Variant report

Variant	esv12906
Chromosome Location	chr5:1880874-1881544
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	BACH1	chr5:1881247-1881808	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr5:1881242-1881816	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr5:1880471-1882435	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr5:1881225-1881327	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F4	chr5:1881463-1881720	MCF10A-Er-Src	breast:	n/a	chr5:1881643-1881650 chr5:1881643-1881650 chr5:1881643-1881650
6	E2F6	chr5:1881272-1882651	H1-hESC	embryonic stem cell:	n/a	chr5:1882416-1882427 chr5:1882410-1882425 chr5:1881643-1881650 chr5:1881643-1881650 chr5:1882417-1882427 chr5:1882415-1882426 chr5:1881643-1881650 chr5:1882245-1882254 chr5:1882411-1882425
7	E2F6	chr5:1881274-1883118	H1-hESC	embryonic stem cell:	n/a	chr5:1882416-1882427 chr5:1882410-1882425 chr5:1881643-1881650 chr5:1881643-1881650 chr5:1882417-1882427 chr5:1882415-1882426 chr5:1881643-1881650 chr5:1882245-1882254 chr5:1882411-1882425
8	E2F6	chr5:1881516-1881701	K562	blood:	n/a	chr5:1881643-1881650 chr5:1881643-1881650 chr5:1881643-1881650
9	EGR1	chr5:1881100-1881710	H1-hESC	embryonic stem cell:	n/a	n/a
10	EGR1	chr5:1881370-1881653	K562	blood:	n/a	n/a
11	EGR1	chr5:1881374-1881641	K562	blood:	n/a	n/a
12	EGR1	chr5:1881148-1881740	H1-hESC	embryonic stem cell:	n/a	n/a
13	ELF1	chr5:1881411-1881688	K562	blood:	n/a	chr5:1881548-1881561
14	EP300	chr5:1881186-1881727	H1-hESC	embryonic stem cell:	n/a	chr5:1881226-1881235
15	FOS	chr5:1881422-1881685	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr5:1881422-1881719	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr5:1881409-1881711	MCF10A-Er-Src	breast:	n/a	n/a
18	FOS	chr5:1881410-1881719	MCF10A-Er-Src	breast:	n/a	n/a
19	GTF2F1	chr5:1881526-1881726	H1-hESC	embryonic stem cell:	n/a	n/a
20	JUND	chr5:1881424-1881608	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUND	chr5:1881270-1881902	H1-hESC	embryonic stem cell:	n/a	n/a
22	JUND	chr5:1881345-1881657	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr5:1881387-1881701	K562	blood:	n/a	n/a
24	MAX	chr5:1881470-1882532	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
25	MAX	chr5:1881356-1884611	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
26	MAX	chr5:1881155-1883265	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
27	MAX	chr5:1881264-1884334	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
28	MAX	chr5:1881127-1883194	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
29	MAZ	chr5:1881337-1881657	K562	blood:	n/a	n/a
30	MYC	chr5:1881528-1881576	MCF10A-Er-Src	breast:	n/a	n/a
31	NANOG	chr5:1881184-1881478	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr5:1881215-1881386	HCT-116	colon:	n/a	n/a
33	POLR2A	chr5:1881481-1891348	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr5:1880513-1880960	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr5:1881479-1881780	MCF-7	breast:	n/a	n/a
36	POLR2A	chr5:1880810-1880907	ProgFib	skin:	n/a	n/a
37	POLR2A	chr5:1881471-1884378	HCT-116	colon:	n/a	n/a
38	POLR2A	chr5:1881436-1881739	HCT-116	colon:	n/a	n/a
39	POLR2A	chr5:1881460-1881668	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr5:1881359-1883606	HCT-116	colon:	n/a	n/a
41	POLR2A	chr5:1881461-1881664	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr5:1881513-1881752	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr5:1881042-1881458	H1-hESC	embryonic stem cell:	n/a	n/a
44	SIN3A	chr5:1881138-1882188	H1-hESC	embryonic stem cell:	n/a	chr5:1881798-1881811
45	SP1	chr5:1881100-1881800	H1-hESC	embryonic stem cell:	n/a	chr5:1881742-1881751 chr5:1881742-1881752 chr5:1881467-1881478 chr5:1881738-1881752 chr5:1881451-1881462 chr5:1881748-1881757 chr5:1881434-1881445 chr5:1881748-1881758 chr5:1881402-1881413 chr5:1881741-1881753 chr5:1881744-1881758
46	SP1	chr5:1881076-1881607	H1-hESC	embryonic stem cell:	n/a	chr5:1881467-1881478 chr5:1881451-1881462 chr5:1881434-1881445 chr5:1881402-1881413
47	SP4	chr5:1881292-1881563	H1-hESC	embryonic stem cell:	n/a	chr5:1881467-1881478 chr5:1881451-1881462 chr5:1881434-1881445 chr5:1881402-1881413
48	STAT3	chr5:1881520-1881696	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr5:1881469-1881741	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr5:1881479-1881696	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:1798942..1801341-chr5:1879541..1882987,3	K562	blood:
2	chr5:1799841..1802509-chr5:1881368..1882987,2	K562	blood:
3	chr17:57923026..57925305-chr5:1880876..1883150,2	MCF-7	breast:
4	chr5:1881475..1885354-chr5:1933918..1938503,4	MCF-7	breast:
5	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
6	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249116	TF binding region
IRX4	TF binding region
ENSG00000171421	chromatin interactions
ENSG00000248994	chromatin interactions
ENSG00000201524	chromatin interactions
ENSG00000145494	chromatin interactions

