Variant report

Variant	rs908789
Chromosome Location	chr2:86612794-86612795
allele	G/T
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:45)

rs_ID	r²[population]
rs10185085	1.00[CHB][hapmap]
rs10208989	0.83[EUR][1000 genomes]
rs1033288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1033289	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036940	1.00[CHB][hapmap]
rs10865481	0.89[CEU][hapmap]
rs11127040	1.00[CHB][hapmap]
rs11127042	1.00[CHB][hapmap]
rs11693352	1.00[CHB][hapmap]
rs11903855	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12617075	0.81[CEU][hapmap]
rs12714183	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12714185	1.00[CHB][hapmap]
rs12714187	1.00[CHB][hapmap]
rs12995117	1.00[CHB][hapmap]
rs13420491	0.82[EUR][1000 genomes]
rs1468039	1.00[CHB][hapmap]
rs1518811	1.00[CHB][hapmap]
rs1964087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1964088	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1964089	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2030259	1.00[CHB][hapmap]
rs2044230	1.00[CHB][hapmap]
rs2113608	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2113609	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3952742	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4832281	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4832282	0.81[CEU][hapmap]
rs4832283	1.00[ASN][1000 genomes]
rs4832285	1.00[CHB][hapmap]
rs4832289	1.00[CHB][hapmap]
rs4832294	1.00[CHB][hapmap]
rs6547677	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6547680	1.00[ASN][1000 genomes]
rs6708398	1.00[ASN][1000 genomes]
rs6710124	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6713586	0.89[ASN][1000 genomes]
rs6714826	1.00[CHB][hapmap]
rs6716701	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6720331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756146	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7573005	1.00[ASN][1000 genomes]
rs7574389	1.00[CHB][hapmap]
rs950780	1.00[CHB][hapmap]
rs966477	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs908789	VPS24	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86609000-86615200	Enhancers	Fetal Lung	lung
2	chr2:86611600-86614000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:86612400-86612800	Enhancers	Fetal Muscle Trunk	muscle

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