Variant report

Variant	nsv539979
Chromosome Location	chr9:7887727-8157591
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	chr9:7974553-7975108	GM12878	blood:	n/a	n/a
2	ATF2	chr9:7976208-7976880	GM12878	blood:	n/a	n/a
3	ATF2	chr9:7976161-7976784	GM12878	blood:	n/a	n/a
4	BACH1	chr9:8072103-8072105	K562	blood:	n/a	n/a
5	BATF	chr9:7906884-7907087	GM12878	blood:	n/a	chr9:7906984-7906995
6	BATF	chr9:7976316-7976827	GM12878	blood:	n/a	n/a
7	BCL11A	chr9:7967937-7968189	H1-hESC	embryonic stem cell:	n/a	n/a
8	BCL11A	chr9:7976366-7976776	GM12878	blood:	n/a	n/a
9	BCL11A	chr9:7976370-7976767	GM12878	blood:	n/a	n/a
10	BCLAF1	chr9:7976212-7976893	GM12878	blood:	n/a	n/a
11	BCLAF1	chr9:7976310-7976902	GM12878	blood:	n/a	n/a
12	BHLHE40	chr9:7976330-7976914	GM12878	blood:	n/a	n/a
13	BRCA1	chr9:7967617-7968226	H1-hESC	embryonic stem cell:	n/a	n/a
14	CEBPB	chr9:7896191-7896530	A549	lung:	n/a	chr9:7896357-7896368 chr9:7896357-7896370 chr9:7896367-7896378 chr9:7896365-7896378
15	CEBPB	chr9:7896202-7896533	HepG2	liver:	n/a	chr9:7896357-7896368 chr9:7896357-7896370 chr9:7896367-7896378 chr9:7896365-7896378
16	CEBPB	chr9:8094887-8095165	HepG2	liver:	n/a	chr9:8095038-8095049 chr9:8095037-8095048
17	CEBPB	chr9:7896194-7896531	IMR90	lung:	n/a	chr9:7896357-7896368 chr9:7896357-7896370 chr9:7896367-7896378 chr9:7896365-7896378
18	CEBPB	chr9:8025772-8025875	A549	lung:	n/a	chr9:8025781-8025798
19	CEBPB	chr9:8135835-8136111	HepG2	liver:	n/a	chr9:8135984-8135997 chr9:8135985-8135996 chr9:8135984-8135997 chr9:8135984-8135995 chr9:8135984-8135995 chr9:8135984-8135997
20	CEBPB	chr9:8093569-8093890	HepG2	liver:	n/a	chr9:8093720-8093731
21	CEBPB	chr9:7896228-7896449	H1-hESC	embryonic stem cell:	n/a	chr9:7896357-7896368 chr9:7896357-7896370 chr9:7896367-7896378 chr9:7896365-7896378
22	CEBPB	chr9:7990037-7990086	H1-hESC	embryonic stem cell:	n/a	n/a
23	CEBPB	chr9:8093596-8093846	A549	lung:	n/a	chr9:8093720-8093731
24	CEBPB	chr9:8122657-8122819	H1-hESC	embryonic stem cell:	n/a	n/a
25	CEBPB	chr9:7937828-7938029	HepG2	liver:	n/a	chr9:7937932-7937943
26	CHD1	chr9:7976189-7977317	GM12878	blood:	n/a	n/a
27	CHD2	chr9:7976199-7976856	GM12878	blood:	n/a	n/a
28	CREB1	chr9:7976212-7976874	GM12878	blood:	n/a	n/a
29	CREB1	chr9:7976111-7976919	GM12878	blood:	n/a	n/a
30	CTCF	chr9:8008097-8008185	Fibrobl	skin:	n/a	n/a
31	CTCF	chr9:7978020-7978170	GM12872	blood:	n/a	n/a
32	CTCF	chr9:8104229-8104263	Lung_OC	lung:	n/a	n/a
33	CTCF	chr9:8108480-8108630	AoAF	blood vessel:	n/a	n/a
34	CTCF	chr9:8058099-8058159	LNCaP	prostate:	n/a	n/a
35	CTCF	chr9:8071238-8071339	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr9:7932600-7932750	AoAF	blood vessel:	n/a	n/a
37	CTCF	chr9:8108534-8108573	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr9:8108519-8108602	Pancreas_OC	pancreas:	n/a	n/a
