Variant report

Variant	rs2525599
Chromosome Location	chr21:15388339-15388340
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs13046630	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13048438	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822383	0.80[EUR][1000 genomes]
rs2822384	0.81[EUR][1000 genomes]
rs34338538	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827720	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611722	0.81[EUR][1000 genomes]
rs60821881	0.85[EUR][1000 genomes]
rs6516571	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129930	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058202	chr21:14706767-15628668	Weak transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1067433	chr21:14736298-15507502	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1055396	chr21:14756514-15507502	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1062639	chr21:14775729-15507502	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	nsv587015	chr21:14957973-15448560	Genic enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
6	nsv913388	chr21:15173846-15400618	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv2508507	chr21:15338129-15397594	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1058072	chr21:15372509-15568171	Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv965972	chr21:15374407-15389737	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2525599	LOC100288738,LOC100293870,LOC390834	cis	brain	BrainEAC
rs2525599	ANKRD20A18P	cis	Esophagus Mucosa	GTEx
rs2525599	LOC100288738,LOC100293870,LOC390834	cis	cerebellar cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15388200-15388400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

Quick Search:

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

what's new

Quick links