Variant report

Variant	rs7519134
Chromosome Location	chr1:85463208-85463209
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:85463111-85463350	MCF-7	breast:	n/a	n/a
2	ZEB1	chr1:85462507-85463768	GM12878	blood:	n/a	n/a
3	EBF1	chr1:85461040-85464248	GM12878	blood:	n/a	chr1:85463075-85463084 chr1:85462912-85462922 chr1:85463073-85463084
4	SIN3AK20	chr1:85462371-85463242	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr1:85459671-85465061	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:85461049-85464327	GM18951	blood:	n/a	n/a
7	MAX	chr1:85462304-85463390	H1-hESC	embryonic stem cell:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
8	SIN3A	chr1:85463064-85463334	GM12878	blood:	n/a	chr1:85463135-85463148
9	POLR2A	chr1:85461494-85464994	GM12892	blood:	n/a	n/a
10	CTCF	chr1:85463160-85463310	GM12873	blood:	n/a	n/a
11	MAX	chr1:85462145-85463701	GM12878	blood:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
12	YY1	chr1:85463006-85463388	GM12892	blood:	n/a	chr1:85463059-85463068 chr1:85463060-85463071 chr1:85463262-85463271
13	CTCF	chr1:85463200-85463350	GM06990	blood:	n/a	n/a
14	CTCF	chr1:85463115-85463357	MCF-7	breast:	n/a	n/a
15	ZNF143	chr1:85462642-85463259	GM12878	blood:	n/a	chr1:85463074-85463092 chr1:85463202-85463220 chr1:85462987-85463005
16	RCOR1	chr1:85463002-85463247	GM12878	blood:	n/a	n/a
17	CTCF	chr1:85463080-85463230	HRE	kidney:	n/a	n/a
18	POLR2A	chr1:85461102-85464291	GM18526	blood:	n/a	n/a
19	ELF1	chr1:85462435-85463628	GM12878	blood:	n/a	chr1:85462980-85462989
20	ZBTB7A	chr1:85462564-85463389	ECC-1	luminal epithelium:	n/a	chr1:85463071-85463079
21	MTA3	chr1:85460680-85464125	GM12878	blood:	n/a	n/a
22	CTBP2	chr1:85462997-85464123	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:85463144-85463315	MCF-7	breast:	n/a	n/a
24	CTCF	chr1:85463129-85463329	GM12891	blood:	n/a	n/a
25	STAT5A	chr1:85460893-85463850	GM12878	blood:	n/a	chr1:85463447-85463455 chr1:85461389-85461400
26	CTCF	chr1:85463140-85463290	GM12873	blood:	n/a	n/a
27	POLR2A	chr1:85459807-85464317	GM12892	blood:	n/a	n/a
28	CTCF	chr1:85463120-85463270	WERI-Rb-1	eye:	n/a	n/a
29	CTCF	chr1:85463120-85463347	GM19240	blood:	n/a	n/a
30	POLR2A	chr1:85462413-85463573	GM12878	blood:	n/a	n/a
31	CTCF	chr1:85463160-85463276	NHEK	skin:	n/a	n/a
32	MAX	chr1:85462319-85463395	A549	lung:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
33	CTCF	chr1:85463207-85463285	LNCaP	prostate:	n/a	n/a
34	MAX	chr1:85462559-85463420	MCF-7	breast:	n/a	chr1:85462813-85462822 chr1:85463085-85463094
35	CTCF	chr1:85463160-85463310	GM06990	blood:	n/a	n/a
36	PAX5	chr1:85462571-85463524	GM12892	blood:	n/a	n/a
37	POLR2A	chr1:85461608-85463709	GM15510	blood:	n/a	n/a
38	RELA	chr1:85461055-85463441	GM15510	blood:	n/a	n/a
39	CTCF	chr1:85463200-85463350	HMEC	breast:	n/a	n/a
40	POLR2A	chr1:85459795-85464999	GM12878	blood:	n/a	n/a
41	CTCF	chr1:85463124-85463242	GM10248	blood:	n/a	n/a
42	MYC	chr1:85463029-85463365	MCF-7	breast:	n/a	chr1:85463085-85463094
43	POLR2A	chr1:85463204-85463210	H1-hESC	embryonic stem cell:	n/a	n/a
44	SIN3A	chr1:85463123-85464120	H1-hESC	embryonic stem cell:	n/a	chr1:85463135-85463148 chr1:85464028-85464039
45	POLR2A	chr1:85462437-85463237	GM10847	blood:	n/a	n/a
46	POLR2A	chr1:85460981-85465011	GM19099	blood:	n/a	n/a
47	CHD2	chr1:85461067-85464026	GM12878	blood:	n/a	chr1:85462833-85462843 chr1:85462244-85462251
48	EP300	chr1:85463028-85463228	GM12878	blood:	n/a	chr1:85463059-85463068
49	CTCF	chr1:85463099-85463352	GM12892	blood:	n/a	n/a
50	CTCF	chr1:85463100-85463250	GM12869	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR63-1	chr1:85463140-85463597	XLOC_000274

