Variant report

Variant	nsv591910
Chromosome Location	chr3:141595613-141596104
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:407)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:407 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:141595510-141595632	HepG2	liver:	n/a	n/a
2	ATF2	chr3:141595404-141595717	H1-hESC	embryonic stem cell:	n/a	n/a
3	ATF2	chr3:141595381-141595748	GM12878	blood:	n/a	n/a
4	BCL3	chr3:141595346-141595694	GM12878	blood:	n/a	chr3:141595421-141595434 chr3:141595550-141595563 chr3:141595558-141595571 chr3:141595604-141595617
5	BCLAF1	chr3:141595244-141596083	GM12878	blood:	n/a	chr3:141595421-141595434 chr3:141595550-141595563 chr3:141595558-141595571 chr3:141595883-141595892 chr3:141595878-141595891 chr3:141595881-141595894 chr3:141595604-141595617 chr3:141595886-141595895
6	BCLAF1	chr3:141595412-141595751	GM12878	blood:	n/a	chr3:141595421-141595434 chr3:141595550-141595563 chr3:141595558-141595571 chr3:141595604-141595617
7	BHLHE40	chr3:141595371-141596427	HepG2	liver:	n/a	chr3:141595604-141595620 chr3:141595582-141595598 chr3:141595929-141595945
8	BHLHE40	chr3:141595930-141596199	A549	lung:	n/a	n/a
9	BHLHE40	chr3:141595074-141596555	GM12878	blood:	n/a	chr3:141595604-141595620 chr3:141595582-141595598 chr3:141595111-141595127 chr3:141595929-141595945
10	BHLHE40	chr3:141595417-141596401	K562	blood:	n/a	chr3:141595604-141595620 chr3:141595582-141595598 chr3:141595929-141595945
11	BRCA1	chr3:141595514-141595647	H1-hESC	embryonic stem cell:	n/a	n/a
12	BRCA1	chr3:141595507-141595687	Hela-S3	cervix:	n/a	n/a
13	CCNT2	chr3:141594962-141596344	K562	blood:	n/a	n/a
14	CEBPB	chr3:141595382-141595635	Hela-S3	cervix:	n/a	n/a
15	CEBPD	chr3:141595401-141595797	K562	blood:	n/a	n/a
16	CEBPD	chr3:141595326-141595698	HepG2	liver:	n/a	n/a
17	CEBPD	chr3:141595381-141595691	HepG2	liver:	n/a	n/a
18	CHD1	chr3:141595430-141596653	H1-hESC	embryonic stem cell:	n/a	chr3:141595830-141595840
19	CHD1	chr3:141596008-141596390	GM12878	blood:	n/a	n/a
20	CHD1	chr3:141594054-141598485	IMR90	lung:	n/a	chr3:141595830-141595840
21	CHD2	chr3:141595354-141595729	GM12878	blood:	n/a	n/a
22	CHD2	chr3:141594356-141595700	Hela-S3	cervix:	n/a	n/a
23	CHD2	chr3:141595997-141596445	Hela-S3	cervix:	n/a	n/a
24	CHD2	chr3:141595443-141595707	HepG2	liver:	n/a	n/a
25	CHD2	chr3:141595492-141595749	K562	blood:	n/a	n/a
26	CHD2	chr3:141595128-141595745	H1-hESC	embryonic stem cell:	n/a	n/a
27	CREB1	chr3:141595295-141595634	A549	lung:	n/a	n/a
28	CREB1	chr3:141594339-141595850	K562	blood:	n/a	n/a
29	CREB1	chr3:141594356-141595865	GM12878	blood:	n/a	n/a
30	CREB1	chr3:141594277-141595878	H1-hESC	embryonic stem cell:	n/a	n/a
31	CREB1	chr3:141594270-141595832	HepG2	liver:	n/a	n/a
32	CREB1	chr3:141594223-141595894	GM12878	blood:	n/a	n/a
33	CREB1	chr3:141594267-141595753	K562	blood:	n/a	n/a
34	CREB1	chr3:141594288-141595836	H1-hESC	embryonic stem cell:	n/a	n/a
35	CREB1	chr3:141594323-141596430	HepG2	liver:	n/a	n/a
36	CREB1	chr3:141594692-141596298	A549	lung:	n/a	n/a
37	CTCF	chr3:141595500-141595650	GM12873	blood:	n/a	n/a
38	CTCF	chr3:141594112-141595727	SK-N-SH	brain:	n/a	chr3:141594498-141594511
39	CTCF	chr3:141595880-141596030	GM12866	blood:	n/a	n/a
40	CTCF	chr3:141595860-141596010	GM12868	blood:	n/a	n/a
41	CTCF	chr3:141595740-141595890	HUVEC	blood vessel:	n/a	n/a
42	CTCF	chr3:141595980-141596130	HCPEpiC	choroid plexus:	n/a	n/a
43	CTCF	chr3:141593822-141595775	A549	lung:	n/a	chr3:141594498-141594511
44	CTCF	chr3:141595419-141595620	MCF-7	breast:	n/a	n/a
45	CTCF	chr3:141595500-141595650	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr3:141595720-141595870	GM12866	blood:	n/a	n/a
47	E2F1	chr3:141594979-141595956	Hela-S3	cervix:	n/a	chr3:141595883-141595893
48	E2F4	chr3:141594391-141595699	K562	blood:	n/a	n/a
49	E2F4	chr3:141595019-141595658	MCF10A-Er-Src	breast:	n/a	n/a
50	E2F6	chr3:141595847-141596204	K562	blood:	n/a	chr3:141596035-141596046 chr3:141595883-141595893 chr3:141595994-141596005

