Variant report

Variant	esv3322354
Chromosome Location	chr3:20228442-20229010
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:20226943-20228838	K562	blood:	n/a	n/a
2	CHD1	chr3:20226793-20228483	GM12878	blood:	n/a	n/a
3	CHD1	chr3:20227929-20228445	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F4	chr3:20225431-20228757	MCF10A-Er-Src	breast:	n/a	chr3:20227701-20227712 chr3:20228378-20228392
5	ELF1	chr3:20227154-20228463	MCF-7	breast:	n/a	chr3:20227453-20227464
6	GATA1	chr3:20227061-20228485	PBDE	blood:	n/a	n/a
7	HCFC1	chr3:20226936-20228532	Hela-S3	cervix:	n/a	n/a
8	IRF1	chr3:20227074-20228463	K562	blood:	n/a	chr3:20228107-20228127 chr3:20227111-20227120 chr3:20228111-20228125
9	JUND	chr3:20227274-20228540	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:20226811-20228497	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr3:20226633-20228740	IMR90	lung:	n/a	n/a
12	MXI1	chr3:20226632-20229279	SK-N-SH	brain:	n/a	n/a
13	MXI1	chr3:20226674-20228494	GM12878	blood:	n/a	n/a
14	MYC	chr3:20226922-20228555	K562	blood:	n/a	n/a
15	NR2F2	chr3:20227122-20228498	K562	blood:	n/a	n/a
16	PML	chr3:20227020-20228448	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:20226431-20229063	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr3:20226670-20229394	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:20227367-20228448	IMR90	lung:	n/a	n/a
20	POLR2A	chr3:20226133-20228701	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:20226822-20229091	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:20226769-20229489	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:20226441-20229232	GM19099	blood:	n/a	n/a
24	POLR2A	chr3:20226840-20229172	GM18505	blood:	n/a	n/a
25	POLR2A	chr3:20226728-20228549	GM15510	blood:	n/a	n/a
26	POLR2A	chr3:20227401-20228857	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:20226888-20228507	GM18526	blood:	n/a	n/a
28	POLR2A	chr3:20227412-20228491	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr3:20227041-20228824	PBDE	blood:	n/a	n/a
30	RAD21	chr3:20226976-20228537	IMR90	lung:	n/a	chr3:20228032-20228041
31	RCOR1	chr3:20227502-20228516	Hela-S3	cervix:	n/a	n/a
32	RCOR1	chr3:20226890-20228566	K562	blood:	n/a	n/a
33	RELA	chr3:20226821-20228520	GM15510	blood:	n/a	n/a
34	RELA	chr3:20227025-20228485	GM19099	blood:	n/a	n/a
35	RELA	chr3:20226886-20228455	GM12878	blood:	n/a	n/a
36	REST	chr3:20227418-20228590	H1-neurons	neurons:	n/a	n/a
37	RUNX3	chr3:20227101-20228603	GM12878	blood:	n/a	chr3:20228433-20228450
38	RUNX3	chr3:20226770-20228498	GM12878	blood:	n/a	chr3:20228433-20228450
39	SIN3AK20	chr3:20226850-20228480	SK-N-SH	brain:	n/a	n/a
40	SIN3AK20	chr3:20226774-20228496	MCF-7	breast:	n/a	n/a
41	SMC3	chr3:20227603-20228470	Hela-S3	cervix:	n/a	n/a
42	STAT3	chr3:20227737-20228474	GM12878	blood:	n/a	n/a
43	STAT3	chr3:20228710-20228743	MCF10A-Er-Src	breast:	n/a	chr3:20228731-20228742
44	STAT5A	chr3:20227164-20228516	K562	blood:	n/a	n/a
45	TBL1XR1	chr3:20226966-20228612	GM12878	blood:	n/a	n/a
46	TBL1XR1	chr3:20227079-20228974	K562	blood:	n/a	n/a
47	TBP	chr3:20226556-20228480	GM12878	blood:	n/a	n/a
48	TBP	chr3:20227459-20228455	HepG2	liver:	n/a	n/a
49	TCF12	chr3:20227094-20228463	A549	lung:	n/a	n/a