Variant related genes	Relation type
MCOLN2	TF binding region
WDR63	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10782534	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10782536	0.83[EUR][1000 genomes]
rs10873669	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873670	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873672	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873676	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873677	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873678	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10873679	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10873682	0.81[EUR][1000 genomes]
rs11161495	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161496	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11161497	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11161498	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161499	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11161501	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161502	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161503	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161504	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161505	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161513	0.81[EUR][1000 genomes]
rs11485283	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11485284	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11799517	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11804248	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12091131	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12130357	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12138711	0.82[EUR][1000 genomes]
rs12730688	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12754569	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1439130	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1837328	0.80[EUR][1000 genomes]
rs2389792	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389793	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486755	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3850430	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3861690	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3895846	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3904965	0.92[ASN][1000 genomes]
rs486751	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs488710	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4907017	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4907018	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4907118	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs495786	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs499539	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs513430	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs515303	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530486	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs531423	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs589653	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs600536	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs603746	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625045	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs631267	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs632545	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs648660	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs650529	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs651916	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6576736	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs662948	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6677091	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685363	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs668860	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6691674	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691970	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700622	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677476	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs679167	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs726708	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72720523	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7516329	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7516610	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7516625	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522851	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541684	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7549346	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7552445	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7553886	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv3515392	chr1:85437980-85465392	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3515393	chr1:85437980-85465392	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
9	esv3410983	chr1:85461789-85464337	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7519134	MCOLN2	cis	Esophagus Muscularis	GTEx
rs7519134	MCOLN2	cis	Artery Aorta	GTEx
rs7519134	MCOLN2	cis	Artery Tibial	GTEx
rs7519134	MCOLN2	cis	Stomach	GTEx
rs7519134	MCOLN2	cis	multi-tissue	Pritchard
rs7519134	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs7519134	MCOLN2	cis	Thyroid	GTEx
rs7519134	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85460400-85463800	Active TSS	GM12878-XiMat	blood
2	chr1:85461200-85463400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr1:85461600-85464400	Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr1:85461800-85463600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:85461800-85464400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:85461800-85464600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr1:85462000-85464200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
8	chr1:85462000-85464400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:85462000-85464400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr1:85462000-85464600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:85462200-85463400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:85462200-85463400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
14	chr1:85462200-85463600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
15	chr1:85462200-85464000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:85462200-85464200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:85462200-85464200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:85462200-85464200	Active TSS	Aorta	Aorta
19	chr1:85462400-85463400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:85462400-85463400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:85462400-85463400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr1:85462400-85463600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:85462400-85463600	Active TSS	NHDF-Ad	bronchial
24	chr1:85462400-85464200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:85462400-85464200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:85462400-85464200	Bivalent/Poised TSS	HSMM	muscle
27	chr1:85462400-85464400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr1:85462400-85464400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:85462400-85464400	Active TSS	Right Atrium	heart
30	chr1:85462600-85463400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:85462600-85463400	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:85462600-85463400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr1:85462600-85463400	Active TSS	Brain Anterior Caudate	brain
34	chr1:85462600-85463400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr1:85462600-85463400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:85462600-85463600	Bivalent Enhancer	Fetal Brain Male	brain
37	chr1:85462600-85464000	Bivalent/Poised TSS	Small Intestine	intestine
38	chr1:85462600-85464200	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr1:85462600-85464200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
40	chr1:85462600-85464200	Bivalent/Poised TSS	NHLF	lung
41	chr1:85462600-85464400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:85462600-85464400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:85462600-85464400	Active TSS	Brain Angular Gyrus	brain
44	chr1:85462600-85464600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:85462800-85463400	Bivalent/Poised TSS	Osteobl	bone
46	chr1:85463000-85463400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:85463000-85463400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
48	chr1:85463000-85463400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:85463000-85463400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr1:85463000-85463400	Flanking Active TSS	Ovary	ovary

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