Variant report

Variant	rs17406644
Chromosome Location	chr1:86508470-86508471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10518360	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518362	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11161727	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12057842	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12077017	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12097262	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12353970	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354099	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12729383	1.00[ASN][1000 genomes]
rs12729890	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12730639	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743320	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743750	1.00[ASN][1000 genomes]
rs12744993	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748730	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750946	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1359419	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17405880	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17405900	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17406104	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17406138	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17406173	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17413771	1.00[ASN][1000 genomes]
rs17414498	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17414519	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17414568	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17414617	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17414884	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415692	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34848727	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4912442	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4912443	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4912455	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912459	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55766419	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56040491	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56229462	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56353901	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392000	0.83[EUR][1000 genomes]
rs59767206	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs648866	1.00[ASN][1000 genomes]
rs6658643	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6703328	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67472012	0.88[ASN][1000 genomes]
rs72716130	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716134	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716145	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72716149	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72958291	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72958294	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72960324	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72960354	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72960374	0.88[ASN][1000 genomes]
rs7411998	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86506600-86508600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:86507800-86520400	Weak transcription	Fetal Lung	lung

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