Variant report

Variant	rs16901868
Chromosome Location	chr5:44479945-44479946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10061166	0.86[EUR][1000 genomes]
rs10941672	0.82[EUR][1000 genomes]
rs10941673	0.83[EUR][1000 genomes]
rs1116180	0.93[EUR][1000 genomes]
rs12186589	0.85[EUR][1000 genomes]
rs12188017	0.96[EUR][1000 genomes]
rs12188390	0.83[EUR][1000 genomes]
rs13355269	0.84[EUR][1000 genomes]
rs13358061	0.81[EUR][1000 genomes]
rs1482695	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1531803	0.87[EUR][1000 genomes]
rs1552184	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17319592	0.99[EUR][1000 genomes]
rs1871950	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2128431	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2330570	0.87[EUR][1000 genomes]
rs28561538	0.86[EUR][1000 genomes]
rs56313556	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57777873	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58261355	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58826391	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60912459	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61399521	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451764	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6869262	0.82[EUR][1000 genomes]
rs6870835	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6884170	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72748041	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72748047	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72748048	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72748056	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748063	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72748065	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748076	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72748082	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72748092	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72750279	0.85[EUR][1000 genomes]
rs73752037	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7733376	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs922853	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs922854	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs922855	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs957739	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3425269	chr5:44461244-44487601	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16901868	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44477800-44480600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:44478000-44480000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
3	chr5:44479200-44480200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
4	chr5:44479200-44480400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
5	chr5:44479200-44480400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr5:44479800-44491800	Weak transcription	Fetal Lung	lung

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