Variant report

Variant	esv3393792
Chromosome Location	chr2:55171448-55173496
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr2:55172506-55172897	GM12878	blood:	n/a	n/a
2	BHLHE40	chr2:55172574-55172896	GM12878	blood:	n/a	n/a
3	BHLHE40	chr2:55172677-55173209	HepG2	liver:	n/a	n/a
4	BHLHE40	chr2:55172717-55172864	K562	blood:	n/a	n/a
5	CEBPB	chr2:55172677-55173194	HepG2	liver:	n/a	n/a
6	CEBPB	chr2:55172900-55173370	MCF-7	breast:	n/a	n/a
7	CEBPB	chr2:55172594-55173269	IMR90	lung:	n/a	n/a
8	CHD2	chr2:55172755-55172825	GM12878	blood:	n/a	n/a
9	EBF1	chr2:55172604-55172806	GM12878	blood:	n/a	n/a
10	EP300	chr2:55172633-55172816	GM12878	blood:	n/a	n/a
11	FOS	chr2:55172592-55172708	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr2:55172953-55173268	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr2:55173019-55173216	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr2:55172975-55173198	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr2:55173025-55173251	MCF10A-Er-Src	breast:	n/a	n/a
16	MAZ	chr2:55172531-55172666	GM12878	blood:	n/a	n/a
17	MXI1	chr2:55172634-55172669	GM12878	blood:	n/a	n/a
18	MYC	chr2:55172940-55173259	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr2:55173052-55173219	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr2:55173169-55173215	ProgFib	skin:	n/a	n/a
21	POLR2A	chr2:55172832-55173252	MCF10A-Er-Src	breast:	n/a	n/a
22	RAD21	chr2:55173098-55173272	IMR90	lung:	n/a	n/a
23	RFX5	chr2:55172817-55172907	HepG2	liver:	n/a	n/a
24	RUNX3	chr2:55172516-55172975	GM12878	blood:	n/a	n/a
25	RUNX3	chr2:55172512-55172930	GM12878	blood:	n/a	n/a
26	STAT1	chr2:55173415-55173451	GM12878	blood:	n/a	n/a
27	STAT3	chr2:55172578-55172681	MCF10A-Er-Src	breast:	n/a	n/a
28	TBL1XR1	chr2:55172685-55172787	GM12878	blood:	n/a	n/a
29	USF2	chr2:55172698-55172835	GM12878	blood:	n/a	n/a
30	USF2	chr2:55173007-55173021	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr2:55172643-55172879	GM12878	blood:	n/a	n/a
32	ZNF217	chr2:55172689-55173357	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:55172992-55173042	SK-N-SH_RA	brain:	n/a
2	chr2:55172992-55173042	HCM	heart:	n/a
3	chr2:55172992-55173042	BJ	skin:	n/a
4	chr2:55172992-55173042	PrEC	prostate:	n/a
5	chr2:55172992-55173042	AG09309	skin:	n/a
6	chr2:55172992-55173042	AG09319	gingival:	n/a
7	chr2:55172992-55173042	Hela-S3	cervix:	n/a
8	chr2:55172992-55173042	AG10803	skin:	n/a
9	chr2:55172992-55173042	GM12892	blood:	n/a
10	chr2:55172992-55173042	HNPCEpiC	eye:	n/a
11	chr2:55172992-55173042	T-47D	breast:	n/a
12	chr2:55172992-55173042	HepG2	liver:	n/a
13	chr2:55172992-55173042	SK-N-MC	brain:	n/a
14	chr2:55172992-55173042	NHDF-neo	bronchial:	n/a
15	chr2:55172992-55173042	GM12891	blood:	n/a
16	chr2:55172992-55173042	H1-hESC	embryonic stem cell:	embryo
17	chr2:55172992-55173042	HIPEpiC	eye:	n/a
18	chr2:55172992-55173042	A549	lung:	n/a
19	chr2:55172992-55173042	RPTEC	kidney:	n/a
20	chr2:55172992-55173042	IMR90	lung:	fetal
21	chr2:55172992-55173042	PFSK-1	brain:	n/a
22	chr2:55172992-55173042	ProgFib	skin:	n/a
23	chr2:55172992-55173042	U87	brain:	n/a
24	chr2:55172992-55173042	HRPEpiC	eye:	n/a
25	chr2:55172992-55173042	MCF10A-Er-Src	breast:	n/a
26	chr2:55172992-55173042	HRCEpiC	kidney:	n/a
27	chr2:55172992-55173042	Hepatocyte	liver:	n/a
28	chr2:55172992-55173042	HPAEpiC	pulmonary alveolar:	n/a
29	chr2:55172992-55173042	ECC-1	luminal epithelium:	n/a
30	chr2:55172992-55173042	ovcar-3	ovarian:	n/a
31	chr2:55172992-55173042	SKMC	muscle:	n/a
32	chr2:55172992-55173042	MCF-7	breast:	n/a
33	chr2:55172992-55173042	BE2_C	brain:	n/a
34	chr2:55172992-55173042	AoSMC	blood vessel:	n/a
35	chr2:55172992-55173042	NHBE	bronchial:	n/a
36	chr2:55172992-55173042	HUVEC	blood vessel:	n/a
37	chr2:55172992-55173042	SK-N-SH	brain:	n/a
38	chr2:55172992-55173042	K562	blood:	n/a
39	chr2:55172992-55173042	AG04449	skin:	fetal
40	chr2:55172992-55173042	AG04450	lung:	fetal
41	chr2:55172992-55173042	NB4	blood:	n/a
42	chr2:55172992-55173042	HAEpiC	amniotic membrane:	n/a
43	chr2:55172992-55173042	HL-60	blood:	n/a
44	chr2:55172992-55173042	HCPEpiC	choroid plexus:	n/a
45	chr2:55172992-55173042	GM19239	blood:	n/a
46	chr2:55172992-55173042	HEEpiC	esophagus:	n/a
47	chr2:55172992-55173042	LNCaP	prostate:	n/a
48	chr2:55172992-55173042	PANC-1	pancreas:	n/a
49	chr2:55172992-55173042	HMEC	breast:	n/a
50	chr2:55172992-55173042	Jurkat	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:90568357..90570526-chr2:55172089..55173609,2	MCF-7	breast:
2	chr2:55171297..55173305-chr2:55180645..55183398,2	K562	blood:
3	chr2:55164941..55167851-chr2:55169428..55172697,4	K562	blood:
4	chr2:39442463..39443026-chr2:55172640..55173316,2	MCF-7	breast:

