Variant report

Variant	esv3518096
Chromosome Location	chr13:50512992-50515056
allele	n/a
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	GATA3	chr13:50512911-50513111	SH-SY5Y	brain:	n/a	n/a
2	HNF4A	chr13:50513076-50513329	HepG2	liver:	n/a	chr13:50513236-50513251 chr13:50513237-50513250 chr13:50513238-50513250 chr13:50513235-50513253 chr13:50513238-50513250 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513237-50513251 chr13:50513233-50513255 chr13:50513238-50513251 chr13:50513236-50513251
3	HNF4A	chr13:50513089-50513325	HepG2	liver:	n/a	chr13:50513236-50513251 chr13:50513237-50513250 chr13:50513238-50513250 chr13:50513235-50513253 chr13:50513238-50513250 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513237-50513251 chr13:50513233-50513255 chr13:50513238-50513251 chr13:50513236-50513251
4	HNF4G	chr13:50513058-50513357	HepG2	liver:	n/a	chr13:50513236-50513251 chr13:50513237-50513250 chr13:50513238-50513250 chr13:50513237-50513252 chr13:50513235-50513253 chr13:50513238-50513250 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513236-50513251 chr13:50513237-50513251 chr13:50513233-50513255 chr13:50513238-50513251 chr13:50513236-50513251
5	POLR2A	chr13:50514307-50514367	GM12878	blood:	n/a	n/a
6	POLR2A	chr13:50514267-50514283	GM12878	blood:	n/a	n/a
7	POLR2A	chr13:50514202-50514254	GM12878	blood:	n/a	n/a
8	SPI1	chr13:50512285-50513016	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:50513235-50513285	HNPCEpiC	eye:	n/a
2	chr13:50513235-50513285	AG04449	skin:	fetal
3	chr13:50513235-50513285	PANC-1	pancreas:	n/a
4	chr13:50513235-50513285	SK-N-MC	brain:	n/a
5	chr13:50513235-50513285	NH-A	brain:	n/a
6	chr13:50513235-50513285	HMEC	breast:	n/a
7	chr13:50513235-50513285	GM12892	blood:	n/a
8	chr13:50513235-50513285	HPAEpiC	pulmonary alveolar:	n/a
9	chr13:50513235-50513285	Caco-2	colon:	n/a
10	chr13:50513235-50513285	MCF10A-Er-Src	breast:	n/a
11	chr13:50513235-50513285	SKMC	muscle:	n/a
12	chr13:50513235-50513285	Jurkat	blood:	n/a
13	chr13:50513235-50513285	HCF	heart:	n/a
14	chr13:50513235-50513285	Hepatocyte	liver:	n/a
15	chr13:50513235-50513285	Hela-S3	cervix:	n/a
16	chr13:50513235-50513285	GM06990	blood:	n/a
17	chr13:50513235-50513285	SK-N-SH	brain:	n/a
18	chr13:50513235-50513285	HAEpiC	amniotic membrane:	n/a
19	chr13:50513235-50513285	GM12891	blood:	n/a
20	chr13:50513235-50513285	BE2_C	brain:	n/a
21	chr13:50513235-50513285	HepG2	liver:	n/a
22	chr13:50513235-50513285	NHDF-neo	bronchial:	n/a
23	chr13:50513235-50513285	HL-60	blood:	n/a
24	chr13:50513235-50513285	AG09309	skin:	n/a
25	chr13:50513235-50513285	AoSMC	blood vessel:	n/a
26	chr13:50513235-50513285	MCF-7	breast:	n/a
27	chr13:50513235-50513285	A549	lung:	n/a
28	chr13:50513235-50513285	HRCEpiC	kidney:	n/a
29	chr13:50513235-50513285	GM12878	blood:	n/a
30	chr13:50513235-50513285	HUVEC	blood vessel:	n/a
31	chr13:50513235-50513285	AG09319	gingival:	n/a
32	chr13:50513235-50513285	HRE	kidney:	n/a
33	chr13:50513235-50513285	ProgFib	skin:	n/a
34	chr13:50513235-50513285	CMK	blood:	n/a
35	chr13:50513235-50513285	HEEpiC	esophagus:	n/a
36	chr13:50513235-50513285	HEK293	kidney:	embryo
37	chr13:50513235-50513285	RPTEC	kidney:	n/a
38	chr13:50513235-50513285	HCM	heart:	n/a
39	chr13:50513235-50513285	GM19239	blood:	n/a
40	chr13:50513235-50513285	ECC-1	luminal epithelium:	n/a
41	chr13:50513235-50513285	NB4	blood:	n/a
42	chr13:50513235-50513285	SK-N-SH_RA	brain:	n/a
43	chr13:50513235-50513285	HIPEpiC	eye:	n/a
44	chr13:50513235-50513285	SAEC	small airway:	n/a
45	chr13:50513235-50513285	T-47D	breast:	n/a
46	chr13:50513235-50513285	IMR90	lung:	fetal
47	chr13:50513235-50513285	LNCaP	prostate:	n/a
48	chr13:50513235-50513285	PrEC	prostate:	n/a
49	chr13:50513235-50513285	HRPEpiC	eye:	n/a
50	chr13:50513235-50513285	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50509646..50512355-chr13:50514189..50517194,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM13-7	chr13:50510782-50513292	NONHSAT033768
2	lnc-TRIM13-7	chr13:50511944-50513226	NONHSAT033769

