Variant report

Variant	rs1564756
Chromosome Location	chr3:69402489-69402490
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629224	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629229	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12631128	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061189	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13075664	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13077078	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1483888	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483889	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483890	0.97[ASN][1000 genomes]
rs1483891	0.97[ASN][1000 genomes]
rs1564757	0.82[CHB][hapmap]
rs1843045	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1843046	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1843049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1843050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2007578	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34184121	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4290808	0.82[CHB][hapmap]
rs4428187	0.82[CHB][hapmap]
rs6419767	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6549207	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6549209	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6762186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6774761	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6774867	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778232	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780513	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6783070	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807930	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs900669	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]
rs900670	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs900671	0.96[ASN][1000 genomes]
rs9825845	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9825849	0.97[AMR][1000 genomes];0.99[EUR][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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69372200-69403800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:69393400-69402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:69394000-69403000	Weak transcription	HSMM	muscle
4	chr3:69397800-69406000	Weak transcription	HSMMtube	muscle
5	chr3:69400200-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:69400200-69405400	Enhancers	Brain Substantia Nigra	brain
7	chr3:69400400-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:69400400-69403400	Active TSS	Right Atrium	heart
9	chr3:69400400-69403400	Flanking Active TSS	Dnd41	blood
10	chr3:69400600-69402800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
12	chr3:69400800-69402600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr3:69401000-69402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:69401000-69403200	Active TSS	Adipose Nuclei	Adipose
15	chr3:69401000-69403800	Weak transcription	NHEK	skin
16	chr3:69401200-69402600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr3:69401200-69402800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr3:69401200-69403000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:69401400-69403000	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:69401400-69403000	Active TSS	HUVEC	blood vessel
21	chr3:69401600-69402800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:69401800-69402800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr3:69401800-69402800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:69401800-69402800	Active TSS	Fetal Muscle Leg	muscle
25	chr3:69401800-69402800	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:69401800-69403200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr3:69401800-69403200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr3:69401800-69404000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:69402000-69402600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
30	chr3:69402000-69402600	Enhancers	Fetal Lung	lung
31	chr3:69402000-69402600	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr3:69402000-69402800	Active TSS	Liver	Liver
33	chr3:69402000-69402800	Active TSS	Fetal Muscle Trunk	muscle
34	chr3:69402000-69402800	Active TSS	Psoas Muscle	Psoas
35	chr3:69402000-69403000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr3:69402000-69403000	Active TSS	Left Ventricle	heart
37	chr3:69402000-69403000	Active TSS	Lung	lung
38	chr3:69402000-69403000	Flanking Active TSS	Thymus	Thymus
39	chr3:69402200-69402600	Active TSS	Aorta	Aorta
40	chr3:69402200-69402800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr3:69402200-69403000	Active TSS	GM12878-XiMat	blood
42	chr3:69402200-69403200	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:69402400-69402800	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr3:69402400-69402800	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr3:69402400-69402800	Active TSS	Brain Cingulate Gyrus	brain
47	chr3:69402400-69402800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr3:69402400-69402800	Active TSS	Stomach Smooth Muscle	stomach
49	chr3:69402400-69403000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:69402400-69403000	Flanking Active TSS	Brain Hippocampus Middle	brain

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