Variant report

Variant	rs1564757
Chromosome Location	chr3:69401804-69401805
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1010315	0.82[CHB][hapmap]
rs10865649	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11128126	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11707515	0.80[JPT][hapmap]
rs11707811	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1483895	0.81[JPT][hapmap]
rs1564756	0.82[CHB][hapmap]
rs17005647	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]
rs1843046	0.80[CHB][hapmap]
rs1843049	0.82[CHB][hapmap]
rs1843050	0.82[CHB][hapmap]
rs1872152	0.86[JPT][hapmap]
rs2007584	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2170800	0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35331889	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4290808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4428187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4855308	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4855389	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56336456	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56741529	0.82[ASN][1000 genomes]
rs59563257	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6419766	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6549203	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762186	0.82[CHB][hapmap]
rs6771772	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6774274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776474	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs68061967	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611647	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612526	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7617464	0.97[ASN][1000 genomes]
rs9310148	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9310149	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9861135	0.82[CHB][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868217	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868990	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.86[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:41 , 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	chr3:69393400-69402600	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	chr3:69400200-69402400	Enhancers	Brain Angular Gyrus	brain
6	chr3:69400200-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:69400200-69405400	Enhancers	Brain Substantia Nigra	brain
8	chr3:69400400-69402200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:69400400-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:69400400-69403400	Active TSS	Right Atrium	heart
11	chr3:69400400-69403400	Flanking Active TSS	Dnd41	blood
12	chr3:69400600-69402200	Enhancers	Primary B cells from cord blood	blood
13	chr3:69400600-69402800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
15	chr3:69400800-69402600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr3:69401000-69402000	Weak transcription	Fetal Lung	lung
17	chr3:69401000-69402000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr3:69401000-69402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:69401000-69403200	Active TSS	Adipose Nuclei	Adipose
20	chr3:69401000-69403800	Weak transcription	NHEK	skin
21	chr3:69401200-69402000	Enhancers	Primary T cells from cord blood	blood
22	chr3:69401200-69402600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr3:69401200-69402800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:69401200-69403000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:69401400-69402000	Enhancers	Brain Anterior Caudate	brain
26	chr3:69401400-69402200	Weak transcription	Aorta	Aorta
27	chr3:69401400-69403000	Enhancers	Primary B cells from peripheral blood	blood
28	chr3:69401400-69403000	Active TSS	HUVEC	blood vessel
29	chr3:69401600-69402000	Enhancers	Thymus	Thymus
30	chr3:69401600-69402800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:69401800-69402000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr3:69401800-69402400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:69401800-69402400	Active TSS	Brain Hippocampus Middle	brain
34	chr3:69401800-69402400	Weak transcription	Fetal Thymus	thymus
35	chr3:69401800-69402800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr3:69401800-69402800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:69401800-69402800	Active TSS	Fetal Muscle Leg	muscle
38	chr3:69401800-69402800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr3:69401800-69403200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr3:69401800-69403200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr3:69401800-69404000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links