Variant report

Variant	rs3759808
Chromosome Location	chr15:51199419-51199420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:160)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:160 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:51199150-51199494	K562	blood:	n/a	n/a
2	POLR2A	chr15:51199140-51201582	GM18505	blood:	n/a	n/a
3	MYC	chr15:51199308-51199431	GM12878	blood:	n/a	n/a
4	ZNF143	chr15:51199111-51201036	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:51199151-51201001	GM12892	blood:	n/a	n/a
6	RELA	chr15:51199073-51201031	GM10847	blood:	n/a	n/a
7	JUN	chr15:51199404-51199529	K562	blood:	n/a	n/a
8	POLR2A	chr15:51199231-51199467	GM12878	blood:	n/a	n/a
9	RUNX3	chr15:51199034-51201100	GM12878	blood:	n/a	n/a
10	RELA	chr15:51199101-51201316	GM15510	blood:	n/a	n/a
11	POLR2A	chr15:51199297-51201667	MCF10A-Er-Src	breast:	n/a	n/a
12	SIN3AK20	chr15:51199187-51199422	HepG2	liver:	n/a	n/a
13	EP300	chr15:51199162-51199486	GM12878	blood:	n/a	n/a
14	ATF2	chr15:51199053-51200228	GM12878	blood:	n/a	n/a
15	RELA	chr15:51199058-51201039	GM19099	blood:	n/a	n/a
16	PML	chr15:51199170-51199783	GM12878	blood:	n/a	n/a
17	MAX	chr15:51199053-51199693	HepG2	liver:	n/a	n/a
18	MXI1	chr15:51199072-51201696	GM12878	blood:	n/a	n/a
19	EP300	chr15:51199153-51200235	GM12878	blood:	n/a	chr15:51200138-51200152
20	POU2F2	chr15:51199116-51199469	GM12878	blood:	n/a	n/a
21	RFX5	chr15:51199197-51199733	GM12878	blood:	n/a	n/a
22	BCL3	chr15:51199221-51199783	GM12878	blood:	n/a	n/a
23	CTCF	chr15:51199290-51201974	A549	lung:	n/a	chr15:51200799-51200808
24	E2F6	chr15:51199146-51199446	K562	blood:	n/a	n/a
25	BCLAF1	chr15:51199038-51201064	GM12878	blood:	n/a	chr15:51200874-51200883 chr15:51200101-51200109 chr15:51200458-51200471
26	MAX	chr15:51199174-51201480	NB4	blood:	n/a	n/a
27	MAX	chr15:51199076-51199495	K562	blood:	n/a	n/a
28	MAX	chr15:51199062-51201501	A549	lung:	n/a	n/a
29	POLR2A	chr15:51199142-51201485	GM19193	blood:	n/a	n/a
30	IRF4	chr15:51199062-51199821	GM12878	blood:	n/a	n/a
31	IKZF1	chr15:51199275-51200040	GM12878	blood:	n/a	n/a
32	YY1	chr15:51199165-51199543	GM12878	blood:	n/a	n/a
33	MAX	chr15:51199160-51199535	K562	blood:	n/a	n/a
34	POLR2A	chr15:51199061-51201049	GM12878	blood:	n/a	n/a
35	POU2F2	chr15:51199136-51199831	GM12891	blood:	n/a	n/a
36	MAX	chr15:51199105-51201256	GM12878	blood:	n/a	n/a
37	TBP	chr15:51199123-51200222	GM12878	blood:	n/a	n/a
38	TBL1XR1	chr15:51199109-51201033	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:51199158-51201545	HepG2	liver:	n/a	n/a
40	BCL11A	chr15:51199186-51199767	GM12878	blood:	n/a	n/a
41	BHLHE40	chr15:51199229-51199485	K562	blood:	n/a	n/a
42	TAF1	chr15:51199241-51199484	GM12878	blood:	n/a	n/a
43	MEF2A	chr15:51199118-51199946	GM12878	blood:	n/a	n/a
44	USF2	chr15:51199214-51200461	GM12878	blood:	n/a	n/a
45	CHD1	chr15:51199147-51201265	GM12878	blood:	n/a	chr15:51200811-51200820 chr15:51200723-51200732 chr15:51200561-51200568
46	TCF12	chr15:51199146-51199468	GM12878	blood:	n/a	n/a
47	BHLHE40	chr15:51199100-51201249	GM12878	blood:	n/a	n/a
48	POU2F2	chr15:51199074-51201126	GM12878	blood:	n/a	chr15:51200290-51200302
49	POLR2A	chr15:51199132-51201313	GM12892	blood:	n/a	n/a
50	STAT5A	chr15:51199079-51201067	GM12878	blood:	n/a	chr15:51200569-51200577