Variant related genes	Relation type
SPRYD7	TF binding region
SPRYD7	CpG island
ENSG00000123178	chromatin interactions

Extended variants
information (count: 61 )
Associated
traits (count: 121 )

Variant overlapped rSNPs/rCNVs (count:61 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs144503481	chr13:50513182-50513183	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs556072344	chr13:50513229-50513230	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs562938209	chr13:50513233-50513234	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs146643614	chr13:50513235-50513236	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs113648456	chr13:50513252-50513253	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs551890590	chr13:50513272-50513273	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs560598746	chr13:50513340-50513341	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs386770915	chr13:50513398-50513399	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs113425684	chr13:50513434-50513435	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs549416291	chr13:50513481-50513482	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs567513881	chr13:50513527-50513528	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs732729	chr13:50513535-50513536	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs544721131	chr13:50513557-50513558	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs547355018	chr13:50513572-50513573	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs189438620	chr13:50513602-50513603	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs544684069	chr13:50513603-50513604	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs558154675	chr13:50513612-50513613	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs35599370	chr13:50513677-50513678	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs397794999	chr13:50513683-50513684	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs147397289	chr13:50513684-50513685	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs140712319	chr13:50513685-50513686	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs181243525	chr13:50513737-50513738	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs538477565	chr13:50513738-50513739	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs553427943	chr13:50513831-50513832	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs565457452	chr13:50513849-50513850	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs535811438	chr13:50513875-50513876	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs541370770	chr13:50513935-50513936	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs563292365	chr13:50513946-50513947	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs561581830	chr13:50513969-50513970	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs576035427	chr13:50514048-50514049	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs184884836	chr13:50514170-50514171	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs143349394	chr13:50514217-50514218	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs530326422	chr13:50514277-50514278	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs578095971	chr13:50514297-50514298	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs189053523	chr13:50514304-50514305	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs544035730	chr13:50514361-50514362	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs181728433	chr13:50514468-50514469	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs562270868	chr13:50514482-50514483	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs542994565	chr13:50514493-50514494	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs561120315	chr13:50514518-50514519	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs531770909	chr13:50514544-50514545	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs561579482	chr13:50514550-50514551	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs575264476	chr13:50514560-50514561	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs147999853	chr13:50514600-50514601	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs532146146	chr13:50514648-50514649	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs140777623	chr13:50514671-50514672	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs563849660	chr13:50514690-50514691	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs565395088	chr13:50514707-50514708	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs535940679	chr13:50514718-50514719	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs554689663	chr13:50514752-50514753	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:121)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Burkitt''s lymphoma	18698080	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Squamous cell cancer	20885788	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Thyroid cancer	19087340	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	17899364	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Colorectal cancer	16774939	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Myoepithelioma	18604193	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Trisomy	24170809	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Alveolar rhabdomyosarcoma	16790082	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Paraganglioma	21461997	CNVD
