Variant report

Variant	rs2960347
Chromosome Location	chr19:38997679-38997680
allele	G/T
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	HCFC1	chr19:38997505-38997701	K562	blood:	n/a	n/a
2	CTCF	chr19:38997425-38997853	K562	blood:	n/a	n/a
3	YY1	chr19:38997512-38997803	GM12891	blood:	n/a	n/a
4	ZMIZ1	chr19:38997249-38997717	K562	blood:	n/a	n/a
5	MAZ	chr19:38997537-38998071	Hela-S3	cervix:	n/a	n/a
6	MAX	chr19:38997445-38997796	SK-N-SH	brain:	n/a	n/a
7	SP1	chr19:38997236-38998197	A549	lung:	n/a	chr19:38997654-38997664 chr19:38997783-38997793 chr19:38997783-38997792 chr19:38997718-38997729 chr19:38997751-38997763 chr19:38997753-38997762 chr19:38997650-38997664 chr19:38997751-38997762 chr19:38997653-38997665 chr19:38997653-38997665 chr19:38997654-38997663 chr19:38997782-38997794 chr19:38997751-38997763 chr19:38997784-38997793 chr19:38997654-38997664 chr19:38997655-38997664 chr19:38997655-38997664 chr19:38997782-38997794
8	SPI1	chr19:38997543-38997974	GM12878	blood:	n/a	n/a
9	CCNT2	chr19:38997459-38997921	K562	blood:	n/a	chr19:38997654-38997663
10	NR2F2	chr19:38997353-38997977	K562	blood:	n/a	n/a
11	E2F6	chr19:38997329-38997921	K562	blood:	n/a	n/a
12	ELF1	chr19:38997378-38998087	K562	blood:	n/a	n/a
13	ELK1	chr19:38997528-38997772	K562	blood:	n/a	n/a
14	MAZ	chr19:38997529-38997923	GM12878	blood:	n/a	n/a
15	MYC	chr19:38997295-38997921	K562	blood:	n/a	n/a
16	SP1	chr19:38997287-38998177	A549	lung:	n/a	chr19:38997654-38997664 chr19:38997783-38997793 chr19:38997783-38997792 chr19:38997718-38997729 chr19:38997751-38997763 chr19:38997753-38997762 chr19:38997650-38997664 chr19:38997751-38997762 chr19:38997653-38997665 chr19:38997653-38997665 chr19:38997654-38997663 chr19:38997782-38997794 chr19:38997751-38997763 chr19:38997784-38997793 chr19:38997654-38997664 chr19:38997655-38997664 chr19:38997655-38997664 chr19:38997782-38997794
17	RCOR1	chr19:38997416-38997952	K562	blood:	n/a	n/a
18	MAX	chr19:38997012-38997947	A549	lung:	n/a	n/a
19	E2F6	chr19:38997332-38997881	A549	lung:	n/a	n/a
20	IRF1	chr19:38997152-38997950	K562	blood:	n/a	chr19:38997782-38997796 chr19:38997751-38997765 chr19:38997653-38997667
21	POLR2A	chr19:38997390-38997787	HCT-116	colon:	n/a	n/a
22	CREB1	chr19:38997433-38997995	A549	lung:	n/a	n/a
23	MAX	chr19:38997361-38997817	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:38997450-38997707	A549	lung:	n/a	n/a
25	POLR2A	chr19:38997423-38997794	HCT-116	colon:	n/a	n/a
26	POLR2A	chr19:38997372-38997798	MCF-7	breast:	n/a	n/a
27	POLR2A	chr19:38997384-38997799	A549	lung:	n/a	n/a
28	SP1	chr19:38997376-38998099	H1-hESC	embryonic stem cell:	n/a	chr19:38997654-38997664 chr19:38997783-38997793 chr19:38997783-38997792 chr19:38997718-38997729 chr19:38997751-38997763 chr19:38997753-38997762 chr19:38997650-38997664 chr19:38997751-38997762 chr19:38997653-38997665 chr19:38997653-38997665 chr19:38997654-38997663 chr19:38997782-38997794 chr19:38997751-38997763 chr19:38997784-38997793 chr19:38997654-38997664 chr19:38997655-38997664 chr19:38997655-38997664 chr19:38997782-38997794
29	TBP	chr19:38997408-38997919	K562	blood:	n/a	n/a
30	IRF1	chr19:38997374-38998356	K562	blood:	n/a	chr19:38997782-38997796 chr19:38997751-38997765 chr19:38997653-38997667
31	MAZ	chr19:38997331-38998333	K562	blood:	n/a	n/a
32	GABPA	chr19:38997358-38997736	K562	blood:	n/a	n/a
33	POLR2A	chr19:38997437-38997724	A549	lung:	n/a	n/a
34	TEAD4	chr19:38997364-38997769	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:38997361-38997822	K562	blood:	n/a	n/a
36	MAX	chr19:38997308-38997820	A549	lung:	n/a	n/a
37	MAX	chr19:38997407-38997907	K562	blood:	n/a	n/a
38	POLR2A	chr19:38997455-38997700	A549	lung:	n/a	n/a
39	TCF12	chr19:38997539-38997756	GM12878	blood:	n/a	chr19:38997618-38997628
40	MAX	chr19:38997379-38997767	K562	blood:	n/a	n/a
41	E2F6	chr19:38997221-38997864	H1-hESC	embryonic stem cell:	n/a	n/a
42	HEY1	chr19:38997388-38997714	K562	blood:	n/a	n/a
43	MAX	chr19:38997351-38997864	MCF-7	breast:	n/a	n/a
44	TCF7L2	chr19:38997127-38997693	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr19:38997392-38997772	MCF-7	breast:	n/a	n/a
46	MAX	chr19:38997448-38997869	ECC-1	luminal epithelium:	n/a	n/a
47	NFYB	chr19:38997632-38997832	Hela-S3	cervix:	n/a	n/a
48	E2F6	chr19:38997050-38997804	K562	blood:	n/a	n/a
49	E2F4	chr19:38997535-38997994	MCF10A-Er-Src	breast:	n/a	n/a
50	SP4	chr19:38997373-38998009	H1-hESC	embryonic stem cell:	n/a	chr19:38997718-38997729 chr19:38997751-38997762 chr19:38997649-38997665 chr19:38997780-38997796 chr19:38997651-38997667

