Variant report

Variant	rs205099
Chromosome Location	chr17:19680089-19680090
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19679774..19681757-chr17:19685256..19686882,2	MCF-7	breast:

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs115326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs118943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123081	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs123082	0.84[EUR][1000 genomes]
rs150122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs157387	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157391	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157392	0.84[EUR][1000 genomes]
rs157393	1.00[CEU][hapmap]
rs157394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157397	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157399	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157400	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157403	0.87[EUR][1000 genomes]
rs157405	1.00[CEU][hapmap]
rs157406	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs157409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs166838	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs166839	0.87[EUR][1000 genomes]
rs169460	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs169512	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169513	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs172186	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182214	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs184006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs192511	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs205087	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs205088	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs205090	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs205092	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs205093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205097	0.97[EUR][1000 genomes]
rs205098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs205100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs205105	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs205106	0.84[EUR][1000 genomes]
rs205107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205108	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs205110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs205111	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs205112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385963	0.87[EUR][1000 genomes]
rs281325	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281326	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281328	0.84[EUR][1000 genomes]
rs281330	0.91[AMR][1000 genomes]
rs281331	0.84[EUR][1000 genomes]
rs281332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281333	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs281334	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs281336	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs281337	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs281338	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281339	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs281340	0.91[ASN][1000 genomes]
rs281341	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs281342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281344	0.84[EUR][1000 genomes]
rs281345	0.84[EUR][1000 genomes]
rs281346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281347	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs281348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281349	0.84[EUR][1000 genomes]
rs281350	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281353	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs281354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281356	0.84[EUR][1000 genomes]
rs281365	0.87[EUR][1000 genomes]
rs3098902	0.84[EUR][1000 genomes]
rs3098905	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098906	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3098907	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3098908	0.84[EUR][1000 genomes]
rs3098909	0.84[EUR][1000 genomes]
rs3101810	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3101811	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3101812	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3101813	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3101814	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs3101815	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34372768	0.87[EUR][1000 genomes]
rs367383	0.87[EUR][1000 genomes]
rs379703	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383948	0.81[EUR][1000 genomes]
rs383951	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs394009	0.88[ASN][1000 genomes]
rs395130	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs421561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs445958	0.81[EUR][1000 genomes]
rs4586510	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924800	0.87[EUR][1000 genomes]
rs4925047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6587203	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7225417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs917519	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1061489	chr17:19654704-19705026	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19666000-19691200	Weak transcription	Spleen	Spleen
2	chr17:19666000-19691800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:19670200-19694200	Weak transcription	Right Ventricle	heart
4	chr17:19670200-19699400	Weak transcription	Psoas Muscle	Psoas
5	chr17:19670400-19683800	Weak transcription	Fetal Brain Male	brain
6	chr17:19673400-19682200	Strong transcription	Fetal Brain Female	brain
7	chr17:19673800-19680200	Weak transcription	HUVEC	blood vessel
8	chr17:19673800-19685000	Weak transcription	HSMM	muscle
9	chr17:19673800-19769800	Weak transcription	NH-A	brain
10	chr17:19674000-19699200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr17:19674000-19699200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr17:19675000-19683800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:19675200-19693000	Weak transcription	Small Intestine	intestine
14	chr17:19675200-19695600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:19675400-19688200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr17:19675600-19683000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:19675600-19684600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:19675600-19691200	Weak transcription	Esophagus	oesophagus
19	chr17:19675600-19693600	Strong transcription	Fetal Muscle Leg	muscle
20	chr17:19676000-19691200	Weak transcription	Fetal Thymus	thymus
21	chr17:19676400-19682000	Strong transcription	Brain Anterior Caudate	brain
22	chr17:19676400-19685400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr17:19676400-19688000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:19676400-19688400	Strong transcription	Fetal Intestine Large	intestine
25	chr17:19676600-19680800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr17:19676800-19681800	Strong transcription	Brain Substantia Nigra	brain
27	chr17:19676800-19683400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:19676800-19683400	Strong transcription	Fetal Lung	lung
29	chr17:19676800-19691800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr17:19676800-19697000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:19676800-19699400	Weak transcription	Thymus	Thymus
32	chr17:19677000-19680800	Strong transcription	NHEK	skin
33	chr17:19677000-19681200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr17:19677000-19685800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:19677000-19687800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:19677000-19688000	Strong transcription	Adipose Nuclei	Adipose
37	chr17:19677200-19680200	Weak transcription	Gastric	stomach
38	chr17:19677200-19685000	Strong transcription	Liver	Liver
39	chr17:19677200-19685200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr17:19677200-19685800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr17:19677200-19691600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:19677400-19687800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:19677400-19696200	Weak transcription	Fetal Heart	heart
44	chr17:19677600-19696200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr17:19677800-19700000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:19678000-19681800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr17:19678000-19698400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr17:19678200-19683200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr17:19678200-19685800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:19678200-19687200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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