Variant report

Variant	rs6762186
Chromosome Location	chr3:69402923-69402924
allele	G/T
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	FOS	chr3:69402640-69403548	HUVEC	blood vessel:	n/a	chr3:69403510-69403520 chr3:69402725-69402734 chr3:69402945-69402957 chr3:69403510-69403520 chr3:69402899-69402908 chr3:69403256-69403268 chr3:69402950-69402961
2	SPI1	chr3:69402615-69402938	GM12891	blood:	n/a	n/a
3	POU2F2	chr3:69402588-69402993	GM12878	blood:	n/a	n/a
4	EP300	chr3:69402740-69403061	GM12878	blood:	n/a	chr3:69402951-69402960
5	BATF	chr3:69402729-69403057	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:69402187-69403065	HUVEC	blood vessel:	n/a	n/a
7	FOS	chr3:69402912-69403111	MCF10A-Er-Src	breast:	n/a	chr3:69402945-69402957 chr3:69402950-69402961
8	BHLHE40	chr3:69402548-69403163	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:69402360-69403237	HUVEC	blood vessel:	n/a	n/a
10	JUN	chr3:69402561-69403377	HUVEC	blood vessel:	n/a	chr3:69402725-69402734 chr3:69402945-69402957 chr3:69402899-69402908 chr3:69403256-69403268
11	POLR2A	chr3:69402542-69402995	GM12891	blood:	n/a	n/a
12	YY1	chr3:69402697-69402925	GM12891	blood:	n/a	n/a
13	CEBPB	chr3:69402911-69403237	Hela-S3	cervix:	n/a	chr3:69403048-69403061
14	STAT3	chr3:69402914-69403067	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr3:69402837-69403179	MCF10A-Er-Src	breast:	n/a	chr3:69402945-69402957 chr3:69402899-69402908 chr3:69402950-69402961
16	FOXM1	chr3:69402730-69403093	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:69400503-69403035	HUVEC	blood vessel:	n/a	n/a
18	BATF	chr3:69402806-69403041	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:69402506-69403074	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr3:69402596-69403021	HUVEC	blood vessel:	n/a	n/a
21	FOS	chr3:69402905-69403105	MCF10A-Er-Src	breast:	n/a	chr3:69402945-69402957 chr3:69402950-69402961
22	POLR2A	chr3:69402399-69403188	HUVEC	blood vessel:	n/a	n/a
23	NFIC	chr3:69402493-69403364	GM12878	blood:	n/a	n/a
24	GATA2	chr3:69402600-69403060	HUVEC	blood vessel:	n/a	n/a
25	TBP	chr3:69402544-69403204	GM12878	blood:	n/a	n/a
26	IKZF1	chr3:69402648-69403139	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1010315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12629224	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12629229	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12631128	0.97[ASN][1000 genomes]
rs13061189	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13075664	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13077078	0.97[ASN][1000 genomes]
rs1483888	0.95[ASN][1000 genomes]
rs1483889	0.95[ASN][1000 genomes]
rs1483890	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1483891	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1564756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1564757	0.82[CHB][hapmap]
rs1843045	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1843046	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1843049	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1843050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2007578	0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs34184121	0.97[ASN][1000 genomes]
rs4290808	0.82[CHB][hapmap]
rs4428187	0.81[CHB][hapmap]
rs6419767	0.97[ASN][1000 genomes]
rs6549207	0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs6549209	0.97[ASN][1000 genomes]
rs6774761	0.97[ASN][1000 genomes]
rs6774867	0.97[ASN][1000 genomes]
rs6778232	0.97[ASN][1000 genomes]
rs6780513	0.98[ASN][1000 genomes]
rs6783070	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6807930	0.97[ASN][1000 genomes]
rs900669	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs900670	0.97[ASN][1000 genomes]
rs900671	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9825845	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9825849	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9861135	1.00[CHB][hapmap];0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1800315	chr3:69374729-69414587	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv520818	chr3:69401248-69421495	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69372200-69403800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:69394000-69403000	Weak transcription	HSMM	muscle
3	chr3:69397800-69406000	Weak transcription	HSMMtube	muscle
4	chr3:69400200-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:69400200-69405400	Enhancers	Brain Substantia Nigra	brain
6	chr3:69400400-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:69400400-69403400	Active TSS	Right Atrium	heart
8	chr3:69400400-69403400	Flanking Active TSS	Dnd41	blood
9	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
10	chr3:69401000-69403200	Active TSS	Adipose Nuclei	Adipose
11	chr3:69401000-69403800	Weak transcription	NHEK	skin
12	chr3:69401200-69403000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:69401400-69403000	Enhancers	Primary B cells from peripheral blood	blood
14	chr3:69401400-69403000	Active TSS	HUVEC	blood vessel
15	chr3:69401800-69403200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr3:69401800-69403200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr3:69401800-69404000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:69402000-69403000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr3:69402000-69403000	Active TSS	Left Ventricle	heart
20	chr3:69402000-69403000	Active TSS	Lung	lung
21	chr3:69402000-69403000	Flanking Active TSS	Thymus	Thymus
22	chr3:69402200-69403000	Active TSS	GM12878-XiMat	blood
23	chr3:69402200-69403200	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:69402400-69403000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:69402400-69403000	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr3:69402400-69403000	Active TSS	Fetal Thymus	thymus
28	chr3:69402600-69403000	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr3:69402600-69403000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:69402600-69403000	Enhancers	Fetal Brain Male	brain
31	chr3:69402600-69403000	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr3:69402600-69403000	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr3:69402600-69403200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:69402600-69403400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:69402600-69403400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:69402800-69403000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:69402800-69403200	Active TSS	Primary B cells from cord blood	blood
38	chr3:69402800-69403200	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr3:69402800-69403200	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:69402800-69403400	Enhancers	Fetal Lung	lung
41	chr3:69402800-69403800	Weak transcription	Brain Angular Gyrus	brain
42	chr3:69402800-69403800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:69402800-69403800	Weak transcription	Hela-S3	cervix
44	chr3:69402800-69404200	Enhancers	Brain Anterior Caudate	brain
45	chr3:69402800-69405000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr3:69402800-69413000	Weak transcription	Aorta	Aorta

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