Variant report

Variant	rs540159
Chromosome Location	chr1:86487655-86487656
allele	A/G
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:79)

rs_ID	r²[population]
rs10493787	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493788	1.00[ASN][1000 genomes]
rs11583563	0.91[ASN][1000 genomes]
rs11588997	0.91[ASN][1000 genomes]
rs11806244	0.82[ASN][1000 genomes]
rs12402809	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408108	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564959	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12566718	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12566940	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12567495	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567549	0.88[EUR][1000 genomes]
rs12744313	0.91[ASN][1000 genomes]
rs12753548	0.91[ASN][1000 genomes]
rs12754154	0.91[ASN][1000 genomes]
rs1408667	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408668	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629358	0.80[AFR][1000 genomes]
rs1698734	0.80[AFR][1000 genomes]
rs1698735	0.80[AFR][1000 genomes]
rs1698736	0.80[AFR][1000 genomes]
rs17405393	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406450	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406471	0.87[EUR][1000 genomes]
rs17406755	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17414470	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415366	0.87[EUR][1000 genomes]
rs2221588	0.84[ASN][1000 genomes]
rs41313268	0.91[ASN][1000 genomes]
rs473232	0.80[AFR][1000 genomes]
rs474106	0.80[AFR][1000 genomes]
rs477862	0.80[AFR][1000 genomes]
rs485816	0.82[AFR][1000 genomes]
rs489325	0.81[AFR][1000 genomes]
rs4912460	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912462	0.87[ASN][1000 genomes]
rs494796	0.80[AFR][1000 genomes]
rs501058	0.80[AFR][1000 genomes]
rs505589	0.80[AFR][1000 genomes]
rs514185	0.81[AFR][1000 genomes]
rs517786	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs557928	0.81[AFR][1000 genomes]
rs565639	0.80[AFR][1000 genomes]
rs565860	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569541	1.00[ASN][1000 genomes]
rs583203	0.81[AFR][1000 genomes]
rs589343	0.81[AFR][1000 genomes]
rs601167	0.81[AFR][1000 genomes]
rs616715	0.80[AFR][1000 genomes]
rs61783511	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61800687	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61800722	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61800724	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61800727	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61800729	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61800732	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61800734	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61802172	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs629683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629719	0.80[AFR][1000 genomes]
rs631935	0.80[AFR][1000 genomes]
rs641712	0.82[AFR][1000 genomes]
rs645271	1.00[ASN][1000 genomes]
rs648355	0.81[AFR][1000 genomes]
rs648366	0.81[AFR][1000 genomes]
rs657026	0.82[AFR][1000 genomes]
rs657540	0.82[AFR][1000 genomes]
rs6665582	0.91[ASN][1000 genomes]
rs6691400	0.82[AFR][1000 genomes]
rs673928	0.80[AFR][1000 genomes]
rs687776	0.86[ASN][1000 genomes]
rs72716135	0.92[EUR][1000 genomes]
rs72716141	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72716150	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72716152	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7414042	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524738	0.84[ASN][1000 genomes]
rs7545716	0.80[ASN][1000 genomes]
rs7548696	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs540159	COL24A1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86484600-86489400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:86487600-86488200	Strong transcription	Fetal Lung	lung

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