50	UBTF	chr3:20226925-20228771	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:20228976-20229026	GM06990	blood:	n/a
2	chr3:20228976-20229026	U87	brain:	n/a
3	chr3:20228976-20229026	PrEC	prostate:	n/a
4	chr3:20228976-20229026	NT2-D1	testis:	n/a
5	chr3:20228976-20229026	SK-N-SH_RA	brain:	n/a
6	chr3:20228976-20229026	Hela-S3	cervix:	n/a
7	chr3:20228976-20229026	HepG2	liver:	n/a
8	chr3:20228976-20229026	ProgFib	skin:	n/a
9	chr3:20228976-20229026	SKMC	muscle:	n/a
10	chr3:20228976-20229026	NB4	blood:	n/a
11	chr3:20228976-20229026	NH-A	brain:	n/a
12	chr3:20228976-20229026	GM12878	blood:	n/a
13	chr3:20228976-20229026	HEK293	kidney:	embryo
14	chr3:20228976-20229026	HNPCEpiC	eye:	n/a
15	chr3:20228976-20229026	HIPEpiC	eye:	n/a
16	chr3:20228976-20229026	GM12892	blood:	n/a
17	chr3:20228976-20229026	H1-hESC	embryonic stem cell:	embryo
18	chr3:20228976-20229026	A549	lung:	n/a
19	chr3:20228976-20229026	SAEC	small airway:	n/a
20	chr3:20228976-20229026	T-47D	breast:	n/a
21	chr3:20228976-20229026	HCM	heart:	n/a
22	chr3:20228976-20229026	HMEC	breast:	n/a
23	chr3:20228976-20229026	PFSK-1	brain:	n/a
24	chr3:20228976-20229026	BJ	skin:	n/a
25	chr3:20228976-20229026	CMK	blood:	n/a
26	chr3:20228976-20229026	HCF	heart:	n/a
27	chr3:20228976-20229026	HRCEpiC	kidney:	n/a
28	chr3:20228976-20229026	SK-N-SH	brain:	n/a
29	chr3:20228976-20229026	IMR90	lung:	fetal
30	chr3:20228976-20229026	HCPEpiC	choroid plexus:	n/a
31	chr3:20228976-20229026	ovcar-3	ovarian:	n/a
32	chr3:20228976-20229026	SK-N-MC	brain:	n/a
33	chr3:20228976-20229026	AG04449	skin:	fetal
34	chr3:20228976-20229026	AoSMC	blood vessel:	n/a
35	chr3:20228976-20229026	HAEpiC	amniotic membrane:	n/a
36	chr3:20228976-20229026	AG09309	skin:	n/a
37	chr3:20228976-20229026	AG10803	skin:	n/a
38	chr3:20228976-20229026	HCT-116	colon:	n/a
39	chr3:20228976-20229026	HRE	kidney:	n/a
40	chr3:20228976-20229026	MCF-7	breast:	n/a
41	chr3:20228976-20229026	LNCaP	prostate:	n/a
42	chr3:20228976-20229026	AG09319	gingival:	n/a
43	chr3:20228976-20229026	RPTEC	kidney:	n/a
44	chr3:20228976-20229026	HL-60	blood:	n/a
45	chr3:20228976-20229026	MCF10A-Er-Src	breast:	n/a
46	chr3:20228976-20229026	NHBE	bronchial:	n/a
47	chr3:20228976-20229026	Hepatocyte	liver:	n/a
48	chr3:20228976-20229026	PANC-1	pancreas:	n/a
49	chr3:20228976-20229026	K562	blood:	n/a
50	chr3:20228976-20229026	GM12891	blood:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:20213813..20216501-chr3:20227432..20229116,2	MCF-7	breast:
2	chr3:20226448..20228980-chr3:20231144..20234755,4	MCF-7	breast:
3	chr3:20212661..20217850-chr3:20224065..20229766,9	K562	blood:
4	chr3:20227937..20230614-chr3:20238703..20240365,2	K562	blood:
5	chr3:20228018..20229588-chr3:20240700..20242261,2	K562	blood:
6	chr3:20227831..20229515-chr3:20229924..20231692,2	MCF-7	breast:
7	chr3:20197490..20199260-chr3:20227955..20230018,2	K562	blood:
8	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
9	chr3:20094893..20096727-chr3:20227964..20230863,2	MCF-7	breast:
10	chr3:20079279..20082964-chr3:20226299..20229620,6	K562	blood:
11	chr3:20225377..20229978-chr3:20232761..20235716,5	K562	blood:
12	chr3:20079527..20082964-chr3:20226742..20229620,4	K562	blood:
13	chr3:20219250..20222131-chr3:20228592..20230370,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KAT2B-1	chr3:20227726-20230848	NONHSAT088617

