Variant report

Variant	rs922854
Chromosome Location	chr5:44452257-44452258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10061166	0.88[EUR][1000 genomes]
rs10941672	0.83[EUR][1000 genomes]
rs10941673	0.85[EUR][1000 genomes]
rs1116180	0.95[EUR][1000 genomes]
rs12186589	0.87[EUR][1000 genomes]
rs12188017	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12188390	0.85[EUR][1000 genomes]
rs13355269	0.86[EUR][1000 genomes]
rs13358061	0.83[EUR][1000 genomes]
rs1482695	0.91[EUR][1000 genomes]
rs1531803	0.89[EUR][1000 genomes]
rs1552184	0.91[EUR][1000 genomes]
rs16901868	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17319592	0.97[EUR][1000 genomes]
rs1871950	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2128431	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2330570	0.89[EUR][1000 genomes]
rs28561538	0.88[EUR][1000 genomes]
rs56313556	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57777873	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58261355	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58826391	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60912459	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61399521	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6451764	0.90[EUR][1000 genomes]
rs6869262	0.83[EUR][1000 genomes]
rs6870835	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6884170	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72748041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748047	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748048	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748056	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72748063	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72748065	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72748076	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748082	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72748092	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72750279	0.87[EUR][1000 genomes]
rs73752037	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7733376	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs922853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs922855	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs957739	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[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	nsv830277	chr5:44383402-44566881	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1024923	chr5:44439853-44528314	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs922854	LOC647121	Cis_chr	lymphoblastoid	RTeQTL
rs922854	MRPS30	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44445000-44453800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:44452000-44453000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:44452200-44453000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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