Variant report

Variant	rs858141
Chromosome Location	chr20:24061950-24061951
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs2005624	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2013710	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2208012	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6036640	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036644	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036645	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036650	0.89[EUR][1000 genomes]
rs6036653	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6036654	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6036664	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6049389	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049390	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049392	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6049394	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6049403	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6049416	0.88[EUR][1000 genomes]
rs6049417	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6049419	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6049432	0.80[CEU][hapmap]
rs721314	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs761865	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs761868	0.80[CEU][hapmap]
rs761869	0.80[CEU][hapmap]
rs858140	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs858144	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs858145	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910775	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs974784	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs974785	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs858141	CST9	cis	parietal	SCAN
rs858141	CST5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24060200-24062200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:24060400-24062200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:24061800-24062000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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