Variant report

Variant	rs2501559
Chromosome Location	chr9:140565196-140565197
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:140481185..140483242-chr9:140565190..140566987,2	K562	blood:
2	chr9:140563248..140567111-chr9:140567384..140570139,4	K562	blood:
3	chr9:140497340..140502310-chr9:140563850..140568927,6	K562	blood:
4	chr9:140484072..140485804-chr9:140563886..140566871,2	K562	blood:
5	chr9:140511684..140515922-chr9:140563311..140567576,10	MCF-7	breast:
6	chr9:140504074..140505804-chr9:140564024..140565554,2	K562	blood:
7	chr9:140513432..140515726-chr9:140563300..140565570,3	MCF-7	breast:
8	chr9:140563812..140566450-chr9:140570445..140574038,3	K562	blood:
9	chr9:140556948..140560022-chr9:140562318..140565265,4	K562	blood:
10	chr9:140478738..140480572-chr9:140563857..140565636,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203993	Chromatin interaction
ENSG00000181090	Chromatin interaction
ENSG00000165724	Chromatin interaction
ENSG00000197070	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10110	0.82[CHB][hapmap]
rs10123486	0.94[ASN][1000 genomes]
rs1045777	0.85[CHB][hapmap]
rs10481734	0.96[ASN][1000 genomes]
rs10732688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10746564	0.96[ASN][1000 genomes]
rs10780179	1.00[CHB][hapmap]
rs10780180	0.84[ASN][1000 genomes]
rs10780181	0.96[ASN][1000 genomes]
rs10780182	0.96[ASN][1000 genomes]
rs10780183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10780184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867049	0.94[ASN][1000 genomes]
rs10867050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10867051	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs10867052	0.98[ASN][1000 genomes]
rs10867053	0.98[ASN][1000 genomes]
rs10867054	0.98[ASN][1000 genomes]
rs11137135	0.82[CHB][hapmap]
rs11137140	1.00[CHB][hapmap]
rs11137141	1.00[CHB][hapmap]
rs11137158	1.00[CHB][hapmap]
rs11137163	1.00[CHB][hapmap]
rs11137167	1.00[CHB][hapmap]
rs11137169	1.00[CHB][hapmap]
rs11137172	1.00[CHB][hapmap]
rs11137177	0.98[ASN][1000 genomes]
rs11137178	0.98[ASN][1000 genomes]
rs11137179	0.98[ASN][1000 genomes]
rs11137182	0.90[ASN][1000 genomes]
rs11137183	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12551649	0.98[ASN][1000 genomes]
rs12683290	0.82[CHB][hapmap]
rs13290032	1.00[JPT][hapmap]
rs13296028	1.00[CHB][hapmap]
rs17496354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1776776	1.00[CHB][hapmap]
rs1891628	1.00[CHB][hapmap]
rs2014103	0.98[ASN][1000 genomes]
rs2094623	1.00[CHB][hapmap]
rs2183138	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2257839	1.00[CHB][hapmap]
rs2297004	1.00[CHB][hapmap]
rs2353770	0.82[AMR][1000 genomes]
rs2501556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2501560	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501567	1.00[CHB][hapmap]
rs2501568	1.00[CHB][hapmap]
rs2987618	1.00[CHB][hapmap]
rs2987621	1.00[CHB][hapmap]
rs36088123	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3849856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3860888	0.89[ASN][1000 genomes]
rs3895387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4246177	1.00[CHB][hapmap]
rs4567119	0.98[ASN][1000 genomes]
rs4962227	1.00[CHB][hapmap]
rs4979638	0.94[ASN][1000 genomes]
rs4979651	0.94[ASN][1000 genomes]
rs4979652	0.94[ASN][1000 genomes]
rs4979653	0.98[ASN][1000 genomes]
rs4979654	0.82[ASN][1000 genomes]
rs4979655	0.96[ASN][1000 genomes]
rs4979656	0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs4979657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7024179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7043932	1.00[CHB][hapmap]
rs821313	1.00[CHB][hapmap]
rs863701	0.82[CHB][hapmap]
rs9410116	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950078	0.82[CHB][hapmap]
rs975978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894499	chr9:139810595-140734161	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
2	nsv531664	chr9:140110329-140725056	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	275 gene(s)	inside rSNPs	diseases
3	nsv531654	chr9:140110329-141033187	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	281 gene(s)	inside rSNPs	diseases
4	nsv932633	chr9:140240417-141053535	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
5	nsv1035524	chr9:140251014-140751633	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv1053628	chr9:140260666-141005637	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
7	nsv534215	chr9:140286134-141008915	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	n/a
8	nsv1035388	chr9:140306746-140654768	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	n/a
9	nsv1039672	chr9:140343466-140707505	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS 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	85 gene(s)	inside rSNPs	n/a
10	nsv540358	chr9:140343466-140707505	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
11	nsv1041512	chr9:140350404-140612859	Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
12	nsv540359	chr9:140350404-140612859	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
13	nsv616023	chr9:140372570-140602887	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
14	nsv531603	chr9:140378700-140590977	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
15	nsv531665	chr9:140378700-141073897	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	n/a
