Variant report

Variant	rs2823790
Chromosome Location	chr21:17807684-17807685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11088585	0.89[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11911745	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11911959	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12483194	0.83[CHB][hapmap]
rs1349226	0.89[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375625	0.96[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1375626	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449517	0.91[CHB][hapmap]
rs1900938	0.81[CHB][hapmap]
rs1974157	0.86[ASN][1000 genomes]
rs1992970	0.91[CHB][hapmap]
rs2017357	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051270	0.92[CEU][hapmap]
rs240453	0.92[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs240461	0.96[CEU][hapmap]
rs240492	0.87[CEU][hapmap];0.89[GIH][hapmap]
rs2823784	0.83[CEU][hapmap];0.95[JPT][hapmap]
rs2823791	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2823795	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];0.99[ASN][1000 genomes]
rs2823798	0.96[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2823799	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2823801	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3928806	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57190849	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61514219	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6517700	0.87[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs8126683	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8126881	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8128973	0.92[CEU][hapmap]
rs9305765	0.96[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs996175	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9979472	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9984548	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
2	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	nsv913416	chr21:17728224-17863882	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv913419	chr21:17775056-17826260	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv470880	chr21:17777827-17820111	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv459100	chr21:17777966-17826260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv587077	chr21:17777966-17826260	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv913420	chr21:17777966-17826260	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv913421	chr21:17786219-17826260	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv913422	chr21:17791751-17826260	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv459101	chr21:17794432-17819036	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv587078	chr21:17794432-17819036	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2823790	CHODL	cis	parietal	SCAN
rs2823790	CHODL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17797200-17813000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr21:17797200-17813400	Weak transcription	Fetal Muscle Leg	muscle
3	chr21:17797800-17808400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr21:17799600-17814000	Weak transcription	Hela-S3	cervix
5	chr21:17801000-17807800	Weak transcription	HUVEC	blood vessel
6	chr21:17804200-17826200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:17805000-17814800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr21:17806600-17808400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr21:17807400-17808800	Enhancers	Liver	Liver
10	chr21:17807400-17808800	Enhancers	Brain Angular Gyrus	brain
11	chr21:17807600-17814000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr21:17807600-17816800	Weak transcription	Brain Germinal Matrix	brain

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