Variant report

Variant	rs3895064
Chromosome Location	chr6:31928238-31928239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:31928160-31928310	NHLF	lung:	n/a	n/a
2	MAZ	chr6:31926085-31928360	IMR90	lung:	n/a	n/a
3	POLR2A	chr6:31928149-31928256	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31928234-31928284	NB4	blood:	n/a
2	chr6:31928234-31928284	HUVEC	blood vessel:	n/a
3	chr6:31928234-31928284	Hela-S3	cervix:	n/a
4	chr6:31928234-31928284	HEK293	kidney:	embryo
5	chr6:31928234-31928284	RPTEC	kidney:	n/a
6	chr6:31928234-31928284	MCF10A-Er-Src	breast:	n/a
7	chr6:31928234-31928284	HPAEpiC	pulmonary alveolar:	n/a
8	chr6:31928234-31928284	SAEC	small airway:	n/a
9	chr6:31928234-31928284	HCM	heart:	n/a
10	chr6:31928234-31928284	AG04449	skin:	fetal
11	chr6:31928234-31928284	GM06990	blood:	n/a
12	chr6:31928234-31928284	AG09309	skin:	n/a
13	chr6:31928234-31928284	T-47D	breast:	n/a
14	chr6:31928234-31928284	HCF	heart:	n/a
15	chr6:31928234-31928284	ovcar-3	ovarian:	n/a
16	chr6:31928234-31928284	SK-N-SH_RA	brain:	n/a
17	chr6:31928234-31928284	SKMC	muscle:	n/a
18	chr6:31928234-31928284	Hepatocyte	liver:	n/a
19	chr6:31928234-31928284	HAEpiC	amniotic membrane:	n/a
20	chr6:31928234-31928284	NH-A	brain:	n/a
21	chr6:31928234-31928284	NT2-D1	testis:	n/a
22	chr6:31928234-31928284	HRCEpiC	kidney:	n/a
23	chr6:31928234-31928284	A549	lung:	n/a
24	chr6:31928234-31928284	HRE	kidney:	n/a
25	chr6:31928234-31928284	GM12892	blood:	n/a
26	chr6:31928234-31928284	HepG2	liver:	n/a
27	chr6:31928234-31928284	U87	brain:	n/a
28	chr6:31928234-31928284	AG04450	lung:	fetal
29	chr6:31928234-31928284	BJ	skin:	n/a
30	chr6:31928234-31928284	GM12878	blood:	n/a
31	chr6:31928234-31928284	BE2_C	brain:	n/a
32	chr6:31928234-31928284	K562	blood:	n/a
33	chr6:31928234-31928284	SK-N-MC	brain:	n/a
34	chr6:31928234-31928284	HMEC	breast:	n/a
35	chr6:31928234-31928284	Caco-2	colon:	n/a
36	chr6:31928234-31928284	HRPEpiC	eye:	n/a
37	chr6:31928234-31928284	HL-60	blood:	n/a
38	chr6:31928234-31928284	NHBE	bronchial:	n/a
39	chr6:31928234-31928284	AG10803	skin:	n/a
40	chr6:31928234-31928284	PrEC	prostate:	n/a
41	chr6:31928234-31928284	AG09319	gingival:	n/a
42	chr6:31928234-31928284	CMK	blood:	n/a
43	chr6:31928234-31928284	MCF-7	breast:	n/a
44	chr6:31928234-31928284	HNPCEpiC	eye:	n/a
45	chr6:31928234-31928284	PANC-1	pancreas:	n/a
46	chr6:31928234-31928284	ECC-1	luminal epithelium:	n/a
47	chr6:31928234-31928284	PFSK-1	brain:	n/a
48	chr6:31928234-31928284	HCT-116	colon:	n/a
49	chr6:31928234-31928284	LNCaP	prostate:	n/a
50	chr6:31928234-31928284	IMR90	lung:	fetal

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31631207..31634109-chr6:31926807..31929140,3	K562	blood:
2	chr6:31844767..31847605-chr6:31925658..31928567,2	MCF-7	breast:
3	chr6:31862879..31872535-chr6:31911667..31928766,47	MCF-7	breast:
4	chr6:31864040..31872511-chr6:31917614..31930102,27	MCF-7	breast:
5	chr6:31894560..31897888-chr6:31924484..31928410,3	K562	blood:
6	chr6:31867075..31869848-chr6:31926953..31928795,2	K562	blood:
7	chr6:31799457..31804164-chr6:31924693..31928301,4	K562	blood:
8	chr6:31867895..31873109-chr6:31925613..31930389,7	K562	blood:
9	chr6:31800911..31802775-chr6:31927377..31929247,2	MCF-7	breast:
10	chr6:31886651..31888947-chr6:31926731..31929141,2	MCF-7	breast:
11	chr6:31742931..31744824-chr6:31926408..31928564,2	K562	blood:

