Variant report

Variant	rs1884658
Chromosome Location	chr20:23126640-23126641
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23126510..23128987-chr20:23134466..23137305,2	MCF-7	breast:
2	chr20:23123944..23126735-chr20:23131086..23132834,2	MCF-7	breast:
3	chr20:23125309..23128497-chr20:23131083..23133976,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11087414	0.87[CHB][hapmap]
rs11697283	0.91[CHB][hapmap]
rs12710326	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4813480	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4815176	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048561	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083011	0.91[CHB][hapmap]
rs6083014	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs6083015	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs6083016	0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6083017	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6113954	0.91[CHB][hapmap]
rs6113957	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6113960	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6515302	0.91[CHB][hapmap]
rs6515304	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7269464	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs755697	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8122415	0.86[CHB][hapmap]
rs844903	0.80[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs844904	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs844905	0.82[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	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1066935	chr20:23123507-23146449	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23118400-23131000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:23119800-23128600	Weak transcription	Gastric	stomach
3	chr20:23120200-23137600	Enhancers	HUVEC	blood vessel
4	chr20:23121000-23128000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:23121000-23144200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr20:23121200-23128800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr20:23121200-23128800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:23121200-23130800	Enhancers	HSMM	muscle
9	chr20:23121600-23127000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr20:23121600-23130800	Enhancers	NH-A	brain
11	chr20:23121600-23138200	Enhancers	Adipose Nuclei	Adipose
12	chr20:23121800-23137600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr20:23121800-23143000	Enhancers	NHDF-Ad	bronchial
14	chr20:23122600-23138000	Enhancers	NHLF	lung
15	chr20:23122800-23128800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:23122800-23130800	Enhancers	Osteobl	bone
17	chr20:23123000-23130200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr20:23123200-23127200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr20:23123400-23129000	Weak transcription	Right Ventricle	heart
20	chr20:23123600-23127000	Weak transcription	Left Ventricle	heart
21	chr20:23123600-23128200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr20:23123600-23128200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr20:23123600-23128600	Weak transcription	Right Atrium	heart
24	chr20:23123600-23132400	Weak transcription	Ovary	ovary
25	chr20:23123800-23128800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr20:23124000-23128000	Weak transcription	A549	lung
27	chr20:23124200-23128200	Enhancers	K562	blood
28	chr20:23124200-23134600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr20:23124400-23127800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr20:23124400-23132800	Weak transcription	Primary T cells from cord blood	blood
31	chr20:23124400-23133000	Weak transcription	Primary B cells from cord blood	blood
32	chr20:23124600-23127600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr20:23124600-23127800	Weak transcription	Hela-S3	cervix
34	chr20:23124600-23128000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr20:23124600-23128400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr20:23124600-23132400	Weak transcription	Fetal Heart	heart
37	chr20:23124600-23132600	Weak transcription	Colon Smooth Muscle	Colon
38	chr20:23124800-23127800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr20:23124800-23128200	Weak transcription	Fetal Thymus	thymus
40	chr20:23125000-23127400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr20:23125000-23127600	Weak transcription	HMEC	breast
42	chr20:23125000-23137600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:23125200-23127000	Enhancers	Brain Hippocampus Middle	brain
44	chr20:23125200-23127200	Enhancers	Spleen	Spleen
45	chr20:23125200-23128200	Weak transcription	NHEK	skin
46	chr20:23125200-23129400	Enhancers	Fetal Muscle Leg	muscle
47	chr20:23125400-23134400	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr20:23125600-23128200	Enhancers	GM12878-XiMat	blood
49	chr20:23125800-23127000	Enhancers	Fetal Lung	lung
50	chr20:23125800-23127600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links