Variant report

Variant	rs881558
Chromosome Location	chr21:40352358-40352359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40347616..40350382-chr21:40351393..40353816,2	MCF-7	breast:
2	chr21:40342214..40345629-chr21:40350907..40355003,4	MCF-7	breast:
3	21:40348344-40365490..21:40748850-40752541	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000232837	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10854393	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10854394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10854395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11088460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12165276	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2410071	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2410072	1.00[EUR][1000 genomes]
rs2410074	1.00[EUR][1000 genomes]
rs2410075	1.00[EUR][1000 genomes]
rs2836793	0.84[ASN][1000 genomes]
rs2836794	0.84[ASN][1000 genomes]
rs2836809	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2836810	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs59075807	0.98[EUR][1000 genomes]
rs60997307	0.83[ASN][1000 genomes]
rs61018306	1.00[EUR][1000 genomes]
rs732339	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs732340	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73906720	1.00[EUR][1000 genomes]
rs8126897	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8129750	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs8131869	0.83[ASN][1000 genomes]
rs8133475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8134059	1.00[EUR][1000 genomes]
rs9636952	1.00[EUR][1000 genomes]
rs973192	1.00[EUR][1000 genomes]
rs973193	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9980120	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9980681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9981682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9982548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9982800	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9983903	0.84[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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40332000-40356800	Weak transcription	Right Atrium	heart
2	chr21:40350400-40354600	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr21:40350400-40354600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr21:40350400-40355000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr21:40350400-40356600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:40350600-40352400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr21:40350600-40352800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr21:40350600-40354600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr21:40351000-40353400	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr21:40351000-40354600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr21:40351000-40354800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr21:40351000-40359600	Enhancers	Primary hematopoietic stem cells	blood
13	chr21:40351200-40352400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr21:40351200-40352400	Enhancers	Hela-S3	cervix
15	chr21:40351200-40353000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr21:40351200-40353800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:40351200-40353800	Enhancers	Thymus	Thymus
18	chr21:40351200-40354000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:40351200-40354600	Enhancers	Fetal Kidney	kidney
20	chr21:40351200-40354600	Enhancers	Fetal Thymus	thymus
21	chr21:40351200-40355200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:40351200-40355200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:40351400-40353600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr21:40351400-40354000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:40351400-40354200	Enhancers	HSMM	muscle
26	chr21:40351400-40354600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:40351600-40352600	Weak transcription	HSMMtube	muscle
28	chr21:40351600-40353800	Flanking Active TSS	Dnd41	blood
29	chr21:40351600-40354200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr21:40351600-40355600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr21:40351600-40356000	Weak transcription	Esophagus	oesophagus
32	chr21:40351600-40357200	Weak transcription	Lung	lung
33	chr21:40351800-40353600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr21:40351800-40354600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr21:40351800-40355200	Enhancers	H9 Cell Line	embryonic stem cell
36	chr21:40351800-40356000	Weak transcription	HMEC	breast
37	chr21:40352000-40352400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr21:40352000-40353600	Weak transcription	HepG2	liver
39	chr21:40352000-40354000	Weak transcription	Placenta	Placenta
40	chr21:40352000-40356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr21:40352000-40356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr21:40352000-40356600	Weak transcription	NHEK	skin
43	chr21:40352200-40353400	Enhancers	Spleen	Spleen
44	chr21:40352200-40353600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr21:40352200-40354800	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links