Variant report

Variant	rs2823858
Chromosome Location	chr21:17903914-17903915
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17903700..17906085-chr21:17908034..17909928,2	K562	blood:

Variant related genes	Relation type
ENSG00000215386	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12481827	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12482215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12482590	0.96[ASN][1000 genomes]
rs12482914	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12483358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12483744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16998685	1.00[EUR][1000 genomes]
rs16998758	1.00[EUR][1000 genomes]
rs16998890	1.00[EUR][1000 genomes]
rs2032286	1.00[EUR][1000 genomes]
rs2155622	1.00[EUR][1000 genomes]
rs2186870	1.00[EUR][1000 genomes]
rs2212561	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2404135	1.00[EUR][1000 genomes]
rs2823823	1.00[JPT][hapmap]
rs2823840	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823841	1.00[EUR][1000 genomes]
rs2823850	1.00[EUR][1000 genomes]
rs2823851	1.00[EUR][1000 genomes]
rs2823857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823860	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2823861	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823864	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28622187	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34151244	0.96[ASN][1000 genomes]
rs35805038	1.00[ASN][1000 genomes]
rs57039340	1.00[EUR][1000 genomes]
rs58981188	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59527462	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7279732	1.00[EUR][1000 genomes]
rs73363436	0.96[ASN][1000 genomes]
rs73367422	0.96[ASN][1000 genomes]
rs73367434	1.00[EUR][1000 genomes]
rs73367453	1.00[EUR][1000 genomes]
rs73367470	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73367472	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73367500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129337	1.00[JPT][hapmap]
rs8129839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8132608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8133774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8134648	1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975878	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9977113	0.96[ASN][1000 genomes]
rs9979076	0.81[AMR][1000 genomes];1.00[EUR][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	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
2	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	esv3405994	chr21:17895130-17912420	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	292 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17887000-17906000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:17892200-17904000	Weak transcription	Ovary	ovary
3	chr21:17894200-17906200	Weak transcription	Left Ventricle	heart
4	chr21:17894200-17906800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:17895000-17904400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr21:17896200-17904400	Weak transcription	Hela-S3	cervix
7	chr21:17897800-17904200	Weak transcription	Esophagus	oesophagus
8	chr21:17898800-17906000	Weak transcription	Psoas Muscle	Psoas
9	chr21:17903200-17904000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr21:17903600-17906800	Enhancers	HUVEC	blood vessel
11	chr21:17903800-17904600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links