Variant report

Variant	rs4384925
Chromosome Location	chr3:54799449-54799450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10865989	0.81[EUR][1000 genomes]
rs1317450	0.83[ASN][1000 genomes]
rs1346407	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1559999	0.96[CEU][hapmap]
rs2360021	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2360026	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732748	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4353779	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs4563383	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs515920	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs517729	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs550210	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs578032	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs583190	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs589281	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs652424	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs661201	0.85[JPT][hapmap]
rs6809466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636321	0.81[CEU][hapmap]
rs838022	0.95[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs934083	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv522779	chr3:54793450-54803521	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
4	nsv524822	chr3:54793450-54803521	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4384925	VPRBP	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54787400-54800200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:54787600-54804600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:54794200-54806800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:54794400-54801400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:54794400-54806600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:54795800-54801200	Weak transcription	Psoas Muscle	Psoas
7	chr3:54796200-54806000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:54798400-54803200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:54798800-54799800	Enhancers	Fetal Stomach	stomach
10	chr3:54799400-54800400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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