Variant report

Variant	nsv892212
Chromosome Location	chr9:7742476-7787532
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	ATF2	chr9:7756002-7756595	GM12878	blood:	n/a	n/a
2	BATF	chr9:7756144-7756427	GM12878	blood:	n/a	chr9:7756282-7756293 chr9:7756283-7756293
3	BATF	chr9:7756144-7756434	GM12878	blood:	n/a	chr9:7756282-7756293 chr9:7756283-7756293
4	BCL11A	chr9:7783624-7783901	GM12878	blood:	n/a	n/a
5	BCL11A	chr9:7784487-7784797	GM12878	blood:	n/a	n/a
6	BHLHE40	chr9:7784514-7784716	GM12878	blood:	n/a	n/a
7	BHLHE40	chr9:7756142-7756553	GM12878	blood:	n/a	n/a
8	BHLHE40	chr9:7762757-7763103	GM12878	blood:	n/a	n/a
9	CEBPB	chr9:7786693-7786871	HepG2	liver:	n/a	chr9:7786745-7786756
10	CHD1	chr9:7756311-7756401	GM12878	blood:	n/a	n/a
11	CHD1	chr9:7784415-7784457	GM12878	blood:	n/a	n/a
12	CHD2	chr9:7784508-7784769	GM12878	blood:	n/a	n/a
13	CHD2	chr9:7748861-7748865	GM12878	blood:	n/a	n/a
14	CTCF	chr9:7769700-7769850	GM12801	blood:	n/a	n/a
15	CTCF	chr9:7787036-7787158	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr9:7765100-7765250	A549	lung:	n/a	n/a
17	CTCF	chr9:7787052-7787124	GM19238	blood:	n/a	n/a
18	CTCF	chr9:7787015-7787115	GM19239	blood:	n/a	n/a
19	CTCF	chr9:7786980-7787130	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr9:7787031-7787109	GM12892	blood:	n/a	n/a
21	CUX1	chr9:7784541-7784917	GM12878	blood:	n/a	n/a
22	CUX1	chr9:7756527-7756659	GM12878	blood:	n/a	n/a
23	EBF1	chr9:7759991-7760214	GM12878	blood:	n/a	chr9:7760069-7760080
24	EBF1	chr9:7756157-7756420	GM12878	blood:	n/a	n/a
25	EBF1	chr9:7783632-7783961	GM12878	blood:	n/a	n/a
26	EBF1	chr9:7784524-7784859	GM12878	blood:	n/a	n/a
27	EBF1	chr9:7756146-7756405	GM12878	blood:	n/a	n/a
28	EBF1	chr9:7783717-7784057	GM12878	blood:	n/a	n/a
29	EP300	chr9:7756111-7756491	GM12878	blood:	n/a	chr9:7756282-7756291 chr9:7756281-7756290
30	EP300	chr9:7784555-7784876	GM12878	blood:	n/a	n/a
31	EP300	chr9:7783599-7783915	GM12878	blood:	n/a	n/a
32	EP300	chr9:7784302-7784955	GM12878	blood:	n/a	n/a
33	EP300	chr9:7783379-7783977	GM12878	blood:	n/a	n/a
34	EP300	chr9:7756081-7756433	GM12878	blood:	n/a	chr9:7756282-7756291 chr9:7756281-7756290
35	FAM48A	chr9:7754080-7754136	GM12878	blood:	n/a	n/a
36	FAM48A	chr9:7779510-7779607	GM12878	blood:	n/a	n/a
37	FOS	chr9:7756166-7756461	MCF10A-Er-Src	breast:	n/a	chr9:7756282-7756291 chr9:7756281-7756290 chr9:7756282-7756290 chr9:7756275-7756287 chr9:7756287-7756296 chr9:7756283-7756290
38	FOS	chr9:7756138-7756417	MCF10A-Er-Src	breast:	n/a	chr9:7756282-7756291 chr9:7756281-7756290 chr9:7756282-7756290 chr9:7756275-7756287 chr9:7756287-7756296 chr9:7756283-7756290
39	FOS	chr9:7756103-7756445	MCF10A-Er-Src	breast:	n/a	chr9:7756282-7756291 chr9:7756281-7756290 chr9:7756282-7756290 chr9:7756275-7756287 chr9:7756287-7756296 chr9:7756283-7756290
40	FOS	chr9:7756137-7756443	MCF10A-Er-Src	breast:	n/a	chr9:7756282-7756291 chr9:7756281-7756290 chr9:7756282-7756290 chr9:7756275-7756287 chr9:7756287-7756296 chr9:7756283-7756290
41	FOS	chr9:7777934-7777970	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr9:7759962-7760167	MCF10A-Er-Src	breast:	n/a	n/a
43	FOXA1	chr9:7782751-7783021	T-47D	breast:	n/a	chr9:7782856-7782871
44	FOXA1	chr9:7782696-7783065	T-47D	breast:	n/a	chr9:7782856-7782871
45	GABPA	chr9:7785260-7785344	HepG2	liver:	n/a	n/a
46	GABPA	chr9:7785258-7785347	HepG2	liver:	n/a	n/a
47	GATA3	chr9:7772793-7772950	SH-SY5Y	brain:	n/a	chr9:7772908-7772918 chr9:7772910-7772917 chr9:7772910-7772917 chr9:7772905-7772921 chr9:7772910-7772917
48	GATA3	chr9:7782777-7783016	T-47D	breast:	n/a	chr9:7782975-7782982
49	GATA3	chr9:7785058-7785274	T-47D	breast:	n/a	n/a
50	IRF3	chr9:7783029-7783047	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:7772004..7774920-chr9:7780666..7782709,2	K562	blood:
2	chr9:7782983..7784835-chr9:7794614..7797331,2	K562	blood:
3	chr9:7772004..7774920-chr9:7780666..7782709,2	K562	blood:
4	chr9:7785236..7788053-chr9:7798343..7800585,2	K562	blood:
5	chr9:7781941..7784534-chr9:7791662..7794254,2	MCF-7	breast:
6	chr9:7767607..7770435-chr9:7773162..7775185,2	K562	blood:
7	chr9:7775868..7780963-chr9:7782182..7785023,5	K562	blood:
8	chr9:7767607..7770435-chr9:7773162..7775185,2	K562	blood:
9	chr9:7775868..7780963-chr9:7782182..7785023,5	K562	blood:
10	chr9:7764096..7766786-chr9:7797842..7799916,2	MCF-7	breast:
11	chr9:7770682..7773341-chr9:7794081..7796235,2	MCF-7	breast:
12	chr9:7785236..7787094-chr9:7798343..7800559,2	K562	blood:
13	chr9:7787126..7791154-chr9:7791178..7794501,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf123-1	chr9:7786105-7786688	ENSG00000273056.1
2	lnc-C9orf123-1	chr9:7787136-7787329	XLOC_007641
3	lnc-C9orf123-1	chr9:7785195-7787329	XLOC_007641
4	lnc-C9orf123-1	chr9:7782483-7782511	XLOC_007641

Variant related genes	Relation type
ENSG00000273056	TF binding region
ENSG00000137038	chromatin interactions
SMARCC2	miRNA target sites
DLST	miRNA target sites

Extended variants
information (count: 1274 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:1274 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs561908635	chr9:7749215-7749216	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs529218924	chr9:7749216-7749217	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs547645957	chr9:7749327-7749328	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs74462295	chr9:7749337-7749338	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs191811150	chr9:7749349-7749350	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs12337599	chr9:7749357-7749358	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs184554661	chr9:7749361-7749362	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs538059759	chr9:7749372-7749373	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs368321333	chr9:7749393-7749394	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs146061056	chr9:7749405-7749406	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs544320415	chr9:7749415-7749416	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs535801869	chr9:7749422-7749423	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs574701802	chr9:7749426-7749427	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs540470180	chr9:7749438-7749439	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs372580530	chr9:7749451-7749452	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs35323148	chr9:7749486-7749487	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs397717341	chr9:7749494-7749495	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs202052322	chr9:7749495-7749496	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs111803805	chr9:7749528-7749529	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs138798065	chr9:7749531-7749532	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs192183419	chr9:7749538-7749539	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs149381746	chr9:7749566-7749567	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs10976548	chr9:7749594-7749595	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs550031551	chr9:7754005-7754006	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs184535744	chr9:7754016-7754017	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs189025841	chr9:7754028-7754029	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs548279316	chr9:7754056-7754057	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs566585392	chr9:7754061-7754062	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs10758897	chr9:7754113-7754114	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs113379302	chr9:7754121-7754122	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs552402565	chr9:7754127-7754128	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs79158920	chr9:7754142-7754143	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs369689732	chr9:7754167-7754168	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs146730445	chr9:7754169-7754170	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs567988316	chr9:7754176-7754177	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs535384916	chr9:7754184-7754185	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs140359785	chr9:7754185-7754186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs112181765	chr9:7754201-7754202	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs145429801	chr9:7754212-7754213	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs146529428	chr9:7754222-7754223	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs149100828	chr9:7754237-7754238	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs558016919	chr9:7754278-7754279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs143657570	chr9:7754313-7754314	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs543372098	chr9:7754321-7754322	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs148079403	chr9:7754330-7754331	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs530049657	chr9:7754375-7754376	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs541859491	chr9:7754394-7754395	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs560110937	chr9:7754404-7754405	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs527809920	chr9:7754422-7754423	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs7022742	chr9:7754451-7754452	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:104)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Developmental delay	21147756	CNVD
