Variant report

Variant	rs12896579
Chromosome Location	chr14:105225130-105225131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:105220777..105225173-chr14:105239104..105243328,5	MCF-7	breast:
2	chr14:105190542..105194071-chr14:105222962..105226590,4	MCF-7	breast:
3	chr14:105199142..105200968-chr14:105223241..105226147,2	K562	blood:
4	chr14:105224057..105226618-chr14:105232704..105234639,2	MCF-7	breast:
5	chr14:105224272..105228850-chr14:105233776..105237208,6	MCF-7	breast:
6	chr14:105222509..105227213-chr14:105256310..105261951,5	MCF-7	breast:
7	chr14:105224474..105226531-chr14:105228594..105231360,2	K562	blood:
8	chr14:105189499..105192092-chr14:105224189..105226467,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185100	Chromatin interaction
ENSG00000258430	Chromatin interaction
ENSG00000142208	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11844508	0.88[EUR][1000 genomes]
rs11850889	0.91[EUR][1000 genomes]
rs12881199	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12885343	0.91[EUR][1000 genomes]
rs12885496	0.91[EUR][1000 genomes]
rs12887774	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12892858	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12894569	0.89[EUR][1000 genomes]
rs12897418	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535133	1.00[ASN][1000 genomes]
rs34369401	1.00[ASN][1000 genomes]
rs35165446	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35455320	0.89[EUR][1000 genomes]
rs35550015	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35590716	0.86[EUR][1000 genomes]
rs35956117	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3730346	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381528	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4983542	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4983545	0.92[EUR][1000 genomes]
rs4983547	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58279280	0.82[AFR][1000 genomes]
rs71421880	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530812	chr14:104775571-105364883	Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv2830002	chr14:105078251-105348552	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv902379	chr14:105086475-105274093	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv902386	chr14:105092479-105233095	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv902387	chr14:105092479-105274093	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv902388	chr14:105092479-105311249	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
9	nsv902389	chr14:105092479-105366499	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
11	nsv902392	chr14:105105769-105274093	Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
12	nsv902394	chr14:105116232-105274093	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv902396	chr14:105119897-105274093	Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv470678	chr14:105126354-105246686	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
15	nsv566052	chr14:105126354-105268228	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
16	nsv470677	chr14:105126354-105348552	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
17	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
18	nsv566053	chr14:105139894-105268228	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
19	nsv902397	chr14:105139894-105268228	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
20	nsv517038	chr14:105146579-105311249	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
21	nsv566057	chr14:105146579-105311249	Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
22	nsv566058	chr14:105148655-105233095	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
23	nsv902403	chr14:105148655-105233095	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
24	nsv820230	chr14:105148655-105246686	ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
25	nsv566059	chr14:105148655-105268228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
26	nsv566060	chr14:105148655-105311249	Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
27	nsv902404	chr14:105148655-105311249	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
28	nsv902405	chr14:105148655-105340643	Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
29	nsv542226	chr14:105153660-105265857	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
30	nsv456455	chr14:105154105-105259734	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
31	nsv566062	chr14:105154105-105259734	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
32	nsv902407	chr14:105154105-105268228	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
33	nsv902408	chr14:105154105-105274093	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
34	nsv902409	chr14:105154105-105311249	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
35	nsv566063	chr14:105154105-105312935	Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
36	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
37	nsv902411	chr14:105163532-105268228	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
38	nsv566069	chr14:105185666-105274538	Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12896579	SIVA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105220200-105234800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:105221000-105225800	Weak transcription	Ovary	ovary
3	chr14:105221000-105229000	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:105221000-105235000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr14:105221200-105225200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:105221200-105225400	Weak transcription	NHDF-Ad	bronchial
7	chr14:105221200-105225600	Strong transcription	Osteobl	bone
8	chr14:105221200-105226400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr14:105221200-105226400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr14:105221200-105227600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr14:105221200-105229200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:105221200-105230200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:105221200-105233600	Weak transcription	HUVEC	blood vessel
14	chr14:105221200-105236000	Weak transcription	Fetal Heart	heart
15	chr14:105221400-105226000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:105221400-105227000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr14:105221400-105235200	Weak transcription	K562	blood
18	chr14:105221600-105225200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr14:105221600-105226000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:105221600-105226200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:105221600-105226400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr14:105221600-105226600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr14:105221600-105226600	Strong transcription	Rectal Smooth Muscle	rectum
24	chr14:105221600-105227400	Strong transcription	NHLF	lung
25	chr14:105221600-105227600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr14:105221600-105227800	Strong transcription	A549	lung
27	chr14:105221600-105228000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:105221600-105228000	Strong transcription	Brain Anterior Caudate	brain
29	chr14:105221600-105228000	Strong transcription	NHEK	skin
30	chr14:105221600-105228400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr14:105221600-105229000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr14:105221600-105229400	Strong transcription	Fetal Stomach	stomach
33	chr14:105221600-105230200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:105221600-105234800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr14:105221600-105253800	Weak transcription	Psoas Muscle	Psoas
36	chr14:105221800-105225400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr14:105221800-105226400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr14:105221800-105226400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr14:105221800-105226400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr14:105221800-105226400	Strong transcription	Hela-S3	cervix
41	chr14:105221800-105227200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr14:105221800-105227200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr14:105221800-105227200	Strong transcription	Colonic Mucosa	Colon
44	chr14:105221800-105227200	Strong transcription	Esophagus	oesophagus
45	chr14:105221800-105227400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:105221800-105228000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr14:105221800-105228000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr14:105221800-105228000	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr14:105221800-105228000	Strong transcription	Lung	lung
50	chr14:105221800-105228600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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