Variant report

Variant	rs6517700
Chromosome Location	chr21:17777827-17777828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1074741	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs11088585	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs11911745	0.96[CEU][hapmap]
rs1349226	0.95[CEU][hapmap];0.87[GIH][hapmap]
rs1375625	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs1375626	0.96[CEU][hapmap]
rs2051270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2155840	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2167060	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs240453	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]
rs240461	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240492	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823784	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2823790	0.87[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs2823798	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs2823799	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2823801	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs8126683	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs8126881	0.96[CEU][hapmap]
rs8128973	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs9305765	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs9979472	1.00[CEU][hapmap];0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv913417	chr21:17762340-17777827	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription	lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv913418	chr21:17767773-17786219	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv979496	chr21:17772425-17789214	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6517700	CHODL	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17761600-17780200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:17771400-17791200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr21:17775400-17782200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr21:17775400-17786600	Weak transcription	Ovary	ovary
5	chr21:17775600-17786000	Weak transcription	Brain Anterior Caudate	brain
6	chr21:17775800-17782000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:17776800-17778400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr21:17777600-17778800	Weak transcription	Adipose Nuclei	Adipose

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