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:51199395-51199445	Hepatocyte	liver:	n/a
2	chr15:51199395-51199445	AG09309	skin:	n/a
3	chr15:51199395-51199445	SAEC	small airway:	n/a
4	chr15:51199395-51199445	PANC-1	pancreas:	n/a
5	chr15:51199395-51199445	HCF	heart:	n/a
6	chr15:51199395-51199445	ECC-1	luminal epithelium:	n/a
7	chr15:51199395-51199445	GM06990	blood:	n/a
8	chr15:51199395-51199445	Jurkat	blood:	n/a
9	chr15:51199395-51199445	BJ	skin:	n/a
10	chr15:51199395-51199445	Hela-S3	cervix:	n/a
11	chr15:51199395-51199445	K562	blood:	n/a
12	chr15:51199395-51199445	HAEpiC	amniotic membrane:	n/a
13	chr15:51199395-51199445	MCF10A-Er-Src	breast:	n/a
14	chr15:51199395-51199445	SK-N-SH_RA	brain:	n/a
15	chr15:51199395-51199445	HIPEpiC	eye:	n/a
16	chr15:51199395-51199445	HL-60	blood:	n/a
17	chr15:51199395-51199445	GM12892	blood:	n/a
18	chr15:51199395-51199445	IMR90	lung:	fetal
19	chr15:51199395-51199445	NT2-D1	testis:	n/a
20	chr15:51199395-51199445	AG09319	gingival:	n/a
21	chr15:51199395-51199445	CMK	blood:	n/a
22	chr15:51199395-51199445	MCF-7	breast:	n/a
23	chr15:51199395-51199445	Caco-2	colon:	n/a
24	chr15:51199395-51199445	GM12891	blood:	n/a
25	chr15:51199395-51199445	ovcar-3	ovarian:	n/a
26	chr15:51199395-51199445	HMEC	breast:	n/a
27	chr15:51199395-51199445	T-47D	breast:	n/a
28	chr15:51199395-51199445	U87	brain:	n/a
29	chr15:51199395-51199445	PFSK-1	brain:	n/a
30	chr15:51199395-51199445	HEEpiC	esophagus:	n/a
31	chr15:51199395-51199445	HCPEpiC	choroid plexus:	n/a
32	chr15:51199395-51199445	NH-A	brain:	n/a
33	chr15:51199395-51199445	HCT-116	colon:	n/a
34	chr15:51199395-51199445	PrEC	prostate:	n/a
35	chr15:51199395-51199445	HEK293	kidney:	embryo
36	chr15:51199395-51199445	HRCEpiC	kidney:	n/a
37	chr15:51199395-51199445	RPTEC	kidney:	n/a
38	chr15:51199395-51199445	LNCaP	prostate:	n/a
39	chr15:51199395-51199445	HNPCEpiC	eye:	n/a
40	chr15:51199395-51199445	HCM	heart:	n/a
41	chr15:51199395-51199445	SKMC	muscle:	n/a
42	chr15:51199395-51199445	GM19239	blood:	n/a
43	chr15:51199395-51199445	SK-N-MC	brain:	n/a
44	chr15:51199395-51199445	AG04450	lung:	fetal
45	chr15:51199395-51199445	NB4	blood:	n/a
46	chr15:51199395-51199445	A549	lung:	n/a
47	chr15:51199395-51199445	AG04449	skin:	fetal
48	chr15:51199395-51199445	HRE	kidney:	n/a
49	chr15:51199395-51199445	BE2_C	brain:	n/a
50	chr15:51199395-51199445	HepG2	liver:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50977442..50979922-chr15:51198976..51201748,2	MCF-7	breast:
2	chr15:51183066..51185706-chr15:51196494..51200802,3	K562	blood:
3	chr15:50977828..50980537-chr15:51197788..51202411,5	MCF-7	breast:
4	chr15:51198585..51200191-chr20:47687011..47688512,2	K562	blood:
5	chr15:51197121..51199959-chr15:51225911..51227445,2	MCF-7	breast:
6	chr15:50645261..50648746-chr15:51197475..51202828,11	MCF-7	breast:
7	chr15:50645568..50648513-chr15:51198882..51201905,4	K562	blood:
8	chr15:50647013..50649194-chr15:51198882..51202798,3	K562	blood:
9	chr15:51190200..51192622-chr15:51197284..51200160,3	K562	blood:
10	chr15:51054845..51057333-chr15:51198137..51200716,3	K562	blood:
11	chr15:50967384..50968440-chr15:51199299..51199841,3	K562	blood:
12	chr15:50977199..50981459-chr15:51198510..51202863,6	K562	blood:
13	chr15:50966474..50968190-chr15:51199130..51200749,2	K562	blood:
14	chr15:51191099..51192622-chr15:51197592..51200160,2	K562	blood:
15	chr15:50977199..50979864-chr15:51198670..51201821,3	K562	blood:
16	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:
17	chr15:51055794..51057333-chr15:51198910..51200716,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPPL2A.1-1	chr15:51199113-51200792	NONHSAT042443

