Variant report

Variant	rs900669
Chromosome Location	chr3:69406802-69406803
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1010315	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631128	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061189	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077078	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483888	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1483889	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1483890	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1483891	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1564756	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17005647	0.82[CHB][hapmap]
rs1843045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1843046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1843049	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1843050	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007584	0.82[CHB][hapmap]
rs34184121	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419767	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549209	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762186	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6774761	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774867	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778232	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780513	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783070	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807930	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900671	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9825845	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9825849	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9861135	0.95[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:28 , 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	chr3:69403000-69414800	Weak transcription	Lung	lung
5	chr3:69403800-69413000	Weak transcription	Thymus	Thymus
6	chr3:69404200-69408200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:69404600-69407000	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:69405000-69408600	Weak transcription	HUVEC	blood vessel
9	chr3:69406000-69407000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:69406000-69407200	Enhancers	Hela-S3	cervix
11	chr3:69406000-69407200	Genic enhancers	NHEK	skin
12	chr3:69406000-69407400	Enhancers	HSMMtube	muscle
13	chr3:69406000-69407600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:69406000-69407600	Enhancers	HMEC	breast
15	chr3:69406200-69407200	Enhancers	Brain Anterior Caudate	brain
16	chr3:69406200-69407400	Enhancers	Brain Hippocampus Middle	brain
17	chr3:69406200-69407600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:69406200-69407600	Enhancers	Fetal Lung	lung
19	chr3:69406200-69408000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:69406200-69408000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:69406400-69407400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:69406600-69407200	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr3:69406600-69408000	Weak transcription	Fetal Thymus	thymus
24	chr3:69406600-69412800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:69406800-69407000	Enhancers	HSMM	muscle
26	chr3:69406800-69409000	Weak transcription	Dnd41	blood
27	chr3:69406800-69413000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:69406800-69413400	Weak transcription	Brain Angular Gyrus	brain

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