Variant report

Variant	nsv526429
Chromosome Location	chr1:245970550-245979357
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	ARID3A	chr1:245974281-245974791	HepG2	liver:	n/a	n/a
2	ATF2	chr1:245970578-245971090	GM12878	blood:	n/a	n/a
3	BATF	chr1:245970698-245971080	GM12878	blood:	n/a	n/a
4	BATF	chr1:245970613-245971062	GM12878	blood:	n/a	n/a
5	BCL3	chr1:245977976-245978245	GM12878	blood:	n/a	n/a
6	BCL3	chr1:245977976-245978280	GM12878	blood:	n/a	n/a
7	BCLAF1	chr1:245970574-245971083	GM12878	blood:	n/a	chr1:245970740-245970749
8	BCLAF1	chr1:245970618-245971063	GM12878	blood:	n/a	chr1:245970740-245970749
9	BHLHE40	chr1:245970679-245971204	GM12878	blood:	n/a	n/a
10	BHLHE40	chr1:245974284-245974638	HepG2	liver:	n/a	n/a
11	CEBPB	chr1:245974350-245974567	HepG2	liver:	n/a	n/a
12	CEBPB	chr1:245974306-245974648	HepG2	liver:	n/a	n/a
13	CEBPB	chr1:245974285-245974663	HepG2	liver:	n/a	n/a
14	CHD2	chr1:245970342-245971030	GM12878	blood:	n/a	n/a
15	CHD2	chr1:245973609-245974590	GM12878	blood:	n/a	n/a
16	CTCF	chr1:245978085-245978195	GM19239	blood:	n/a	n/a
17	CTCF	chr1:245972885-245972959	LNCaP	prostate:	n/a	n/a
18	EBF1	chr1:245970267-245970595	GM12878	blood:	n/a	n/a
19	EBF1	chr1:245970655-245970948	GM12878	blood:	n/a	n/a
20	EBF1	chr1:245971378-245971698	GM12878	blood:	n/a	n/a
21	EBF1	chr1:245973542-245974573	GM12878	blood:	n/a	chr1:245973640-245973649
22	EBF1	chr1:245970265-245971082	GM12878	blood:	n/a	n/a
23	EBF1	chr1:245971518-245972036	GM12878	blood:	n/a	n/a
24	EBF1	chr1:245972615-245972750	GM12878	blood:	n/a	n/a
25	EBF1	chr1:245970634-245971007	GM12878	blood:	n/a	n/a
26	EGR1	chr1:245970243-245970572	K562	blood:	n/a	chr1:245970388-245970398 chr1:245970386-245970400 chr1:245970388-245970399 chr1:245970384-245970398 chr1:245970388-245970398 chr1:245970387-245970400 chr1:245970388-245970399
27	ELF1	chr1:245970483-245971151	GM12878	blood:	n/a	chr1:245970929-245970940
28	ELF1	chr1:245970691-245971045	K562	blood:	n/a	chr1:245970929-245970940
29	ELK1	chr1:245970537-245971009	GM12878	blood:	n/a	chr1:245970740-245970749 chr1:245970740-245970749
30	EP300	chr1:245971282-245971637	SK-N-SH_RA	brain:	n/a	n/a
31	EP300	chr1:245971265-245971694	SK-N-SH_RA	brain:	n/a	n/a
32	EP300	chr1:245976613-245976903	SK-N-SH_RA	brain:	n/a	n/a
33	EP300	chr1:245970394-245972062	SK-N-SH	brain:	n/a	chr1:245971762-245971771 chr1:245970741-245970748 chr1:245970397-245970413
34	EP300	chr1:245970375-245971053	GM12878	blood:	n/a	chr1:245970741-245970748 chr1:245970397-245970413
35	EP300	chr1:245970718-245971142	GM12878	blood:	n/a	chr1:245970741-245970748
36	EP300	chr1:245974035-245974556	GM12878	blood:	n/a	n/a
37	EP300	chr1:245976622-245976842	SK-N-SH_RA	brain:	n/a	n/a
38	EP300	chr1:245974238-245974732	HepG2	liver:	n/a	n/a
39	EP300	chr1:245974246-245974669	HepG2	liver:	n/a	n/a
40	EP300	chr1:245976497-245977218	SK-N-SH	brain:	n/a	n/a
41	EP300	chr1:245974199-245974678	HepG2	liver:	n/a	n/a
42	FOXA1	chr1:245974184-245974643	HepG2	liver:	n/a	n/a
43	FOXA1	chr1:245974255-245974694	HepG2	liver:	n/a	n/a
44	FOXA1	chr1:245974216-245974942	HepG2	liver:	n/a	n/a
45	FOXA1	chr1:245974149-245974793	HepG2	liver:	n/a	n/a
46	FOXA2	chr1:245974131-245974964	HepG2	liver:	n/a	n/a
47	FOXA2	chr1:245974236-245974687	HepG2	liver:	n/a	n/a
48	FOXM1	chr1:245970682-245971062	GM12878	blood:	n/a	n/a
49	FOXM1	chr1:245970471-245971106	GM12878	blood:	n/a	n/a
50	GABPA	chr1:245970249-245971187	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:245965294..245968068-chr1:245973609..245975680,2	K562	blood:
2	chr1:245967776..245970325-chr1:245971274..245973112,2	K562	blood:
3	chr1:245978284..245980210-chr1:245986167..245988754,2	K562	blood:
4	chr1:245958486..245963819-chr1:245964384..245971753,7	K562	blood:

