Variant report

Variant	rs1893573
Chromosome Location	chr21:27965706-27965707
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13433431	0.96[YRI][hapmap]
rs13433470	0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1543775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2135305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2830275	1.00[ASW][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2830280	0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2830282	1.00[AMR][1000 genomes]
rs2830295	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2830296	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2830298	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2830299	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2830300	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2830301	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28401356	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28404770	0.90[AFR][1000 genomes]
rs28525622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28572488	0.83[AMR][1000 genomes]
rs28624518	0.83[AMR][1000 genomes]
rs28678819	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57821067	1.00[AMR][1000 genomes]
rs7277524	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7283190	0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73351185	1.00[AMR][1000 genomes]
rs73351190	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73353008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8127446	0.83[AMR][1000 genomes]
rs8128689	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8129932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8129933	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8130654	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8133538	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9974221	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9975467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9975732	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9978127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9979121	0.89[AFR][1000 genomes]
rs9979986	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9980194	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9980419	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9984233	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9989934	0.88[AFR][1000 genomes];1.00[AMR][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	nsv1056506	chr21:27332898-28049880	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv544412	chr21:27332898-28049880	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv544413	chr21:27942060-28065995	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1893573	CAPS	trans	brain	seeQTL
rs1893573	SLC47A2	trans	brain	seeQTL
rs1893573	DYNLRB2	trans	brain	seeQTL
rs1893573	C1orf194	trans	brain	seeQTL
rs1893573	ZMYND10	trans	brain	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:27961000-27966200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr21:27961000-27966200	Weak transcription	NHEK	skin
3	chr21:27964400-27966200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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