Variant report

Variant	rs239023
Chromosome Location	chr21:17702346-17702347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs151580	0.82[JPT][hapmap]
rs239015	0.82[JPT][hapmap]
rs239020	1.00[ASN][1000 genomes]
rs239021	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239025	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs239027	1.00[EUR][1000 genomes]
rs239029	0.82[JPT][hapmap]
rs239030	0.82[JPT][hapmap]
rs239031	0.82[JPT][hapmap]
rs239032	0.82[JPT][hapmap]
rs239033	1.00[EUR][1000 genomes]
rs239034	0.82[JPT][hapmap]
rs239072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs239405	0.82[JPT][hapmap]
rs2823751	0.82[JPT][hapmap]
rs73892955	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	nsv834051	chr21:17564843-17721764	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17692000-17703000	Weak transcription	Ovary	ovary
2	chr21:17696800-17702600	Weak transcription	Osteobl	bone
3	chr21:17697600-17702600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr21:17697600-17703000	Weak transcription	Fetal Brain Female	brain
5	chr21:17697800-17702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:17700800-17703600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:17701000-17702600	Enhancers	Brain Anterior Caudate	brain
8	chr21:17701000-17703200	Enhancers	Brain Substantia Nigra	brain
9	chr21:17701000-17703600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr21:17701200-17702400	Weak transcription	Brain Angular Gyrus	brain
11	chr21:17701200-17703400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr21:17701400-17702600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr21:17701400-17709200	Weak transcription	Fetal Muscle Leg	muscle
14	chr21:17701600-17703000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr21:17701800-17702600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr21:17701800-17703200	Enhancers	Hela-S3	cervix
17	chr21:17701800-17724400	Weak transcription	Psoas Muscle	Psoas
18	chr21:17702200-17702600	Enhancers	Brain Hippocampus Middle	brain
19	chr21:17702200-17702800	Enhancers	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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