Variant report

Variant	rs10016506
Chromosome Location	chr4:56396674-56396675
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56393770..56396745-chr4:56397077..56399857,3	K562	blood:
2	chr4:56394810..56399339-chr4:56410958..56414096,4	K562	blood:

Variant related genes	Relation type
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10002541	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005989	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10009593	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10026692	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10034433	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1011095	0.86[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs10462035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133376	0.84[JPT][hapmap]
rs11133379	0.86[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133382	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11133383	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133394	1.00[ASN][1000 genomes]
rs11133399	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11133404	0.83[CHB][hapmap]
rs11726609	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733864	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735267	0.86[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11931061	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11935806	0.81[CHB][hapmap]
rs11939815	0.86[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947476	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947623	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12499623	0.81[CHB][hapmap]
rs12512220	0.87[CHB][hapmap]
rs12646078	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12647034	0.84[EUR][1000 genomes]
rs13102385	0.86[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13121235	0.85[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13128582	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138697	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13152650	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522106	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522107	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522108	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522110	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522111	0.85[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17085889	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873092	0.86[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1965467	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1980273	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2130036	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2140077	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2177127	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap]
rs2177129	0.86[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412646	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412647	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412663	0.82[CEU][hapmap];0.89[CHB][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28445925	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28448438	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28463765	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28469692	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28514423	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28525309	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28572116	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28582059	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28670674	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28673496	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28713343	0.81[EUR][1000 genomes]
rs28790098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899037	0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs35767091	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3736544	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736545	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805147	0.86[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805152	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805154	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805157	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817444	0.85[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828481	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4371676	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4580704	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473005	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs480479	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs4864998	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865008	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865010	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap]
rs4865018	0.89[CHB][hapmap];0.88[YRI][hapmap]
rs59804446	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60797008	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60992571	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62303714	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62309727	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554280	0.82[EUR][1000 genomes]
rs6554286	0.85[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554292	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6810948	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811520	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812042	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815516	0.86[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817267	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6817663	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6819660	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824057	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824955	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6825994	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827359	0.87[CHB][hapmap]
rs6829182	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6832769	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6834676	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837710	0.86[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839788	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846427	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6850524	0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs6851838	0.85[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6853192	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726967	0.86[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7660054	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap]
rs7660808	0.81[EUR][1000 genomes]
rs7667849	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668147	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7670225	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673908	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677526	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680941	0.83[CHB][hapmap]
rs7684810	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9312662	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9312664	0.87[CHB][hapmap]
rs9684708	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9997288	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9998038	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998146	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56361600-56411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56372600-56405200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:56385000-56403400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:56386000-56398600	Weak transcription	Fetal Stomach	stomach
5	chr4:56387800-56398800	Weak transcription	Left Ventricle	heart
6	chr4:56391600-56397800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:56391600-56398400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:56391600-56400600	Weak transcription	HSMM	muscle
9	chr4:56391600-56403400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:56391600-56405600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:56391600-56405600	Weak transcription	Osteobl	bone
12	chr4:56391600-56405800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:56391600-56408800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:56391600-56409400	Weak transcription	NHDF-Ad	bronchial
15	chr4:56391800-56399800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:56391800-56409400	Weak transcription	HMEC	breast
17	chr4:56391800-56409400	Weak transcription	NHEK	skin
18	chr4:56391800-56409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:56393200-56408000	Weak transcription	K562	blood
20	chr4:56394600-56397000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr4:56394800-56397200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr4:56394800-56403400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:56395600-56397000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:56396200-56406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:56396400-56396800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:56396400-56397000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
27	chr4:56396600-56396800	ZNF genes & repeats	Psoas Muscle	Psoas
28	chr4:56396600-56397000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:56396600-56397600	ZNF genes & repeats	Fetal Lung	lung

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