Variant report

Variant	rs12566940
Chromosome Location	chr1:86535863-86535864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493787	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10493788	0.91[ASN][1000 genomes]
rs11583563	1.00[ASN][1000 genomes]
rs11588997	1.00[ASN][1000 genomes]
rs11806244	0.91[ASN][1000 genomes]
rs12402809	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12408108	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12564959	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12566718	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567495	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12567549	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12744313	1.00[ASN][1000 genomes]
rs12753548	1.00[ASN][1000 genomes]
rs12754154	1.00[ASN][1000 genomes]
rs1408667	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1408668	0.91[ASN][1000 genomes]
rs17405393	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17406450	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17406471	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17406755	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17414470	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17415366	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2221588	0.92[ASN][1000 genomes]
rs41313268	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912460	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4912462	0.96[ASN][1000 genomes]
rs517786	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540159	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs565860	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs569541	0.91[ASN][1000 genomes]
rs61783511	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61800687	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61800722	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61800724	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61800727	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61800729	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61800732	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61800734	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802172	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629683	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs645271	0.91[ASN][1000 genomes]
rs6665582	1.00[ASN][1000 genomes]
rs72716135	0.88[EUR][1000 genomes]
rs72716141	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72716150	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716152	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414042	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7524738	0.92[ASN][1000 genomes]
rs7545716	0.88[ASN][1000 genomes]
rs7548696	1.00[ASN][1000 genomes]

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	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525678	chr1:86487914-86549498	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1797916	chr1:86529538-86556298	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86534000-86536000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:86534000-86536600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:86535600-86544600	Weak transcription	Fetal Lung	lung

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