Variant related genes	Relation type
SMYD3	TF binding region

Extended variants
information (count: 403 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:403 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4654285	chr1:245970550-245970551	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs148324851	chr1:245970564-245970565	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs72766646	chr1:245970603-245970604	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs374457065	chr1:245970628-245970629	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs554655992	chr1:245970637-245970638	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs111653396	chr1:245970654-245970655	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs117947158	chr1:245970655-245970656	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs533998034	chr1:245970668-245970669	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs60244015	chr1:245970671-245970672	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs571917297	chr1:245970674-245970675	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs547472644	chr1:245970739-245970740	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs116630781	chr1:245970753-245970754	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs111423539	chr1:245970807-245970808	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs539255793	chr1:245970843-245970844	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs576651502	chr1:245970852-245970853	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs147063964	chr1:245970856-245970857	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs558079796	chr1:245970911-245970912	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs535744145	chr1:245970919-245970920	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs191179048	chr1:245970927-245970928	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs576232260	chr1:245970943-245970944	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs555373861	chr1:245970970-245970971	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs572086354	chr1:245970990-245970991	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs541061633	chr1:245971014-245971015	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs564146252	chr1:245971019-245971020	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs543808170	chr1:245971031-245971032	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs183680919	chr1:245971032-245971033	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs546069021	chr1:245971058-245971059	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs563104258	chr1:245971064-245971065	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs200906871	chr1:245971112-245971113	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs61831343	chr1:245971113-245971114	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs35324111	chr1:245971115-245971116	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs112141189	chr1:245971116-245971117	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs186779555	chr1:245971117-245971118	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs377536031	chr1:245971123-245971124	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs192412152	chr1:245971124-245971125	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs5782369	chr1:245971130-245971131	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs143854286	chr1:245971158-245971159	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs73134723	chr1:245971161-245971162	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs147319544	chr1:245971162-245971163	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs140021735	chr1:245971183-245971184	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs533476538	chr1:245971268-245971269	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs74891666	chr1:245971301-245971302	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs185746940	chr1:245971308-245971309	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs535354136	chr1:245971326-245971327	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs146217578	chr1:245971331-245971332	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs555683403	chr1:245971348-245971349	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs550946467	chr1:245971373-245971374	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs190204080	chr1:245971379-245971380	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs542299008	chr1:245971439-245971440	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs573077430	chr1:245971449-245971450	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	20729466	CNVD
Testicular germ cell tumor	18059402	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-small cell lung cancer	21829676	CNVD
Multiple myeloma	16616336	CNVD
Ovarian cancer	21720365	CNVD
Glioblastoma multiforme	22291905	CNVD
Myelofibrosis	22110671	CNVD
Disease	21936942	CNVD
laryngomalacia	21936942	CNVD
GLUT3 deficiency syndrome	20509907	CNVD
Developmental delay	21373258	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Developmental delay	19490664	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD
Autism	20841430	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:154 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245949200-245999600	Weak transcription	Gastric	stomach
2	chr1:245955200-245970800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:245961800-245980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:245962000-245972600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:245964600-245971200	Weak transcription	Fetal Heart	heart
6	chr1:245964800-245973800	Weak transcription	Fetal Stomach	stomach
7	chr1:245968200-245972600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:245968400-245975200	Weak transcription	Placenta	Placenta
9	chr1:245968400-245985800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:245969600-245974000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:245969600-245975800	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:245969800-245970600	Enhancers	Colonic Mucosa	Colon
13	chr1:245969800-245970600	Weak transcription	Fetal Brain Female	brain
14	chr1:245969800-245972600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:245970200-245970800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:245970200-245970800	Enhancers	NHDF-Ad	bronchial
17	chr1:245970200-245972000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:245970200-245974200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:245970200-245974400	Enhancers	Primary B cells from cord blood	blood
20	chr1:245970400-245970600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:245970400-245970600	ZNF genes & repeats	Aorta	Aorta
22	chr1:245970400-245970600	Enhancers	Duodenum Mucosa	Duodenum
23	chr1:245970400-245970600	Enhancers	Fetal Muscle Trunk	muscle
24	chr1:245970400-245970600	Enhancers	Fetal Muscle Leg	muscle
25	chr1:245970400-245970800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:245970400-245970800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:245970400-245970800	Enhancers	Ovary	ovary
28	chr1:245970400-245970800	Enhancers	Stomach Mucosa	stomach
29	chr1:245970400-245970800	Enhancers	Spleen	Spleen
30	chr1:245970400-245971000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:245970400-245971000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:245970400-245971000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:245970400-245971000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:245970400-245971000	Enhancers	K562	blood
35	chr1:245970400-245971000	Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:245970400-245971000	Enhancers	NH-A	brain
37	chr1:245970400-245971200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:245970400-245971200	Enhancers	Osteobl	bone
39	chr1:245970400-245971600	Enhancers	Primary hematopoietic stem cells	blood
40	chr1:245970400-245971600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:245970400-245971800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:245970400-245971800	Flanking Active TSS	GM12878-XiMat	blood
43	chr1:245970400-245972000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr1:245970400-245972000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:245970400-245973800	Enhancers	HepG2	liver
46	chr1:245970400-245975400	Enhancers	Fetal Brain Male	brain
47	chr1:245970600-245970800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:245970600-245970800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr1:245970600-245970800	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr1:245970600-245971600	Enhancers	Fetal Brain Female	brain

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