Variant report

Variant	rs9869925
Chromosome Location	chr3:69401124-69401125
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11128125	0.80[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1564758	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1976064	0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2003264	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2005546	0.80[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2008239	1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34397489	0.99[ASN][1000 genomes]
rs6549200	0.90[CHB][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs6549204	0.98[ASN][1000 genomes]
rs6549213	0.82[CHB][hapmap]
rs6763080	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6774290	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781841	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6802833	0.99[ASN][1000 genomes]
rs6808107	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7610748	0.91[ASN][1000 genomes]
rs7615137	0.86[ASN][1000 genomes]
rs7640281	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820308	0.92[CEU][hapmap];0.80[CHB][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9820322	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9844501	0.86[CEU][hapmap]
rs9867072	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9872564	0.80[CHB][hapmap]
rs9876410	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9882259	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	nsv876935	chr3:69307942-69401248	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:35 , 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	chr3:69400200-69401800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr3:69400200-69402400	Enhancers	Brain Angular Gyrus	brain
7	chr3:69400200-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:69400200-69405400	Enhancers	Brain Substantia Nigra	brain
9	chr3:69400400-69401200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:69400400-69401400	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr3:69400400-69401800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr3:69400400-69401800	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:69400400-69401800	Enhancers	Fetal Thymus	thymus
14	chr3:69400400-69402200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:69400400-69403400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:69400400-69403400	Active TSS	Right Atrium	heart
17	chr3:69400400-69403400	Flanking Active TSS	Dnd41	blood
18	chr3:69400600-69401200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:69400600-69401400	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr3:69400600-69402200	Enhancers	Primary B cells from cord blood	blood
21	chr3:69400600-69402800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
23	chr3:69400800-69401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:69400800-69401200	Enhancers	Brain Hippocampus Middle	brain
25	chr3:69400800-69401400	Enhancers	Aorta	Aorta
26	chr3:69400800-69401600	Weak transcription	Thymus	Thymus
27	chr3:69400800-69402600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr3:69401000-69401400	Flanking Active TSS	HUVEC	blood vessel
29	chr3:69401000-69401600	Enhancers	Fetal Heart	heart
30	chr3:69401000-69401800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:69401000-69402000	Weak transcription	Fetal Lung	lung
32	chr3:69401000-69402000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:69401000-69402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:69401000-69403200	Active TSS	Adipose Nuclei	Adipose
35	chr3:69401000-69403800	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links