188312743-188313492	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:188312759-188313342	GM12892	blood:	n/a	n/a
22	POLR2A	chr2:188312670-188313378	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr2:188312768-188313322	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:188312739-188313304	GM12891	blood:	n/a	n/a
25	POLR2A	chr2:188312441-188313343	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr2:188312776-188313337	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr2:188312804-188313365	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr2:188312137-188313376	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr2:188312521-188313491	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr2:188312706-188313461	GM12891	blood:	n/a	n/a
31	POLR2A	chr2:188312760-188313347	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr2:188312792-188313334	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:188312626-188313309	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:188312976-188313305	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr2:188312735-188313362	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr2:188312534-188313372	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr2:188312642-188313327	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr2:188312757-188313332	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:188312735-188313381	U87	brain:	n/a	n/a
40	POLR2A	chr2:188312684-188313399	HUVEC	blood vessel:	n/a	n/a
41	RAD21	chr2:188312691-188313333	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr2:188312806-188313336	ECC-1	luminal epithelium:	n/a	n/a
43	RAD21	chr2:188312754-188313315	H1-hESC	embryonic stem cell:	n/a	n/a
44	REST	chr2:188312532-188313422	H1-neurons	neurons:	n/a	n/a
45	RFX5	chr2:188312858-188313305	GM12878	blood:	n/a	n/a
46	SETDB1	chr2:188312868-188313537	U2OS	brain:	n/a	n/a
47	SMC3	chr2:188312762-188313308	GM12878	blood:	n/a	n/a
48	SP1	chr2:188312820-188313379	H1-hESC	embryonic stem cell:	n/a	n/a
49	STAT3	chr2:188312991-188313377	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr2:188313053-188313368	MCF10A-Er-Src	breast:	n/a	n/a

No data

Variant related genes	Relation type
CALCRL	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 50 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370723747	chr2:188313321-188313322	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs372951936	chr2:188313323-188313324	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs149173056	chr2:188313324-188313325	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs5837038	chr2:188313354-188313355	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs71017394	chr2:188313363-188313364	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs533596990	chr2:188313375-188313376	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs555303880	chr2:188313402-188313403	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs111638822	chr2:188313517-188313518	Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs13405040	chr2:188313582-188313583	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs185610080	chr2:188313594-188313595	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs2041777	chr2:188313645-188313646	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:50)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
Colorectal cancer	16272173	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Glioblastoma	21080181	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Facial dysmorphism	20548289	CNVD
Mental retardation	20548289	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21183584	CNVD
Sudden cardiac death	19188705	CNVD
Autism	19329560	CNVD
Urothelial carcinoma	21177765	CNVD
Intellectual disability	22102821	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Tetralogy of Fallot	22912587	CNVD

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188310800-188313400	Active TSS	GM12878-XiMat	blood
2	chr2:188310800-188313600	Active TSS	Right Atrium	heart
3	chr2:188311000-188313400	Active TSS	Adipose Nuclei	Adipose
4	chr2:188311000-188313400	Active TSS	Stomach Smooth Muscle	stomach
5	chr2:188311200-188313400	Active TSS	Ovary	ovary
6	chr2:188311400-188313400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:188311400-188313400	Active TSS	Psoas Muscle	Psoas
8	chr2:188311600-188313400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:188311800-188313400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:188311800-188313400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:188312000-188313400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:188312000-188313400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:188312000-188313400	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr2:188312000-188313400	Active TSS	Thymus	Thymus
15	chr2:188312000-188313600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:188312200-188313400	Active TSS	Brain Angular Gyrus	brain
17	chr2:188312200-188313400	Active TSS	Brain Cingulate Gyrus	brain
18	chr2:188312400-188313400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:188312400-188313400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:188312400-188313600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:188312600-188313400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:188312600-188313400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:188312800-188313400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr2:188312800-188313400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:188312800-188313400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:188312800-188313400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr2:188312800-188313400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr2:188312800-188313400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:188312800-188313400	Flanking Active TSS	HMEC	breast
30	chr2:188312800-188313600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:188312800-188313600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:188312800-188313600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:188312800-188313600	Flanking Active TSS	Fetal Lung	lung
34	chr2:188312800-188313600	Flanking Active TSS	NHEK	skin
35	chr2:188313000-188313400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr2:188313000-188313400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:188313000-188313400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:188313000-188313400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:188313000-188313400	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:188313000-188313400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr2:188313000-188313400	Enhancers	Fetal Thymus	thymus
42	chr2:188313000-188313400	Enhancers	HSMM	muscle
43	chr2:188313000-188313400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr2:188313000-188313400	Flanking Active TSS	Osteobl	bone
45	chr2:188313000-188313600	Flanking Active TSS	HUVEC	blood vessel
46	chr2:188313000-188326200	Weak transcription	Right Ventricle	heart
47	chr2:188313200-188313400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:188313200-188313400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr2:188313200-188313400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:188313200-188313400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links