Variant report

Variant	rs58983540
Chromosome Location	chr3:17620816-17620817
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11916993	1.00[AFR][1000 genomes]
rs11917279	0.94[AFR][1000 genomes]
rs11923225	0.83[AFR][1000 genomes]
rs11925079	0.94[AFR][1000 genomes]
rs56975774	0.89[AFR][1000 genomes]
rs57167178	0.94[AFR][1000 genomes]
rs59007406	0.94[AFR][1000 genomes]
rs59994592	0.83[AFR][1000 genomes]
rs60535468	0.94[AFR][1000 genomes]
rs73153022	0.94[AFR][1000 genomes]
rs73155232	0.94[AFR][1000 genomes]
rs73160960	0.95[AFR][1000 genomes]
rs73161449	0.94[AFR][1000 genomes]
rs73161460	0.94[AFR][1000 genomes]
rs73165737	1.00[AFR][1000 genomes]
rs73165787	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv915606	chr3:17357042-17668263	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv999460	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv536510	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17608000-17621600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr3:17608600-17621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:17613600-17621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:17614800-17623400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:17616000-17663600	Weak transcription	Left Ventricle	heart
6	chr3:17618600-17623800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:17619200-17622800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr3:17619200-17624000	Enhancers	NHEK	skin
9	chr3:17619400-17621000	Enhancers	A549	lung
10	chr3:17619400-17621600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:17619400-17622400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:17619400-17623800	Enhancers	HMEC	breast
13	chr3:17619600-17621600	Enhancers	Osteobl	bone
14	chr3:17619600-17621800	Enhancers	HUVEC	blood vessel
15	chr3:17619600-17622000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:17619600-17622400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:17619800-17621000	Weak transcription	Brain Angular Gyrus	brain
18	chr3:17619800-17631600	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:17620000-17621000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:17620000-17622400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:17620000-17631600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:17620200-17621000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:17620200-17621400	Enhancers	Primary B cells from cord blood	blood
24	chr3:17620200-17622800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:17620200-17627400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:17620400-17622800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:17620600-17621400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:17620600-17622600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:17620800-17622000	Enhancers	Primary T cells from cord blood	blood
30	chr3:17620800-17622200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:17620800-17622200	Flanking Active TSS	GM12878-XiMat	blood
32	chr3:17620800-17622600	Enhancers	Primary B cells from peripheral blood	blood
33	chr3:17620800-17623200	Enhancers	Dnd41	blood
34	chr3:17620800-17623400	Enhancers	K562	blood
35	chr3:17620800-17623600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:17620800-17623800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links