Variant report

Variant	rs743018
Chromosome Location	chr20:25053105-25053106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13036777	0.82[EUR][1000 genomes]
rs2207632	0.90[YRI][hapmap]
rs2387577	0.90[YRI][hapmap]
rs2892313	0.88[AFR][1000 genomes]
rs4813546	0.90[YRI][hapmap]
rs4813547	0.83[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4815366	0.89[YRI][hapmap]
rs6050290	0.83[EUR][1000 genomes]
rs6115024	0.94[ASW][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs6115026	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs743018	LOC284788	cis	cerebellum	SCAN
rs743018	VSX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25046400-25057200	Weak transcription	Brain Substantia Nigra	brain
2	chr20:25046800-25057400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr20:25046800-25058200	Weak transcription	Right Atrium	heart
4	chr20:25048600-25056800	Weak transcription	Gastric	stomach
5	chr20:25048800-25057200	Weak transcription	Pancreas	Pancrea
6	chr20:25050600-25053400	Bivalent Enhancer	HepG2	liver
7	chr20:25052200-25053200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr20:25052200-25053800	Enhancers	A549	lung
9	chr20:25052400-25053200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:25052400-25053200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr20:25052400-25053200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:25052600-25053400	Enhancers	HMEC	breast
13	chr20:25052600-25053600	Bivalent Enhancer	NHEK	skin
14	chr20:25052800-25053200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr20:25052800-25053400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr20:25052800-25053600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:25053000-25053200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr20:25053000-25053200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr20:25053000-25053600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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