Variant report

Variant	rs2823704
Chromosome Location	chr21:17631152-17631153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11088580	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11088581	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11911170	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11911298	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12053753	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13048000	0.90[EUR][1000 genomes]
rs1389071	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1389072	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389074	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1492957	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1492958	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1492960	0.96[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1786836	0.85[JPT][hapmap]
rs2131404	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251006	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2251012	0.94[AMR][1000 genomes]
rs238946	0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs238962	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs238963	0.98[EUR][1000 genomes]
rs238964	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs238999	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs239009	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs239010	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2823684	0.93[JPT][hapmap]
rs2823686	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2823688	1.00[JPT][hapmap]
rs2823689	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2823690	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2823691	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2823692	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823693	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2823694	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2823695	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823696	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823697	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823698	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2823699	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2823700	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2823701	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2823702	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823703	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823705	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2823706	0.92[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs2823707	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823708	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823709	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2823710	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823711	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823712	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2823713	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823714	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2823715	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2823716	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2823717	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823718	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823719	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2823720	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2823721	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2823722	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2823723	0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2823724	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2823725	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823726	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2823727	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2823728	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2823729	0.91[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2823731	0.92[EUR][1000 genomes]
rs4381854	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4465860	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57097865	0.90[ASN][1000 genomes]
rs60963357	0.90[ASN][1000 genomes]
rs61333624	0.98[ASN][1000 genomes]
rs6517695	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7278407	0.89[ASN][1000 genomes]
rs73357138	0.86[ASN][1000 genomes]
rs8126809	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8128157	0.88[ASN][1000 genomes]
rs9637001	0.83[AMR][1000 genomes]
rs9808741	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9977984	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834051	chr21:17564843-17721764	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823704	ZNF438	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17619000-17631200	Weak transcription	Brain Hippocampus Middle	brain
2	chr21:17623400-17633400	Weak transcription	Hela-S3	cervix
3	chr21:17626800-17636200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:17626800-17636600	Weak transcription	Ovary	ovary
5	chr21:17628400-17632200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr21:17630800-17631200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:17631000-17631400	Weak transcription	Brain Substantia Nigra	brain
8	chr21:17631000-17631400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr21:17631000-17631800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr21:17631000-17631800	Enhancers	Fetal Brain Male	brain
11	chr21:17631000-17631800	Active TSS	Psoas Muscle	Psoas

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