Variant report

Variant	rs55960393
Chromosome Location	chr6:88221391-88221392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88220208..88222197-chr6:88226588..88230676,3	MCF-7	breast:
2	chr6:88217873..88220227-chr6:88221102..88223244,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 196 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:190)

rs_ID	r²[population]
rs10080513	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11962998	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13193193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13193303	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13193470	0.89[ASN][1000 genomes]
rs13193703	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13193911	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13193927	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13196538	0.89[ASN][1000 genomes]
rs13196755	0.89[ASN][1000 genomes]
rs13197090	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13198094	0.89[ASN][1000 genomes]
rs13198372	0.89[ASN][1000 genomes]
rs13200106	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13202825	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13203056	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13203649	0.89[ASN][1000 genomes]
rs13203790	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13203957	0.89[ASN][1000 genomes]
rs13204592	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13204861	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13205357	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13206240	0.89[ASN][1000 genomes]
rs13206485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13206536	0.89[ASN][1000 genomes]
rs13206957	0.89[ASN][1000 genomes]
rs13208201	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13208550	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13208933	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13210643	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13211439	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13211720	0.89[AMR][1000 genomes]
rs13211892	0.89[ASN][1000 genomes]
rs13212076	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13212089	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213285	0.89[ASN][1000 genomes]
rs13213812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13215013	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13215887	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13216482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13216724	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13216727	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16879475	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16879490	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16879507	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16879510	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16879517	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16879528	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16879532	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171399	0.84[AMR][1000 genomes]
rs17455002	0.89[ASN][1000 genomes]
rs17504209	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17504475	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17504517	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2273130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273131	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2307383	0.89[ASN][1000 genomes]
rs2307389	0.89[ASN][1000 genomes]
rs2307393	0.89[ASN][1000 genomes]
rs28360511	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28381452	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28381487	0.89[ASN][1000 genomes]
rs28381518	0.89[ASN][1000 genomes]
rs28381552	0.89[ASN][1000 genomes]
rs28385570	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28385591	0.89[ASN][1000 genomes]
rs28385632	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34006571	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34007246	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34008333	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34054042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34054261	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34107692	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34154420	0.89[ASN][1000 genomes]
rs34220026	0.89[ASN][1000 genomes]
rs34369446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34385811	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34395299	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34423353	0.89[ASN][1000 genomes]
rs34455158	0.89[ASN][1000 genomes]
rs34540725	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34547532	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34650015	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34727395	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34926624	0.89[ASN][1000 genomes]
rs34941612	0.89[ASN][1000 genomes]
rs35031351	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35056836	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35058527	0.89[ASN][1000 genomes]
rs35116392	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35145047	0.89[ASN][1000 genomes]
rs35234062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35237504	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35289945	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35303040	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35317752	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35324020	0.89[ASN][1000 genomes]
rs35350424	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35363104	0.80[EUR][1000 genomes]
rs35396056	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35465301	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35494431	0.89[ASN][1000 genomes]
rs35504787	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35593940	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35610797	0.87[EUR][1000 genomes]
rs35679038	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35688969	0.89[ASN][1000 genomes]
rs35866706	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35903880	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35917348	0.89[ASN][1000 genomes]
rs35925514	0.89[ASN][1000 genomes]
rs35946241	0.89[ASN][1000 genomes]
rs35972482	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36020402	0.89[ASN][1000 genomes]
rs36041712	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36090981	0.89[ASN][1000 genomes]
rs3734908	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3757369	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3757371	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3823469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4409162	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4587137	0.87[EUR][1000 genomes]
rs55751639	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55759644	0.89[ASN][1000 genomes]
rs55765303	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55766457	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55880748	0.89[ASN][1000 genomes]
rs56004408	0.89[ASN][1000 genomes]
rs56031077	0.89[ASN][1000 genomes]
rs57526195	0.89[ASN][1000 genomes]
rs59361639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60313720	0.89[ASN][1000 genomes]
rs62417663	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417666	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417673	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417674	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417675	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417676	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417680	0.89[ASN][1000 genomes]
rs62417686	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417689	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417692	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417693	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417699	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417701	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62417715	0.89[ASN][1000 genomes]
rs62417718	0.89[ASN][1000 genomes]
rs62417720	0.89[ASN][1000 genomes]
rs62417727	0.89[ASN][1000 genomes]
rs62417753	0.89[ASN][1000 genomes]
rs62419372	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62419373	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62419377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62419378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62419386	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6900057	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6902069	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6905345	0.87[EUR][1000 genomes]
rs6905480	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6911442	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6911548	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6917424	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926321	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6927654	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6927826	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6929542	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6940675	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71548716	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7738268	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7739772	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7740476	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7741170	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7742607	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7744190	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7749032	0.89[ASN][1000 genomes]
rs7750528	0.89[ASN][1000 genomes]
rs7750775	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7750877	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7754550	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7757446	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7759422	0.89[ASN][1000 genomes]
rs7759648	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7760840	0.84[EUR][1000 genomes]
rs7760919	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7770458	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7771832	0.89[ASN][1000 genomes]
rs9444507	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450703	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450714	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88183600-88226000	Weak transcription	Gastric	stomach
2	chr6:88183800-88225400	Weak transcription	Aorta	Aorta
3	chr6:88183800-88227400	Weak transcription	Right Ventricle	heart
4	chr6:88184000-88224200	Weak transcription	Hela-S3	cervix
5	chr6:88188600-88221600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:88191200-88227400	Weak transcription	Spleen	Spleen
7	chr6:88193600-88227600	Weak transcription	Pancreas	Pancrea
8	chr6:88193800-88221400	Weak transcription	Ovary	ovary
9	chr6:88193800-88227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:88194000-88226200	Weak transcription	Lung	lung
11	chr6:88194000-88249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:88194200-88221400	Weak transcription	Colonic Mucosa	Colon
13	chr6:88194600-88228200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:88198800-88223600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:88200600-88227400	Weak transcription	Small Intestine	intestine
16	chr6:88205200-88224600	Weak transcription	Stomach Mucosa	stomach
17	chr6:88207200-88242600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr6:88210000-88223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:88210200-88223600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:88210200-88224400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:88210200-88231400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:88210200-88232800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:88210200-88240600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr6:88210400-88235000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr6:88210800-88224600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:88210800-88224600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:88210800-88230800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:88210800-88230800	Strong transcription	Fetal Thymus	thymus
29	chr6:88210800-88231400	Strong transcription	Osteobl	bone
30	chr6:88210800-88235000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:88211000-88223000	Strong transcription	Primary B cells from cord blood	blood
32	chr6:88211000-88231400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:88211000-88235000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:88211000-88235200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:88211000-88241200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:88211200-88230800	Strong transcription	Liver	Liver
37	chr6:88211800-88224600	Strong transcription	HUVEC	blood vessel
38	chr6:88212000-88245200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:88212600-88221600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:88212800-88224000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:88212800-88227400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:88213000-88224200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr6:88213000-88224600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:88213000-88225400	Weak transcription	Brain Substantia Nigra	brain
45	chr6:88213000-88226200	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:88213400-88223200	Weak transcription	Fetal Intestine Small	intestine
47	chr6:88213400-88227200	Weak transcription	Psoas Muscle	Psoas
48	chr6:88213400-88227400	Weak transcription	Esophagus	oesophagus
49	chr6:88214000-88224200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:88214000-88231400	Strong transcription	NH-A	brain

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