Variant report

Variant	rs2838979
Chromosome Location	chr21:47117969-47117970
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11089019	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11908836	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11911348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs2015400	0.93[CEU][hapmap]
rs2330328	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs2838977	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2839008	0.87[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs2839023	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs2839024	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs28801527	0.87[ASN][1000 genomes]
rs4819138	0.80[CHB][hapmap]
rs4819142	0.90[CHB][hapmap]
rs4819147	0.90[ASN][1000 genomes]
rs4819160	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs725930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs7278258	0.82[CHB][hapmap]
rs7280089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs73232733	0.97[EUR][1000 genomes]
rs73232736	0.97[EUR][1000 genomes]
rs73232746	0.90[ASN][1000 genomes]
rs741954	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs8133338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9798668	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs9976490	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9977594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9982063	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9982174	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9984438	0.87[CEU][hapmap];0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers 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	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1056995	chr21:47094147-47120504	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
10	nsv1062702	chr21:47095762-47169369	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
11	nsv544493	chr21:47095762-47169369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2838979	PCBP3	cis	cerebellum	SCAN
rs2838979	KRTAP10-5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47102600-47138400	Weak transcription	Fetal Thymus	thymus
2	chr21:47116800-47118200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr21:47117000-47118000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:47117600-47121200	Enhancers	NHDF-Ad	bronchial
5	chr21:47117800-47119600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr21:47117800-47121000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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