No data

Variant related genes	Relation type
AP4E1	TF binding region
AP4E1	CpG island
ENSG00000138600	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000243027	Chromatin interaction
ENSG00000092439	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070815	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631037	0.92[EUR][1000 genomes]
rs11633226	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635054	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439323	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619684	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619685	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755423	0.92[ASN][1000 genomes]
rs3803369	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3886394	0.83[EUR][1000 genomes]
rs4775912	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775914	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289295	0.82[EUR][1000 genomes]
rs7170736	0.81[EUR][1000 genomes]
rs72742336	0.82[EUR][1000 genomes]
rs72742362	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742383	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72744339	0.92[EUR][1000 genomes]
rs9806270	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription 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 target site	82 gene(s)	inside rSNPs	diseases
2	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1042372	chr15:50846461-51208891	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv542386	chr15:50846461-51208891	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv516168	chr15:51114437-51217361	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	esv3446414	chr15:51199106-51199455	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
16	esv3514487	chr15:51199157-51199446	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
17	esv3514488	chr15:51199157-51199446	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51177800-51199600	Weak transcription	Ovary	ovary
2	chr15:51185800-51199800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:51194800-51200000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:51195400-51199600	Weak transcription	Fetal Stomach	stomach
5	chr15:51195600-51199600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:51196000-51199600	Weak transcription	Fetal Brain Female	brain
7	chr15:51197600-51199600	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:51198800-51200000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr15:51199000-51199600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:51199000-51199600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:51199000-51199600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:51199000-51199600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:51199000-51199600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:51199000-51199600	Enhancers	Brain Cingulate Gyrus	brain
15	chr15:51199000-51199600	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr15:51199000-51199600	Flanking Active TSS	Dnd41	blood
17	chr15:51199000-51199800	Active TSS	HepG2	liver
18	chr15:51199000-51199800	Flanking Active TSS	NHEK	skin
19	chr15:51199000-51200000	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr15:51199000-51200000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr15:51199000-51200000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:51199000-51200000	Flanking Active TSS	HMEC	breast
23	chr15:51199000-51200200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:51199000-51200200	Flanking Active TSS	Liver	Liver
25	chr15:51199000-51201400	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr15:51199000-51202000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr15:51199000-51202400	Active TSS	GM12878-XiMat	blood
28	chr15:51199200-51199600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr15:51199200-51199600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr15:51199200-51199600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr15:51199200-51199600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:51199200-51199600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:51199200-51199600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr15:51199200-51199600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr15:51199200-51199600	Enhancers	Brain Anterior Caudate	brain
36	chr15:51199200-51199600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:51199200-51199600	Enhancers	Brain Substantia Nigra	brain
38	chr15:51199200-51199600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr15:51199200-51199600	Enhancers	Fetal Heart	heart
40	chr15:51199200-51199600	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr15:51199200-51199600	Enhancers	Fetal Muscle Leg	muscle
42	chr15:51199200-51199600	Enhancers	Placenta	Placenta
43	chr15:51199200-51199600	Enhancers	Gastric	stomach
44	chr15:51199200-51199600	Enhancers	Left Ventricle	heart
45	chr15:51199200-51199600	Enhancers	Lung	lung
46	chr15:51199200-51199600	Enhancers	Pancreas	Pancrea
47	chr15:51199200-51199600	Enhancers	Psoas Muscle	Psoas
48	chr15:51199200-51199600	Active TSS	Rectal Smooth Muscle	rectum
49	chr15:51199200-51199600	Enhancers	Right Atrium	heart
50	chr15:51199200-51199600	Enhancers	Right Ventricle	heart

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