Variant report

Variant	rs4671519
Chromosome Location	chr2:63820398-63820399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:63814719..63818163-chr2:63820081..63823220,6	MCF-7	breast:
2	chr2:63814652..63820726-chr2:63822860..63830564,18	K562	blood:
3	chr2:63814544..63817562-chr2:63819288..63824360,10	K562	blood:
4	chr2:63815568..63817310-chr2:63819288..63820984,2	K562	blood:

Variant related genes	Relation type
ENSG00000143951	Chromatin interaction
ENSG00000014641	Chromatin interaction

Extended variants
information (count: 183 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs10168545	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10170988	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10171223	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10176522	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1023820	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10469944	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10469945	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1082363	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10865337	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10865338	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10865339	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10865341	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11125977	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125978	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs112194	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11693909	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11898615	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12105140	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1255	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12713494	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713496	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12990914	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1348803	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1348806	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1356390	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1374308	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1446563	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1446564	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1446565	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1446569	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1550860	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs166384	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs166385	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs171901	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs171902	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs174485	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs185499	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1867847	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1867849	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs187801	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1900303	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs190519	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs196123	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs196124	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs196125	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2028883	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2028887	0.91[EUR][1000 genomes]
rs2084200	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2121350	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2121351	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2121353	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2166494	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2166497	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2176415	0.84[EUR][1000 genomes]
rs2292793	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2305157	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2422011	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2592386	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2592387	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2592388	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2604613	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2604614	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2604615	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2604617	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262470	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs262471	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs262472	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs262473	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs262474	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262475	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262476	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262477	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs262478	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs262479	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs262480	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262481	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs262482	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262483	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262484	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262485	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262486	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262487	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262488	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262489	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs262490	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs262491	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs262492	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs262493	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs262494	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262495	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs262501	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs262502	0.92[EUR][1000 genomes]
rs262503	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs262504	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262505	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs262506	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs262507	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs262508	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262509	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262510	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262511	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262512	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262513	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262514	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262515	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs262516	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262517	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs262518	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262519	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262520	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262521	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262523	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262524	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262525	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs262526	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262527	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262528	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262529	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262530	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262531	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262532	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs262533	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262536	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262537	0.81[EUR][1000 genomes]
rs262538	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs262539	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2901614	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3980466	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4255949	0.82[EUR][1000 genomes]
rs4671064	0.83[EUR][1000 genomes]
rs4671065	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671066	0.85[EUR][1000 genomes]
rs4671067	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671068	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671069	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671503	0.87[EUR][1000 genomes]
rs4671505	0.88[EUR][1000 genomes]
rs4671508	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4671509	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4671512	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671514	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4671515	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671516	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671517	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546004	0.87[EUR][1000 genomes]
rs6546005	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6546007	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6546009	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6546011	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6546016	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6546017	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6546018	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6546019	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6706123	0.94[EUR][1000 genomes]
rs6708804	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6717031	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6724160	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6732791	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6734648	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6736029	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6736411	0.87[EUR][1000 genomes]
rs6738190	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6754730	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68183503	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7563623	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7570031	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7571017	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7571325	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7576316	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7577952	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7581630	0.87[EUR][1000 genomes]
rs7584404	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7606045	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7607257	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7608470	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7608513	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs959195	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs964880	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs964903	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9789351	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs989527	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1792289	chr2:63812148-63900292	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4671519	MDH1	cis	Adipose Subcutaneous	GTEx
rs4671519	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63816600-63830200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:63816800-63831000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:63817000-63820400	Weak transcription	Ovary	ovary
4	chr2:63817000-63827000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:63817000-63827000	Weak transcription	Spleen	Spleen
6	chr2:63817000-63827400	Weak transcription	Lung	lung
7	chr2:63817000-63828800	Weak transcription	Pancreas	Pancrea
8	chr2:63817000-63830200	Weak transcription	Esophagus	oesophagus
9	chr2:63817000-63831800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:63817200-63820400	Weak transcription	Fetal Lung	lung
11	chr2:63817200-63820400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:63817200-63821200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:63817200-63823400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:63817200-63828000	Weak transcription	Aorta	Aorta
15	chr2:63817200-63834400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:63817400-63820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:63817400-63821600	Weak transcription	Fetal Kidney	kidney
18	chr2:63817400-63821800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:63817400-63831600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:63817600-63820600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:63817600-63820600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:63817600-63821200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:63817600-63821600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:63817600-63828600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:63817800-63820600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:63818000-63820600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:63818000-63821200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:63818000-63821200	Weak transcription	HSMM	muscle
29	chr2:63818000-63822000	Weak transcription	Brain Substantia Nigra	brain
30	chr2:63818000-63822000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:63818000-63822400	Weak transcription	Thymus	Thymus
32	chr2:63818000-63834800	Strong transcription	Fetal Thymus	thymus
33	chr2:63818000-63835400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:63818200-63820600	Weak transcription	Placenta	Placenta
35	chr2:63818400-63820400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr2:63818400-63820600	Weak transcription	Hela-S3	cervix
37	chr2:63818400-63820600	Weak transcription	NH-A	brain
38	chr2:63818400-63820600	Weak transcription	NHEK	skin
39	chr2:63818400-63821200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:63818400-63821600	Weak transcription	Osteobl	bone
41	chr2:63818400-63821800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:63818400-63823000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:63818400-63824000	Strong transcription	HUVEC	blood vessel
44	chr2:63818400-63828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:63818400-63829800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:63818400-63831000	Weak transcription	Gastric	stomach
47	chr2:63818400-63831800	Weak transcription	Colonic Mucosa	Colon
48	chr2:63818400-63831800	Weak transcription	Small Intestine	intestine
49	chr2:63818600-63820400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:63818600-63821200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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