No.	Distal block	Cell Line	Cell type
1	chr19:38966809..38968842-chr19:38996344..38998675,2	K562	blood:
2	chr19:38942941..38945544-chr19:38995924..38999103,4	K562	blood:
3	chr19:38996337..38999179-chr19:39339414..39341961,3	K562	blood:
4	chr19:38995901..38997990-chr19:39057193..39059011,2	K562	blood:
5	chr19:38996312..38998030-chr19:39136647..39139239,2	K562	blood:
6	chr19:38996424..38999346-chr19:39017618..39019958,2	K562	blood:
7	chr19:38990098..38992675-chr19:38995996..38998496,3	K562	blood:
8	chr19:38991175..38993486-chr19:38996742..38999270,3	K562	blood:
9	chr19:38878587..38880206-chr19:38996146..38998236,2	K562	blood:
10	chr19:38892294..38894337-chr19:38997304..39000049,2	MCF-7	breast:
11	chr19:38995826..38998096-chr19:39027051..39028960,2	K562	blood:
12	chr19:38892986..38895865-chr19:38996015..38998025,2	K562	blood:
13	chr19:38996233..38998057-chr19:39033853..39035583,2	K562	blood:
14	chr19:38892071..38894486-chr19:38996089..38998025,2	K562	blood:
15	chr19:38996461..38998048-chr19:39086974..39089806,2	K562	blood:
16	chr19:38997159..38998011-chr9:35531211..35531711,2	NB4	blood:
17	chr19:38863683..38866676-chr19:38996103..38998198,2	K562	blood:
18	chr19:38984014..38986656-chr19:38996185..38997730,2	K562	blood:
19	chr19:38983899..38986656-chr19:38994778..38998627,3	K562	blood:
20	chr19:38994667..38998309-chr19:39006613..39008813,3	K562	blood:

Variant related genes	Relation type
RYR1	TF binding region
ENSG00000269445	Chromatin interaction
ENSG00000267291	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000268055	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11880187	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469695	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469699	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1473249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071089	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163823	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2229144	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2229146	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2459634	0.80[EUR][1000 genomes]
rs2915949	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2915950	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2915951	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915953	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915954	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915959	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960330	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2960331	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960332	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2960333	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2960334	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960340	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2960342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960343	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960346	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2960348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802515	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58360688	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv911666	chr19:38948356-39014184	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2960347	CAPN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38934800-39005600	Strong transcription	Fetal Muscle Leg	muscle
2	chr19:38940000-39006400	Weak transcription	HSMM	muscle
3	chr19:38960800-39034400	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr19:38963000-39033000	Strong transcription	Skeletal Muscle Male	skeletal muscle
5	chr19:38976800-39005400	Weak transcription	Brain Anterior Caudate	brain
6	chr19:38981600-39005600	Weak transcription	Brain Substantia Nigra	brain
7	chr19:38981800-39005400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:38982200-39005600	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
10	chr19:38988200-39005400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr19:38989400-39000000	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr19:38989800-38999200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:38996200-39007800	Weak transcription	Right Atrium	heart
14	chr19:38997000-38997800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr19:38997000-38997800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr19:38997000-38997800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr19:38997000-38997800	Enhancers	Spleen	Spleen
18	chr19:38997000-38998800	Genic enhancers	H1 Cell Line	embryonic stem cell
19	chr19:38997200-38997800	Enhancers	Colonic Mucosa	Colon
20	chr19:38997200-38998000	Bivalent Enhancer	Placenta	Placenta
21	chr19:38997200-38998400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
22	chr19:38997200-38998400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:38997200-38998600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr19:38997200-38998600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:38997400-38997800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:38997400-38997800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr19:38997400-38997800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:38997400-38997800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr19:38997400-38997800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:38997400-38997800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:38997400-38997800	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr19:38997400-38997800	Bivalent Enhancer	Fetal Stomach	stomach
33	chr19:38997400-38997800	Enhancers	Lung	lung
34	chr19:38997400-38997800	Enhancers	Pancreas	Pancrea
35	chr19:38997400-38997800	Bivalent Enhancer	Right Ventricle	heart
36	chr19:38997400-38997800	Enhancers	Stomach Mucosa	stomach
37	chr19:38997400-38997800	Enhancers	Thymus	Thymus
38	chr19:38997400-38998000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:38997400-38998400	Enhancers	Primary B cells from peripheral blood	blood
40	chr19:38997400-38998400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:38997400-38998400	Enhancers	Ovary	ovary
42	chr19:38997400-38998400	Enhancers	HMEC	breast
43	chr19:38997400-38998600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:38997600-38997800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr19:38997600-38997800	Enhancers	Adipose Nuclei	Adipose
46	chr19:38997600-38998200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:38997600-38998200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:38997600-38998200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr19:38997600-38998200	Active TSS	A549	lung
50	chr19:38997600-38998200	Weak transcription	HSMMtube	muscle

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