Variant report

Variant	rs34225441
Chromosome Location	chr3:48308891-48308892
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48297107..48298627-chr3:48307362..48309456,2	K562	blood:
2	chr3:48282900..48284446-chr3:48308562..48310138,2	MCF-7	breast:
3	chr3:48308597..48312699-chr3:48540055..48542560,3	MCF-7	breast:
4	chr3:48281394..48283876-chr3:48308645..48311446,2	MCF-7	breast:
5	chr3:48303362..48306921-chr3:48308084..48310713,4	MCF-7	breast:
6	chr3:48308211..48311790-chr3:48318412..48322138,4	K562	blood:
7	chr3:48298868..48300972-chr3:48308573..48310773,2	MCF-7	breast:
8	chr3:48308151..48311606-chr3:48472406..48476834,4	MCF-7	breast:
9	chr3:48308211..48310337-chr3:48320094..48322138,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164054	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000229759	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1045482	0.83[EUR][1000 genomes]
rs11130162	0.83[EUR][1000 genomes]
rs11130163	0.83[EUR][1000 genomes]
rs11130164	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11706221	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11706277	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11707606	0.83[EUR][1000 genomes]
rs11707997	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11709691	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710257	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11710861	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714176	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11714944	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715776	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715799	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11715876	0.82[EUR][1000 genomes]
rs11716371	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11716848	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11717716	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11718329	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11718350	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11719365	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11928691	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13059037	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13060020	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13061269	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13066044	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13066758	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13067450	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13068265	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13068288	0.80[EUR][1000 genomes]
rs13069029	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13070210	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13071960	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13072018	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13079728	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13081169	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13081633	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13082158	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13082859	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13084616	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13085251	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13087929	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13090538	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13094727	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13095983	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13097450	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13100815	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17647717	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17786132	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2125482	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2361685	0.83[EUR][1000 genomes]
rs2541	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3197223	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34076262	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34523942	0.94[EUR][1000 genomes]
rs34589064	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34630841	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34728236	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34749846	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34946886	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35190747	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35297395	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35297486	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35411187	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35414021	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35456569	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35778847	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35802497	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35944878	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36020562	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36064160	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36075665	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36092070	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36121690	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3729577	0.83[EUR][1000 genomes]
rs3731487	0.83[EUR][1000 genomes]
rs3731489	0.83[EUR][1000 genomes]
rs3731497	0.83[EUR][1000 genomes]
rs3731513	0.83[EUR][1000 genomes]
rs3731515	0.83[EUR][1000 genomes]
rs3731534	0.83[EUR][1000 genomes]
rs3731550	0.82[EUR][1000 genomes]
rs3731555	0.82[EUR][1000 genomes]
rs3937	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4130522	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4131361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4131362	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4371540	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4392440	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4404473	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4420898	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4479622	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4511915	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4511916	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4541431	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4619808	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4632568	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6442110	0.83[EUR][1000 genomes]
rs6442111	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6775179	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6782166	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6787500	0.83[EUR][1000 genomes]
rs6791930	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6793150	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6793223	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6793239	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6794644	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6796343	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800492	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6801801	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804986	0.91[EUR][1000 genomes]
