Variant report

Variant	rs240453
Chromosome Location	chr21:17789829-17789830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1074741	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs11088585	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs11911745	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11911959	0.82[EUR][1000 genomes]
rs1349226	1.00[CEU][hapmap];0.89[GIH][hapmap];0.82[EUR][1000 genomes]
rs1375625	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs1375626	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1992970	0.84[CEU][hapmap]
rs2017357	0.81[EUR][1000 genomes]
rs2051270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs240455	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs240459	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240461	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs240492	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs2823784	0.91[CEU][hapmap]
rs2823790	0.92[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2823791	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2823798	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs2823799	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2823801	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs3928806	0.85[EUR][1000 genomes]
rs57190849	0.83[EUR][1000 genomes]
rs61514219	0.82[EUR][1000 genomes]
rs6517700	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs8126683	0.95[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8126881	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8128973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9305765	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs996175	0.84[EUR][1000 genomes]
rs9979472	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9980917	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9984548	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs240453	CHODL	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17771400-17791200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:17781200-17790400	Weak transcription	NH-A	brain
3	chr21:17788400-17790600	Weak transcription	Right Atrium	heart
4	chr21:17788400-17790800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr21:17788600-17790400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr21:17788600-17790600	Weak transcription	Brain Angular Gyrus	brain
7	chr21:17788800-17791000	Weak transcription	Ovary	ovary
8	chr21:17789400-17790000	Weak transcription	Brain Anterior Caudate	brain
9	chr21:17789400-17790000	Enhancers	Brain Germinal Matrix	brain
10	chr21:17789400-17791200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr21:17789600-17790400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr21:17789600-17791000	Enhancers	Fetal Brain Male	brain
13	chr21:17789600-17791400	Enhancers	Brain Hippocampus Middle	brain
14	chr21:17789800-17790200	Weak transcription	Liver	Liver
15	chr21:17789800-17790800	Weak transcription	Brain Cingulate Gyrus	brain

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