Variant report

Variant	rs964553
Chromosome Location	chr3:69419499-69419500
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13320477	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17005675	0.92[CEU][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17005685	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17005687	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005689	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17005691	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005694	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17005696	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17005699	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17005713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17416638	0.81[AMR][1000 genomes]
rs2314987	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs2872808	0.85[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4241387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5026329	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56653941	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56682655	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57343519	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58937767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59683429	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60969945	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72940765	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72940769	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72940771	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72940775	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72940779	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72940783	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72940785	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs881031	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][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	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
3	esv2760780	chr3:69413876-69513947	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69416600-69420400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:69416800-69419800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:69416800-69420400	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr3:69416800-69420600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:69417000-69420600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:69417000-69420600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:69417200-69420600	Flanking Active TSS	Dnd41	blood
8	chr3:69417200-69421000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:69417400-69420800	Enhancers	Fetal Lung	lung
10	chr3:69417800-69419600	Weak transcription	Spleen	Spleen
11	chr3:69417800-69420800	Weak transcription	Aorta	Aorta
12	chr3:69418600-69419800	Enhancers	Brain Germinal Matrix	brain
13	chr3:69418800-69420000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr3:69418800-69420200	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:69418800-69420200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:69418800-69420600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:69418800-69421400	Enhancers	Fetal Heart	heart
18	chr3:69419000-69419600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:69419000-69419600	Active TSS	NHDF-Ad	bronchial
20	chr3:69419000-69419800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:69419000-69419800	Flanking Active TSS	HMEC	breast
22	chr3:69419000-69419800	Flanking Active TSS	HUVEC	blood vessel
23	chr3:69419000-69419800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:69419000-69420000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:69419000-69420000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr3:69419000-69420200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:69419000-69420600	Flanking Active TSS	NHEK	skin
28	chr3:69419000-69421400	Enhancers	Brain Angular Gyrus	brain
29	chr3:69419200-69419600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:69419200-69419600	Flanking Active TSS	Fetal Thymus	thymus
31	chr3:69419200-69419800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr3:69419200-69419800	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr3:69419200-69419800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr3:69419200-69419800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:69419200-69419800	Flanking Active TSS	Thymus	Thymus
36	chr3:69419200-69420000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:69419200-69420000	Enhancers	Fetal Brain Male	brain
38	chr3:69419200-69420400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr3:69419200-69420600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:69419200-69421000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:69419200-69421200	Enhancers	Placenta	Placenta
42	chr3:69419400-69419600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr3:69419400-69419600	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:69419400-69419600	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:69419400-69419600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:69419400-69419600	Enhancers	Adipose Nuclei	Adipose
47	chr3:69419400-69419600	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr3:69419400-69419600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr3:69419400-69419600	Active TSS	NHLF	lung
50	chr3:69419400-69419800	Flanking Active TSS	Primary B cells from cord blood	blood

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