No data

Variant related genes	Relation type
EML6	TF binding region
EML6	CpG island
ENSG00000214595	chromatin interactions

Extended variants
information (count: 89 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:89 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556517368	chr2:55171458-55171459	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs572902852	chr2:55171484-55171485	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs542015040	chr2:55171525-55171526	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs561772866	chr2:55171553-55171554	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs143772562	chr2:55171574-55171575	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs114325879	chr2:55171584-55171585	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs148129580	chr2:55171609-55171610	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs556720174	chr2:55171612-55171613	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs563329802	chr2:55171635-55171636	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs186536486	chr2:55171689-55171690	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs545953798	chr2:55171764-55171765	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs559800940	chr2:55171815-55171816	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs559181630	chr2:55171822-55171823	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs116415146	chr2:55171826-55171827	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs548756119	chr2:55171839-55171840	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs568697386	chr2:55171910-55171911	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs531212291	chr2:55171919-55171920	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs192595276	chr2:55171942-55171943	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs115087921	chr2:55171943-55171944	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs370583641	chr2:55171953-55171954	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs78583495	chr2:55172002-55172003	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs566551756	chr2:55172021-55172022	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs77089440	chr2:55172030-55172031	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs555517772	chr2:55172036-55172037	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs575131117	chr2:55172040-55172041	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs562209352	chr2:55172051-55172052	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs375221089	chr2:55172058-55172059	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs544067766	chr2:55172101-55172102	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs557653028	chr2:55172102-55172103	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs77360704	chr2:55172129-55172130	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs79843619	chr2:55172130-55172131	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs201445389	chr2:55172157-55172158	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs559529845	chr2:55172219-55172220	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs369585970	chr2:55172257-55172258	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs200524142	chr2:55172261-55172262	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs371154819	chr2:55172323-55172324	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs112343649	chr2:55172332-55172333	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs577871389	chr2:55172338-55172339	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs374586298	chr2:55172339-55172340	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs539806230	chr2:55172391-55172392	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs199594380	chr2:55172418-55172419	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs559733785	chr2:55172428-55172429	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs113374367	chr2:55172440-55172441	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs145395103	chr2:55172468-55172469	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs573374649	chr2:55172487-55172488	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs541991379	chr2:55172496-55172497	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs185804628	chr2:55172497-55172498	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs190324594	chr2:55172511-55172512	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs137930538	chr2:55172523-55172524	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs75010292	chr2:55172536-55172537	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:77)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:156 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55166200-55172800	Weak transcription	Gastric	stomach
2	chr2:55168600-55172600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:55169000-55172400	Weak transcription	HepG2	liver
5	chr2:55169000-55172600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:55169000-55172600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:55169000-55172600	Weak transcription	Pancreas	Pancrea
8	chr2:55169000-55172800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:55169200-55172200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:55169200-55172400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:55169200-55172400	Weak transcription	HMEC	breast
12	chr2:55169600-55172600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:55169800-55171600	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:55169800-55172600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:55169800-55172600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:55169800-55172800	Weak transcription	Esophagus	oesophagus
17	chr2:55170000-55171800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:55170000-55172400	Weak transcription	HSMM	muscle
19	chr2:55170000-55172800	Weak transcription	Lung	lung
20	chr2:55170200-55171800	Enhancers	Dnd41	blood
21	chr2:55170400-55171800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:55170400-55172400	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:55170400-55190400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:55170600-55172800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:55170800-55172600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:55171200-55171600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:55171400-55172600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:55171600-55171800	Enhancers	Brain Hippocampus Middle	brain
29	chr2:55171800-55172000	Enhancers	Brain Angular Gyrus	brain
30	chr2:55171800-55172000	Enhancers	Brain Anterior Caudate	brain
31	chr2:55171800-55172200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:55171800-55172200	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:55172000-55172400	Weak transcription	Brain Angular Gyrus	brain
34	chr2:55172000-55172400	Weak transcription	Brain Anterior Caudate	brain
35	chr2:55172200-55172400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:55172200-55172600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr2:55172200-55172600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55172200-55174200	Enhancers	Brain Hippocampus Middle	brain
39	chr2:55172400-55172600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:55172400-55172600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:55172400-55172600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:55172400-55172600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:55172400-55172600	Enhancers	Brain Anterior Caudate	brain
44	chr2:55172400-55172600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:55172400-55172600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:55172400-55172600	Enhancers	HepG2	liver
47	chr2:55172400-55172600	Flanking Active TSS	HSMM	muscle
48	chr2:55172400-55172800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:55172400-55173800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:55172400-55173800	Enhancers	HMEC	breast

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