Extended variants
information (count: 30 )
Associated
traits (count: 113 )

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs199581237	chr5:1880881-1880882	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs148912115	chr5:1880885-1880886	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs2232376	chr5:1880891-1880892	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs201446504	chr5:1880898-1880899	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs528019826	chr5:1880913-1880914	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs138268066	chr5:1880922-1880923	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs200041586	chr5:1880928-1880929	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs531947910	chr5:1880953-1880954	Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs550078975	chr5:1881041-1881042	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs539117428	chr5:1881049-1881050	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs571715947	chr5:1881054-1881055	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs532458997	chr5:1881064-1881065	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs547850214	chr5:1881068-1881069	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs71871413	chr5:1881171-1881172	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs111961905	chr5:1881174-1881175	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs111619755	chr5:1881179-1881180	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs185463	chr5:1881216-1881217	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs186634968	chr5:1881302-1881303	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs191461387	chr5:1881303-1881304	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs10474731	chr5:1881355-1881356	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs567535559	chr5:1881367-1881368	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs538068907	chr5:1881374-1881375	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
23	rs13162179	chr5:1881378-1881379	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs11949517	chr5:1881400-1881401	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
25	rs577678266	chr5:1881426-1881427	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
26	rs200336602	chr5:1881430-1881431	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
27	rs374837024	chr5:1881432-1881433	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
28	rs544769786	chr5:1881433-1881434	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
29	rs143666424	chr5:1881434-1881435	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
30	rs372271512	chr5:1881435-1881436	Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:113)

Disease	PMID	Source
Biliary cancer	19435499	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16608533	CNVD
Cervical cancer	16585170	CNVD
Glioblastoma multiforme	22286061	CNVD
Lung cancer	17925434	CNVD
Ovarian cancer	20844748	CNVD
Cervical squamous cell carcinoma	21590768	CNVD
Non-small cell lung cancer	21829676	CNVD
Intracranial ependymoma	16609018	CNVD
Breast cancer	19181860	CNVD
prenatal diagnosis	20453657	CNVD
Developmental delay	19490664	CNVD
Human papillomavirus	17975027	CNVD
Acute monocytic leukemia	16498392	CNVD
Gastric cancer	16891809	CNVD
Intracranial aneurysm	16715129	CNVD
Emphysema	19352772	CNVD
Chordoma	18071362	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Lung cancer	21911935	CNVD
Cri-du chat syndrome	21549014	CNVD
Melanoma	18172304	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Sudden cardiac death	19188705	CNVD
renal disease	17924346	CNVD
abnormal development	18461090	CNVD
Lung cancer	19547694	CNVD
Cri-du chat syndrome	22283845	CNVD
Disorders of sex development	21048976	CNVD
Non-small cell lung cancer	20864512	CNVD
Cancer	21183584	CNVD
Honadal dysgenesis	21048976	CNVD
Cancer	16751803	CNVD
Breast cancer	17133270	CNVD
Hepatocellular carcinoma	22174799	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Salivary gland tumor	18059337	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Kartagener syndrome	16639409	CNVD
Medulloblastoma	21979893	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	16783165	CNVD
Thyroid cancer	19087340	CNVD
Liposarcoma	21253554	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cervical Cancer	21857958	CNVD
Cervical cancer	21062161	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Oral cancer	21386901	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Ewing''s sarcoma	17952124	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Cervical cancer	18559093	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	21509527	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	21364760	CNVD
Cancer	20164919	CNVD
Oral cancer	22144094	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Urothelial carcinoma	21177765	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Multiple myeloma	17550852	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Developmental delay	21147756	CNVD
prenatal diagnosis	22389664	CNVD
Bladder cancer	21909424	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Breast cancer	21858162	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Melanoma	22183965	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	22495311	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Schizophrenia	23813976	CNVD
Ependymoma	20639864	CNVD

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1876600-1882400	Weak transcription	Right Atrium	heart
2	chr5:1877200-1881200	Strong transcription	HMEC	breast
3	chr5:1877200-1881600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:1877200-1881600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:1877200-1881600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:1878400-1881600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:1878600-1883000	Enhancers	Fetal Heart	heart
8	chr5:1879000-1881000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:1879800-1885200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr5:1880400-1882200	Weak transcription	Pancreas	Pancrea
11	chr5:1880600-1881600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
12	chr5:1880600-1881600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:1880800-1881000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
14	chr5:1880800-1881200	Bivalent Enhancer	Fetal Stomach	stomach
15	chr5:1880800-1881600	Weak transcription	NHEK	skin
16	chr5:1880800-1881800	Weak transcription	Right Ventricle	heart
17	chr5:1880800-1882800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:1880800-1887800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr5:1881000-1881200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr5:1881000-1881200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:1881000-1881200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:1881200-1881400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
23	chr5:1881200-1881600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:1881200-1881600	Weak transcription	HMEC	breast
25	chr5:1881200-1885200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr5:1881400-1882000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:1881400-1882200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr5:1881400-1882400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:1881400-1884400	Bivalent Enhancer	Fetal Brain Male	brain
30	chr5:1881400-1886800	Bivalent Enhancer	Fetal Stomach	stomach

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