16	nsv868924	chr9:140407572-141053525	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA miRNA target site	70 gene(s)	inside rSNPs	n/a
17	nsv1039933	chr9:140408112-141005637	Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
18	nsv531666	chr9:140409395-141015925	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised 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 miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
19	nsv831763	chr9:140439831-140614021	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS 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	60 gene(s)	inside rSNPs	n/a
20	esv3398333	chr9:140451462-140814795	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	60 gene(s)	inside rSNPs	n/a
21	nsv1052036	chr9:140452641-141018985	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
22	nsv540365	chr9:140452641-141018985	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
23	nsv949702	chr9:140466816-141027939	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	n/a
24	nsv531667	chr9:140468821-140936261	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
25	nsv531668	chr9:140492807-140986221	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	n/a
26	nsv531669	chr9:140514663-140852911	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	n/a
27	nsv1053192	chr9:140532404-141005637	Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
28	nsv540366	chr9:140532404-141005637	Weak transcription Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
29	nsv532478	chr9:140535164-140786943	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	n/a
30	nsv894676	chr9:140536098-140734161	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
31	nsv534573	chr9:140550908-140757122	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140534600-140572600	Weak transcription	Small Intestine	intestine
2	chr9:140548400-140567600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:140555000-140571200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr9:140558400-140566600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:140559600-140567600	Weak transcription	Osteobl	bone
6	chr9:140560800-140566800	Weak transcription	NHEK	skin
7	chr9:140560800-140567400	Weak transcription	NHDF-Ad	bronchial
8	chr9:140561200-140568000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:140561600-140567000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:140561800-140565200	Weak transcription	Fetal Lung	lung
11	chr9:140561800-140567600	Weak transcription	Fetal Kidney	kidney
12	chr9:140561800-140572800	Weak transcription	Dnd41	blood
13	chr9:140562000-140567000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:140562000-140567000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:140562000-140567200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr9:140562000-140569000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:140562000-140573800	Weak transcription	HUVEC	blood vessel
18	chr9:140562800-140567400	Weak transcription	Brain Anterior Caudate	brain
19	chr9:140563400-140565400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:140563600-140565400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:140563600-140565400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr9:140563600-140565600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:140563800-140565400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr9:140563800-140565600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:140563800-140566400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr9:140563800-140566600	Genic enhancers	Fetal Intestine Small	intestine
27	chr9:140564000-140565400	Enhancers	Stomach Mucosa	stomach
28	chr9:140564000-140565600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:140564000-140566600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:140564000-140566600	Enhancers	Ovary	ovary
31	chr9:140564000-140566600	Weak transcription	Hela-S3	cervix
32	chr9:140564000-140567400	Weak transcription	Brain Substantia Nigra	brain
33	chr9:140564000-140567400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:140564000-140567600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:140564000-140567600	Weak transcription	Brain Angular Gyrus	brain
36	chr9:140564000-140591200	Weak transcription	Aorta	Aorta
37	chr9:140564200-140565600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr9:140564200-140565600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:140564200-140565600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr9:140564200-140565600	Enhancers	Fetal Muscle Leg	muscle
41	chr9:140564200-140565800	Enhancers	Gastric	stomach
42	chr9:140564200-140566600	Enhancers	Fetal Intestine Large	intestine
43	chr9:140564200-140566600	Enhancers	Pancreas	Pancrea
44	chr9:140564200-140566600	Enhancers	Right Ventricle	heart
45	chr9:140564200-140566800	Weak transcription	Primary B cells from cord blood	blood
46	chr9:140564200-140567000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:140564200-140567000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr9:140564200-140567600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:140564200-140567600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:140564200-140567600	Weak transcription	Thymus	Thymus

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