Variant report

Variant	rs17005647
Chromosome Location	chr3:69406181-69406182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10865649	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11128126	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11707515	0.80[JPT][hapmap]
rs11707811	0.89[ASN][1000 genomes]
rs12629224	0.82[CHB][hapmap]
rs12629229	0.82[CHB][hapmap]
rs13075664	0.83[CHB][hapmap]
rs1483895	0.81[JPT][hapmap]
rs1564757	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1843045	0.82[CHB][hapmap]
rs1843046	0.86[CHB][hapmap]
rs1872152	0.86[JPT][hapmap]
rs2007578	0.82[CHB][hapmap]
rs2007584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2170800	0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs35331889	0.85[ASN][1000 genomes]
rs4290808	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4428187	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855308	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4855389	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs56336456	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59563257	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62254082	0.85[ASN][1000 genomes]
rs6419766	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6549203	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6549207	0.83[CHB][hapmap]
rs6771772	0.84[ASN][1000 genomes]
rs6774274	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6776474	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs68061967	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611647	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612526	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617464	0.92[ASN][1000 genomes]
rs900669	0.82[CHB][hapmap]
rs9310148	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9310149	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9861135	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868217	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868990	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
2	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:69402800-69413000	Weak transcription	Aorta	Aorta
4	chr3:69403000-69406200	Weak transcription	Fetal Thymus	thymus
5	chr3:69403000-69406200	Weak transcription	Left Ventricle	heart
6	chr3:69403000-69414800	Weak transcription	Lung	lung
7	chr3:69403400-69406200	Weak transcription	Fetal Lung	lung
8	chr3:69403800-69406200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:69403800-69406600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:69403800-69413000	Weak transcription	Thymus	Thymus
11	chr3:69404000-69406200	Weak transcription	HSMM	muscle
12	chr3:69404200-69406400	Weak transcription	Brain Angular Gyrus	brain
13	chr3:69404200-69408200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:69404400-69406200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:69404400-69406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:69404600-69407000	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:69404800-69406200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:69404800-69406200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:69404800-69406200	Weak transcription	Dnd41	blood
20	chr3:69405000-69406200	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:69405000-69406200	Weak transcription	Right Atrium	heart
22	chr3:69405000-69408600	Weak transcription	HUVEC	blood vessel
23	chr3:69405800-69406400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:69405800-69406800	Enhancers	Brain Substantia Nigra	brain
25	chr3:69406000-69406400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:69406000-69406600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr3:69406000-69406800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:69406000-69407000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:69406000-69407200	Enhancers	Hela-S3	cervix
30	chr3:69406000-69407200	Genic enhancers	NHEK	skin
31	chr3:69406000-69407400	Enhancers	HSMMtube	muscle
32	chr3:69406000-69407600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:69406000-69407600	Enhancers	HMEC	breast

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