Lung cancer	18438408	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Metastatic melanoma	18483359	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	16783165	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Pancreatic cancer	21811587	CNVD
Chordoma	21215367	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Renal cell carcinoma	21215367	CNVD
Bipolar disorder	19114987	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:233 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7749200-7749600	Enhancers	Fetal Lung	lung
2	chr9:7754000-7755400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:7754200-7755400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr9:7754800-7755000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:7754800-7755000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:7754800-7755000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:7754800-7755200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:7754800-7755400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:7754800-7755400	Enhancers	HSMMtube	muscle
10	chr9:7755000-7756400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:7755400-7756400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:7755600-7756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:7755600-7756800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:7755800-7757200	Enhancers	GM12878-XiMat	blood
15	chr9:7756000-7756600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:7756000-7756800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr9:7756200-7757200	Enhancers	HMEC	breast
18	chr9:7756400-7756600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr9:7756400-7756800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:7756400-7757000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:7756400-7757200	Enhancers	NHEK	skin
22	chr9:7756400-7757400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:7756600-7757200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:7757200-7763000	Weak transcription	GM12878-XiMat	blood
25	chr9:7759400-7760400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:7759400-7760600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:7762600-7763200	Enhancers	Primary B cells from peripheral blood	blood
28	chr9:7762800-7763200	Enhancers	Primary B cells from cord blood	blood
29	chr9:7763000-7763200	Enhancers	GM12878-XiMat	blood
30	chr9:7765000-7768800	Weak transcription	HSMMtube	muscle
31	chr9:7768800-7769400	Enhancers	HSMMtube	muscle
32	chr9:7769200-7769400	Enhancers	Fetal Muscle Leg	muscle
33	chr9:7769400-7769800	Weak transcription	HSMMtube	muscle
34	chr9:7769800-7770600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr9:7769800-7771000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:7769800-7771000	Enhancers	HSMMtube	muscle
37	chr9:7770000-7770800	Enhancers	Fetal Lung	lung
38	chr9:7770200-7771000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:7770400-7770600	Enhancers	Primary hematopoietic stem cells	blood
40	chr9:7770400-7770600	Enhancers	Brain Germinal Matrix	brain
41	chr9:7771200-7771400	Enhancers	Brain Germinal Matrix	brain
42	chr9:7775200-7776600	Enhancers	HSMMtube	muscle
43	chr9:7776000-7776400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:7776200-7776800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:7776400-7780400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:7776600-7777000	Weak transcription	HSMMtube	muscle
47	chr9:7777000-7778000	Enhancers	Brain Germinal Matrix	brain
48	chr9:7777000-7778200	Enhancers	HSMMtube	muscle
49	chr9:7777600-7779200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:7777800-7778200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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