No data

Variant related genes	Relation type
SGOL1	TF binding region
SGOL1	CpG island
ENSG00000252442	chromatin interactions
ENSG00000129810	chromatin interactions
ENSG00000163576	chromatin interactions
ENSG00000144566	chromatin interactions
ENSG00000237485	chromatin interactions
ENSG00000114166	chromatin interactions

Extended variants
information (count: 22 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs114760018	chr3:20228446-20228447	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
2	rs553145878	chr3:20228453-20228454	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
3	rs138668145	chr3:20228500-20228501	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
4	rs574973889	chr3:20228588-20228589	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
5	rs36041171	chr3:20228598-20228599	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
6	rs79463437	chr3:20228613-20228614	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
7	rs112941085	chr3:20228619-20228620	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
8	rs187481345	chr3:20228657-20228658	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
9	rs376838781	chr3:20228672-20228673	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
10	rs576109124	chr3:20228734-20228735	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
11	rs543408301	chr3:20228753-20228754	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
12	rs1995722	chr3:20228770-20228771	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs192723897	chr3:20228780-20228781	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
14	rs541385633	chr3:20228793-20228794	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
15	rs17006713	chr3:20228844-20228845	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs529812049	chr3:20228845-20228846	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
17	rs548371287	chr3:20228860-20228861	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
18	rs77332067	chr3:20228865-20228866	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
19	rs184557622	chr3:20228913-20228914	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
20	rs552128914	chr3:20228916-20228917	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
21	rs149318824	chr3:20228997-20228998	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a
22	rs530100229	chr3:20229000-20229001	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD

Chromatin state (count:224 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20224600-20229000	Active TSS	GM12878-XiMat	blood
2	chr3:20225800-20228600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:20225800-20228600	Active TSS	K562	blood
4	chr3:20225800-20228800	Active TSS	HMEC	breast
5	chr3:20225800-20229000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:20226000-20228600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr3:20226000-20228600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:20226000-20228600	Active TSS	Thymus	Thymus
9	chr3:20226000-20228800	Active TSS	NHDF-Ad	bronchial
10	chr3:20226000-20229000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:20226000-20229000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:20226000-20229000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:20226200-20228800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:20226200-20228800	Active TSS	NHEK	skin
15	chr3:20226200-20229000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:20226200-20229200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr3:20226200-20229200	Active TSS	NHLF	lung
18	chr3:20226400-20228600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:20226400-20228600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:20226400-20228600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:20226400-20228800	Active TSS	Fetal Stomach	stomach
22	chr3:20226400-20229000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:20226400-20229000	Active TSS	Fetal Intestine Large	intestine
24	chr3:20226400-20229200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:20226600-20228600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:20226600-20228600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:20226600-20228600	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:20226600-20228800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr3:20226600-20228800	Active TSS	A549	lung
30	chr3:20226600-20229000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:20226600-20229000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:20226600-20229600	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:20226800-20228600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr3:20226800-20228600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:20226800-20228600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:20226800-20228600	Active TSS	Fetal Kidney	kidney
37	chr3:20226800-20228600	Active TSS	Fetal Muscle Trunk	muscle
38	chr3:20226800-20228600	Active TSS	HSMMtube	muscle
39	chr3:20226800-20228800	Active TSS	Colonic Mucosa	Colon
40	chr3:20226800-20228800	Active TSS	Colon Smooth Muscle	Colon
41	chr3:20226800-20229000	Active TSS	Fetal Intestine Small	intestine
42	chr3:20226800-20229200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:20227000-20228600	Active TSS	Aorta	Aorta
44	chr3:20227000-20228600	Active TSS	Left Ventricle	heart
45	chr3:20227000-20228600	Active TSS	Small Intestine	intestine
46	chr3:20227000-20228600	Active TSS	Stomach Mucosa	stomach
47	chr3:20227000-20228800	Active TSS	Fetal Brain Male	brain
48	chr3:20227000-20228800	Active TSS	Psoas Muscle	Psoas
49	chr3:20227000-20228800	Bivalent/Poised TSS	HepG2	liver
50	chr3:20227000-20229000	Active TSS	Brain Inferior Temporal Lobe	brain

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