Variant report

Variant	rs6023080
Chromosome Location	chr20:52880574-52880575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13039589	0.81[EUR][1000 genomes]
rs13039601	0.81[EUR][1000 genomes]
rs13042527	0.84[EUR][1000 genomes]
rs13045683	0.84[EUR][1000 genomes]
rs1477725	0.88[EUR][1000 genomes]
rs1477736	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs17223034	0.89[MEX][hapmap]
rs1964861	0.86[CEU][hapmap]
rs2023531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28404865	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28435070	0.84[EUR][1000 genomes]
rs28526259	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28676447	0.83[EUR][1000 genomes]
rs28707344	0.84[EUR][1000 genomes]
rs28795767	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs292129	0.92[EUR][1000 genomes]
rs6013946	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023083	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6023080	DOK5	cis	parietal	SCAN
rs6023080	PFDN4	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52872800-52883800	Weak transcription	Pancreas	Pancrea
2	chr20:52874200-52883600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr20:52874200-52884000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr20:52878800-52881200	Enhancers	Fetal Lung	lung
5	chr20:52879600-52881000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:52879600-52881200	Enhancers	Fetal Stomach	stomach
7	chr20:52879800-52880600	Weak transcription	Ovary	ovary
8	chr20:52879800-52883800	Weak transcription	Osteobl	bone
9	chr20:52880000-52880600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr20:52880400-52880600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr20:52880400-52880800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:52880400-52883400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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Input of quick search could be:

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

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