No data

Variant related genes	Relation type
NELFE	TF binding region
SKIV2L	TF binding region
MIR1236	TF binding region
NELFE	CpG island
SKIV2L	CpG island
MIR1236	CpG island
ENSG00000263020	Chromatin interaction
ENSG00000201823	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000204385	Chromatin interaction
ENSG00000244255	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204366	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000204438	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs2071290	1.00[AFR][1000 genomes]
rs2075563	1.00[AMR][1000 genomes]
rs2075701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2242568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2269428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2280773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34467149	1.00[AMR][1000 genomes]
rs3749960	1.00[AMR][1000 genomes]
rs3749961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3749963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4711281	1.00[AFR][1000 genomes]
rs4713492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713504	1.00[AFR][1000 genomes]
rs4947252	1.00[ASN][1000 genomes]
rs4959020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4959022	1.00[AFR][1000 genomes]
rs4959023	1.00[AFR][1000 genomes]
rs4959082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57967962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58478632	0.85[AMR][1000 genomes]
rs58912491	1.00[AFR][1000 genomes]
rs59002496	1.00[ASN][1000 genomes]
rs60149397	0.83[ASN][1000 genomes]
rs60900316	1.00[ASN][1000 genomes]
rs7383256	1.00[AMR][1000 genomes]
rs9800604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS 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 miRNA target site	370 gene(s)	inside rSNPs	diseases
2	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
3	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
5	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
7	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
9	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
10	nsv601950	chr6:31785438-32492308	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
11	nsv601951	chr6:31785438-32496748	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
12	nsv601955	chr6:31785453-32484368	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
13	nsv601956	chr6:31785453-32492308	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
14	nsv601961	chr6:31868322-32484368	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
15	nsv427751	chr6:31871512-32092843	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	91 gene(s)	inside rSNPs	diseases
16	nsv428141	chr6:31871512-32092843	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
17	esv2758043	chr6:31871512-32209113	Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
18	esv2759415	chr6:31871512-32209113	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
19	nsv830628	chr6:31887554-31947600	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
20	nsv933250	chr6:31905060-32008005	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
21	nsv934279	chr6:31905060-32013902	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
22	nsv884512	chr6:31908470-31933161	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
23	nsv884513	chr6:31922575-32066025	Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
24	nsv884514	chr6:31923052-31958960	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
25	nsv932869	chr6:31924496-32013902	Weak transcription Genic enhancers Enhancers Flanking Active TSS 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	73 gene(s)	inside rSNPs	diseases
26	nsv933913	chr6:31924682-32009282	Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
27	nsv284	chr6:31925739-31996721	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
28	nsv5247	chr6:31925739-32023216	Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31927400-31928800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:31927400-31928800	Weak transcription	Aorta	Aorta
3	chr6:31927400-31929600	Weak transcription	Psoas Muscle	Psoas
4	chr6:31927400-31938800	Weak transcription	Right Atrium	heart
5	chr6:31927600-31928400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:31927600-31928400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:31927600-31928400	Enhancers	Right Ventricle	heart
8	chr6:31927600-31928400	Genic enhancers	Thymus	Thymus
9	chr6:31927600-31928600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:31927600-31928600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:31927600-31928600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:31927600-31928800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:31927600-31929000	Weak transcription	Left Ventricle	heart
14	chr6:31927600-31929400	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr6:31927600-31937000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:31927600-31939400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:31927800-31928400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:31927800-31928400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:31927800-31928400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:31927800-31928400	Genic enhancers	Primary T cells from cord blood	blood
21	chr6:31927800-31928400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
22	chr6:31927800-31928400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:31927800-31928400	Genic enhancers	Liver	Liver
24	chr6:31927800-31928400	Weak transcription	Fetal Lung	lung
25	chr6:31927800-31928600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:31927800-31928600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:31927800-31928600	Weak transcription	Fetal Brain Male	brain
28	chr6:31927800-31928800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:31927800-31928800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:31927800-31929200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:31927800-31929400	Weak transcription	Small Intestine	intestine
32	chr6:31927800-31929400	Weak transcription	HSMMtube	muscle
33	chr6:31927800-31929400	Weak transcription	HUVEC	blood vessel
34	chr6:31927800-31934800	Weak transcription	Fetal Heart	heart
35	chr6:31927800-31935400	Weak transcription	Stomach Mucosa	stomach
36	chr6:31927800-31937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:31927800-31938400	Strong transcription	Lung	lung
38	chr6:31927800-31938600	Strong transcription	NHEK	skin
39	chr6:31928000-31928400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:31928000-31928400	Genic enhancers	Colonic Mucosa	Colon
41	chr6:31928000-31928400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:31928000-31928400	Weak transcription	Esophagus	oesophagus
43	chr6:31928000-31928400	Weak transcription	Gastric	stomach
44	chr6:31928000-31928400	Genic enhancers	Spleen	Spleen
45	chr6:31928000-31928400	Weak transcription	HMEC	breast
46	chr6:31928000-31928400	Genic enhancers	K562	blood
47	chr6:31928000-31928400	Weak transcription	NH-A	brain
48	chr6:31928000-31928600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:31928000-31928600	Genic enhancers	Dnd41	blood
50	chr6:31928000-31928600	Transcr. at gene 5' and 3'	Hela-S3	cervix

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