Variant report

Variant	rs2823960
Chromosome Location	chr21:18045539-18045540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11088586	0.81[AMR][1000 genomes]
rs1116415	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1129247	0.80[EUR][1000 genomes]
rs12626359	0.81[AMR][1000 genomes]
rs12626360	0.82[AMR][1000 genomes]
rs12627437	0.81[AMR][1000 genomes]
rs12627532	0.82[AMR][1000 genomes]
rs2027624	0.82[AMR][1000 genomes]
rs2027625	0.82[AMR][1000 genomes]
rs2154727	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2211987	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2211988	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2211990	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2823929	0.82[AMR][1000 genomes]
rs2823930	0.82[AMR][1000 genomes]
rs2823931	0.82[AMR][1000 genomes]
rs2823932	0.80[EUR][1000 genomes]
rs2823933	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2823959	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823962	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823963	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823964	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823965	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4485639	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4485640	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7277443	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279043	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7281422	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7281452	0.94[EUR][1000 genomes]
rs7282138	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8130313	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8133801	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8134596	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8134854	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9784203	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974183	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9984100	0.82[AMR][1000 genomes]
rs9984105	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv834052	chr21:17967385-18142224	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv915742	chr21:18022813-18339999	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv913423	chr21:18023205-18057633	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
6	nsv913424	chr21:18026703-18057633	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
7	nsv587079	chr21:18035045-18050542	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
8	nsv913425	chr21:18035045-18057633	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
9	nsv459102	chr21:18039145-18050542	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
10	nsv587080	chr21:18039145-18050542	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2823960	AP000473.8	cis	Thyroid	GTEx
rs2823960	AP000473.8	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:18045400-18046600	Weak transcription	Liver	Liver

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