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:141595655-141595705	PFSK-1	brain:	n/a
2	chr3:141595655-141595705	HCPEpiC	choroid plexus:	n/a
3	chr3:141595655-141595705	H1-hESC	embryonic stem cell:	embryo
4	chr3:141595655-141595705	HUVEC	blood vessel:	n/a
5	chr3:141595655-141595705	GM12878	blood:	n/a
6	chr3:141595655-141595705	HL-60	blood:	n/a
7	chr3:141595655-141595705	HEK293	kidney:	embryo
8	chr3:141595655-141595705	SK-N-MC	brain:	n/a
9	chr3:141595655-141595705	HMEC	breast:	n/a
10	chr3:141595655-141595705	Hepatocyte	liver:	n/a
11	chr3:141595655-141595705	HCF	heart:	n/a
12	chr3:141595655-141595705	GM19239	blood:	n/a
13	chr3:141595655-141595705	AG04450	lung:	fetal
14	chr3:141595655-141595705	IMR90	lung:	fetal
15	chr3:141595655-141595705	T-47D	breast:	n/a
16	chr3:141595655-141595705	HCM	heart:	n/a
17	chr3:141595655-141595705	HNPCEpiC	eye:	n/a
18	chr3:141595655-141595705	Hela-S3	cervix:	n/a
19	chr3:141595655-141595705	HCT-116	colon:	n/a
20	chr3:141595655-141595705	NH-A	brain:	n/a
21	chr3:141595655-141595705	AG04449	skin:	fetal
22	chr3:141595655-141595705	NHBE	bronchial:	n/a
23	chr3:141595655-141595705	AoSMC	blood vessel:	n/a
24	chr3:141595655-141595705	NHDF-neo	bronchial:	n/a
25	chr3:141595655-141595705	HEEpiC	esophagus:	n/a
26	chr3:141595655-141595705	SK-N-SH	brain:	n/a
27	chr3:141595655-141595705	HRPEpiC	eye:	n/a
28	chr3:141595655-141595705	BJ	skin:	n/a
29	chr3:141595655-141595705	ECC-1	luminal epithelium:	n/a
30	chr3:141595655-141595705	PANC-1	pancreas:	n/a
31	chr3:141595655-141595705	AG09319	gingival:	n/a
32	chr3:141595655-141595705	U87	brain:	n/a
33	chr3:141595655-141595705	K562	blood:	n/a
34	chr3:141595655-141595705	AG10803	skin:	n/a
35	chr3:141595655-141595705	Jurkat	blood:	n/a
36	chr3:141595655-141595705	HRCEpiC	kidney:	n/a
37	chr3:141595655-141595705	SK-N-SH_RA	brain:	n/a
38	chr3:141595655-141595705	CMK	blood:	n/a
39	chr3:141595655-141595705	HRE	kidney:	n/a
40	chr3:141595655-141595705	HepG2	liver:	n/a
41	chr3:141595655-141595705	MCF10A-Er-Src	breast:	n/a
42	chr3:141595655-141595705	AG09309	skin:	n/a
43	chr3:141595655-141595705	BE2_C	brain:	n/a
44	chr3:141595655-141595705	PrEC	prostate:	n/a
45	chr3:141595655-141595705	MCF-7	breast:	n/a
46	chr3:141595655-141595705	Caco-2	colon:	n/a
47	chr3:141595655-141595705	NT2-D1	testis:	n/a
48	chr3:141595655-141595705	ProgFib	skin:	n/a
49	chr3:141595655-141595705	ovcar-3	ovarian:	n/a
50	chr3:141595655-141595705	HPAEpiC	pulmonary alveolar:	n/a

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
2	chr3:141296186..141298105-chr3:141594416..141596281,2	MCF-7	breast:
3	chr1:149223784..149224456-chr3:141595271..141595955,2	Hela-S3	cervix:
4	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
5	chr3:141595410..141595997-chr5:41869285..41870151,2	Hela-S3	cervix:
6	chr1:6662875..6663586-chr3:141595164..141595828,2	HCT-116	colon:
7	chr3:141455674..141460093-chr3:141592801..141597430,19	MCF-7	breast:
8	chr3:141594460..141597483-chr3:141621419..141624479,3	K562	blood:
9	chr16:31470762..31471597-chr3:141595023..141595997,2	Hela-S3	cervix:
10	chr3:141593925..141596999-chr3:141621116..141624479,3	K562	blood:
11	chr12:54674483..54675446-chr3:141595145..141596027,2	Hela-S3	cervix:
12	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
13	chr1:26758364..26759241-chr3:141595118..141595810,2	HCT-116	colon:
14	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
15	chr3:141296069..141298248-chr3:141594604..141596170,2	K562	blood:
16	chr3:141582963..141586740-chr3:141593075..141596909,5	MCF-7	breast:
17	chr3:141456960..141457566-chr3:141595354..141595954,2	K562	blood:
18	chr3:141592835..141597303-chr3:141629979..141635181,8	MCF-7	breast:

