Variant report

Variant	rs460420
Chromosome Location	chr21:28183652-28183653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs456604	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs456954	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs457752	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs461141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs465000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs465253	0.82[AFR][1000 genomes]
rs465401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1066328	chr21:28179782-28200710	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs460420	ATP5J	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28174000-28185400	Weak transcription	HSMMtube	muscle
2	chr21:28174600-28187800	Weak transcription	Osteobl	bone
3	chr21:28177800-28186800	Weak transcription	NHLF	lung
4	chr21:28178200-28185800	Weak transcription	Ovary	ovary
5	chr21:28179800-28187800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr21:28182600-28192200	Weak transcription	NHEK	skin
7	chr21:28183000-28183800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr21:28183000-28183800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr21:28183000-28183800	Enhancers	Fetal Stomach	stomach
10	chr21:28183000-28184400	Enhancers	Hela-S3	cervix
11	chr21:28183000-28185600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr21:28183400-28183800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr21:28183400-28183800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr21:28183400-28183800	Enhancers	Brain Substantia Nigra	brain
15	chr21:28183600-28187600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:28183600-28187600	Weak transcription	NHDF-Ad	bronchial
17	chr21:28183600-28188000	Weak transcription	Brain Hippocampus Middle	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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