Pheochromocytoma	21461997	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Prostate cancer	19242612	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	17245344	CNVD
Colorectal cancer	21586687	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Retinoblastoma	19183342	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Developmental delay	21147756	CNVD
Melanoma	18172304	CNVD
Retinoblastoma	21504564	CNVD
Chronic lymphocytic leukemia	21795749	CNVD
Chronic lymphocytic leukemia	17805327	CNVD
Mental retardation	17502991	CNVD
Retinoblastoma	17502991	CNVD
Bipolar disorder	18458673	CNVD
Liposarcoma	21253554	CNVD
T-cell lymphomas	19863542	CNVD
Cervical cancer	21062161	CNVD
microdeletion syndrome	19284877	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Multiple myeloma	19135901	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Prostate cancer	16461572	CNVD
Merkel cell carcinoma	19020549	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
lymphocytic leukemia	21291569	CNVD
Multiple myeloma	17550852	CNVD
Glioblastoma multiforme	19435819	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Congenital anomalies of the kidney and urinary tract	20467480	CNVD
Breast cancer	21858162	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute myeloid leukemia	17237825	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Myelofibrosis	22110671	CNVD
Hereditary prostate cancer	22028916	CNVD
Glioblastoma multiforme	22286061	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Prostate cancer	17217626	CNVD
Ovarian cancer	21781307	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	21922591	CNVD
Metanephric adenoma	20802469	CNVD
Sezary syndrome	18413736	CNVD
Breast cancer	21990379	CNVD
Colorectal cancer	21645411	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50511400-50513000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:50511400-50537800	Weak transcription	Left Ventricle	heart
3	chr13:50511600-50513000	Enhancers	Primary hematopoietic stem cells	blood
4	chr13:50511600-50513000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr13:50511600-50513000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr13:50511600-50513000	Weak transcription	Fetal Kidney	kidney
7	chr13:50511600-50513400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr13:50511600-50513400	Enhancers	Brain Anterior Caudate	brain
9	chr13:50511600-50513800	Enhancers	HepG2	liver
10	chr13:50511600-50514600	Enhancers	Fetal Intestine Large	intestine
11	chr13:50511600-50517800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr13:50511800-50513200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr13:50511800-50513400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr13:50511800-50514200	Enhancers	Fetal Intestine Small	intestine
15	chr13:50512200-50513200	Weak transcription	Fetal Heart	heart
16	chr13:50512200-50514000	Enhancers	Adipose Nuclei	Adipose
17	chr13:50512400-50513000	Enhancers	Colonic Mucosa	Colon
18	chr13:50512400-50513000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr13:50512600-50513000	Enhancers	Liver	Liver
20	chr13:50512600-50513000	Weak transcription	Brain Germinal Matrix	brain
21	chr13:50512600-50513400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:50512600-50513400	Enhancers	Esophagus	oesophagus
23	chr13:50512600-50513400	Enhancers	Ovary	ovary
24	chr13:50512600-50514200	Enhancers	Fetal Lung	lung
25	chr13:50512600-50514400	Weak transcription	HSMMtube	muscle
26	chr13:50512600-50515600	Weak transcription	Stomach Mucosa	stomach
27	chr13:50512800-50513000	Weak transcription	Fetal Muscle Leg	muscle
28	chr13:50512800-50513600	Enhancers	Duodenum Mucosa	Duodenum
29	chr13:50512800-50513800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr13:50512800-50513800	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr13:50512800-50513800	Enhancers	NHLF	lung
32	chr13:50513000-50513400	Flanking Active TSS	Liver	Liver
33	chr13:50513000-50513400	Enhancers	Brain Germinal Matrix	brain
34	chr13:50513000-50513400	Enhancers	Fetal Muscle Leg	muscle
35	chr13:50513000-50513400	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr13:50513000-50513800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:50513000-50513800	Enhancers	Fetal Kidney	kidney
38	chr13:50513000-50514200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr13:50513200-50513400	Enhancers	Fetal Muscle Trunk	muscle
40	chr13:50513200-50513600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr13:50513200-50513800	Enhancers	Fetal Heart	heart
42	chr13:50513400-50513600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr13:50513400-50514000	Enhancers	Stomach Smooth Muscle	stomach
44	chr13:50513400-50514200	Enhancers	Liver	Liver
45	chr13:50513400-50532600	Weak transcription	Ovary	ovary
46	chr13:50513400-50532800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:50513600-50513800	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr13:50513600-50514200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr13:50513800-50514400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr13:50513800-50515400	Weak transcription	Fetal Heart	heart

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