No data

Variant related genes	Relation type
ATP1B3	TF binding region
ATP1B3	CpG island
ENSG00000260267	chromatin interactions
ENSG00000114125	chromatin interactions
ENSG00000248668	chromatin interactions
ENSG00000155903	chromatin interactions
ENSG00000200389	chromatin interactions
ENSG00000228398	chromatin interactions
ENSG00000206737	chromatin interactions
ENSG00000162413	chromatin interactions
ENSG00000117682	chromatin interactions
ENSG00000135486	chromatin interactions
ENSG00000069849	chromatin interactions
ENSG00000140691	chromatin interactions

Extended variants
information (count: 23 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11539491	chr3:141595613-141595614	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
2	rs368376011	chr3:141595618-141595619	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
3	rs371057028	chr3:141595629-141595630	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
4	rs375615647	chr3:141595638-141595639	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
5	rs375562362	chr3:141595655-141595656	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
6	rs367864943	chr3:141595668-141595669	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
7	rs566342270	chr3:141595671-141595672	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
8	rs371693282	chr3:141595685-141595686	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
9	rs144037516	chr3:141595712-141595713	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
10	rs145984073	chr3:141595739-141595740	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
11	rs576427663	chr3:141595758-141595759	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
12	rs374773348	chr3:141595782-141595783	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
13	rs369969729	chr3:141595784-141595785	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
14	rs201050651	chr3:141595787-141595788	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
15	rs574273384	chr3:141595843-141595844	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
16	rs7616510	chr3:141595883-141595884	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs559933523	chr3:141595890-141595891	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
18	rs572209352	chr3:141595930-141595931	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
19	rs550369866	chr3:141596037-141596038	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs201610346	chr3:141596069-141596070	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs554389113	chr3:141596089-141596090	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
22	rs549879776	chr3:141596091-141596092	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
23	rs138405755	chr3:141596100-141596101	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:133 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141593400-141596600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:141593400-141597400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:141593400-141597600	Active TSS	Fetal Kidney	kidney
4	chr3:141593400-141597600	Active TSS	HMEC	breast
5	chr3:141593400-141597600	Active TSS	NHLF	lung
6	chr3:141593400-141598000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:141593600-141596400	Active TSS	Pancreas	Pancrea
8	chr3:141593600-141597000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:141593600-141597000	Active TSS	Placenta	Placenta
10	chr3:141593600-141597200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:141593600-141597600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:141593600-141598400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:141593800-141596400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:141593800-141596600	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr3:141593800-141596600	Active TSS	Brain Anterior Caudate	brain
16	chr3:141593800-141596800	Active TSS	Brain Hippocampus Middle	brain
17	chr3:141593800-141596800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr3:141593800-141596800	Active TSS	Fetal Brain Female	brain
19	chr3:141593800-141596800	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr3:141593800-141596800	Active TSS	Thymus	Thymus
21	chr3:141593800-141597200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:141593800-141597200	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:141593800-141597200	Active TSS	NH-A	brain
24	chr3:141593800-141597200	Active TSS	NHDF-Ad	bronchial
25	chr3:141593800-141597400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:141593800-141597400	Active TSS	Stomach Smooth Muscle	stomach
27	chr3:141593800-141597400	Active TSS	HSMMtube	muscle
28	chr3:141593800-141597600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:141593800-141597600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr3:141593800-141597600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:141593800-141597600	Active TSS	Fetal Intestine Large	intestine
32	chr3:141593800-141597600	Active TSS	HSMM	muscle
33	chr3:141593800-141598000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:141593800-141598000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:141593800-141598000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:141593800-141598400	Active TSS	H1 Cell Line	embryonic stem cell
37	chr3:141594000-141596000	Active TSS	Primary hematopoietic stem cells	blood
38	chr3:141594000-141596200	Active TSS	Rectal Smooth Muscle	rectum
39	chr3:141594000-141596600	Active TSS	Brain Substantia Nigra	brain
40	chr3:141594000-141596800	Active TSS	Brain Angular Gyrus	brain
41	chr3:141594000-141597600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr3:141594000-141597600	Active TSS	Fetal Muscle Leg	muscle
43	chr3:141594000-141597600	Active TSS	Right Ventricle	heart
44	chr3:141594000-141598000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr3:141594200-141596800	Active TSS	Brain Germinal Matrix	brain
46	chr3:141594200-141597000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:141594200-141597600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:141594200-141598000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:141594200-141598000	Active TSS	Colonic Mucosa	Colon
50	chr3:141594400-141596200	Active TSS	Primary B cells from cord blood	blood

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