rs6806112	0.81[EUR][1000 genomes]
rs71323391	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71323394	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71323395	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71323396	0.90[EUR][1000 genomes]
rs71323397	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs745116	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7614532	0.93[EUR][1000 genomes]
rs7621785	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7624450	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7632297	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7636461	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644414	0.84[EUR][1000 genomes]
rs7645425	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7647817	0.83[EUR][1000 genomes]
rs7648720	0.95[EUR][1000 genomes]
rs7652233	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7653152	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653336	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9311421	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936426	0.83[EUR][1000 genomes]
rs936427	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818937	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9819094	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9825637	0.91[EUR][1000 genomes]
rs9830016	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9831531	0.83[EUR][1000 genomes]
rs9833309	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9834095	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9837228	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847953	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850672	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9853804	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs34225441	CDC25A	cis	Muscle Skeletal	GTEx
rs34225441	CDC25A	cis	Artery Tibial	GTEx
rs34225441	MRPS18AP1	cis	Thyroid	GTEx
rs34225441	ZNF589	cis	Nerve Tibial	GTEx
rs34225441	ZNF589	cis	Thyroid	GTEx
rs34225441	MRPS18AP1	cis	lung	GTEx
rs34225441	ZNF589	cis	lung	GTEx
rs34225441	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs34225441	ZNF589	cis	Esophagus Muscularis	GTEx
rs34225441	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs34225441	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs34225441	MRPS18AP1	cis	Artery Aorta	GTEx
rs34225441	NME6	cis	Nerve Tibial	GTEx
rs34225441	MRPS18AP1	cis	Stomach	GTEx
rs34225441	ZNF589	cis	Adipose Subcutaneous	GTEx
rs34225441	CDC25A	cis	Adipose Subcutaneous	GTEx
rs34225441	SPINK8	cis	Whole Blood	GTEx
rs34225441	NME6	cis	Esophagus Muscularis	GTEx
rs34225441	ZNF589	cis	Artery Aorta	GTEx
rs34225441	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs34225441	ZNF589	cis	Esophagus Mucosa	GTEx
rs34225441	CDC25A	cis	Thyroid	GTEx
rs34225441	ZNF589	cis	Artery Tibial	GTEx
rs34225441	NME6	cis	Muscle Skeletal	GTEx
rs34225441	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs34225441	NME6	cis	multi-tissue	Pritchard
rs34225441	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs34225441	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs34225441	NME6	cis	Artery Tibial	GTEx
rs34225441	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs34225441	MRPS18AP1	cis	Artery Tibial	GTEx
rs34225441	FCF1P2	cis	Artery Tibial	GTEx
rs34225441	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs34225441	MRPS18AP1	cis	Nerve Tibial	GTEx
rs34225441	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs34225441	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs34225441	ZNF589	cis	Stomach	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48283200-48309800	Weak transcription	Fetal Lung	lung
2	chr3:48283400-48310000	Weak transcription	NH-A	brain
3	chr3:48283400-48315200	Weak transcription	Ovary	ovary
4	chr3:48283600-48309600	Weak transcription	Fetal Intestine Large	intestine
5	chr3:48283800-48309400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:48283800-48310400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:48285600-48312400	Weak transcription	Psoas Muscle	Psoas
8	chr3:48285800-48310200	Weak transcription	Fetal Brain Male	brain
9	chr3:48285800-48311000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:48286400-48309400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:48288600-48312800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:48289200-48312000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:48289200-48312600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:48290000-48309400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:48292800-48309400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:48293200-48311400	Weak transcription	Placenta	Placenta
17	chr3:48296000-48311000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr3:48296200-48311600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:48296600-48311000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:48296600-48312000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:48297400-48312000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:48297600-48311800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:48297800-48312400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:48298400-48309600	Weak transcription	Brain Angular Gyrus	brain
25	chr3:48298400-48309800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:48299000-48309200	Weak transcription	Stomach Mucosa	stomach
27	chr3:48299600-48310400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr3:48299600-48311800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:48299600-48312600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:48300200-48309200	Strong transcription	Fetal Thymus	thymus
31	chr3:48300200-48312200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:48300400-48310400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:48301000-48309200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:48301000-48309400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:48301200-48309400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:48301200-48309600	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:48301600-48310000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:48301800-48309400	Weak transcription	Right Ventricle	heart
39	chr3:48302000-48309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:48302800-48312800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:48303000-48309400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:48303000-48317400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:48303400-48309600	Weak transcription	Primary B cells from cord blood	blood
44	chr3:48303800-48309400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:48304000-48311600	Weak transcription	A549	lung
46	chr3:48304200-48309800	Weak transcription	NHDF-Ad	bronchial
47	chr3:48304200-48311200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:48304600-48309400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:48304600-48309600	Weak transcription	Hela-S3	cervix
50	chr3:48304800-48314000	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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