Variant report

Variant	rs6920511
Chromosome Location	chr6:4744063-4744064
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1933225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6931832	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs6937790	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs6941758	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9328272	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9378411	0.83[JPT][hapmap]
rs9378910	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9392631	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9392632	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9392635	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9405771	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9405772	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs9405773	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs9405774	0.92[CHB][hapmap];0.93[JPT][hapmap]

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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017938	chr6:4729592-4774914	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6920511	CAGE1	cis	cerebellum	SCAN
rs6920511	TEK	trans	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4741600-4744400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:4741800-4744400	Enhancers	NHEK	skin
3	chr6:4742000-4744400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:4743000-4744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:4743400-4744800	Enhancers	Fetal Intestine Large	intestine
6	chr6:4743600-4745000	Enhancers	Fetal Intestine Small	intestine

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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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