39	CTCF	chr9:8088981-8089022	GM12892	blood:	n/a	n/a
40	CTCF	chr9:7981000-7981150	RPTEC	kidney:	n/a	n/a
41	CTCF	chr9:8000380-8000530	GM12865	blood:	n/a	n/a
42	CTCF	chr9:7981085-7981273	GM12878	blood:	n/a	n/a
43	CTCF	chr9:8071240-8071390	BE2_C	brain:	n/a	n/a
44	CTCF	chr9:8078680-8078830	GM12866	blood:	n/a	n/a
45	CTCF	chr9:7945720-7945804	HepG2	liver:	n/a	n/a
46	CTCF	chr9:8108420-8108570	HMF	breast:	n/a	n/a
47	CTCF	chr9:8153479-8153544	GM13976	blood:	n/a	n/a
48	CTCF	chr9:8134371-8134501	Pancreas_OC	pancreas:	n/a	n/a
49	CTCF	chr9:7974758-7974851	Spleen_OC	spleen:	n/a	n/a
50	CTCF	chr9:8000160-8000204	LNCaP	prostate:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:8106136..8108592-chr9:8119218..8121466,2	K562	blood:
2	chr9:8106136..8108592-chr9:8119218..8121466,2	K562	blood:
3	chr13:56158216..56158765-chr9:8154008..8154641,2	MCF-7	breast:
4	chr11:107728772..107729298-chr9:8021237..8021737,2	HCT-116	colon:
5	chr9:7740039..7741870-chr9:7890019..7892015,2	K562	blood:
6	chr11:107727967..107730044-chr9:8019737..8022718,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-16	chr9:8085728-8085987	uc_249_+
2	lnc-C9orf123-4	chr9:7960355-7960662	NONHSAT130186
3	lnc-C9orf123-7	chr9:7950413-7950662	NONHSAT130185
4	lnc-C9orf123-2	chr9:7925545-7926107	XLOC_007642
5	lnc-C9orf123-7	chr9:7950830-7951080	NONHSAT130185
6	lnc-C9orf123-2	chr9:7927003-7927686	NONHSAT130182
7	lnc-C9orf123-8	chr9:8085728-8085987	uc_249_-
8	lnc-C9orf123-2	chr9:7925551-7925625	NONHSAT130182
9	lnc-KDM4C-7	chr9:7925578-7930367	XLOC_007279
10	lnc-C9orf123-4	chr9:7960830-7961080	XLOC_007643
11	lnc-C9orf123-2	chr9:7924794-7924818	XLOC_007642
12	lnc-KDM4C-7	chr9:7960826-7961234	XLOC_007279
13	lnc-C9orf123-4	chr9:7960830-7961188	NONHSAT130186
14	lnc-PTPRD-8	chr9:7888299-7888380	NONHSAT130179
15	lnc-C9orf123-4	chr9:7960413-7960662	XLOC_007643

Variant related genes	Relation type
ENSG00000226376	TF binding region
TMEM261	TF binding region
ENSG00000231902	TF binding region
ENSG00000110660	chromatin interactions
AURKA	miRNA target sites
C7orf59	miRNA target sites
FGFR1	miRNA target sites
MINA	miRNA target sites

Extended variants
information (count: 7247 )
Associated
traits (count: 105 )

Variant overlapped rSNPs/rCNVs (count:7247 , 50 per page) page: 1 2 3 4 5 6 7 ... 145

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553815094	chr9:7888303-7888304	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs190947402	chr9:7888330-7888331	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs538714164	chr9:7888373-7888374	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs552991368	chr9:7889238-7889239	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs77384614	chr9:7889240-7889241	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs559773131	chr9:7889263-7889264	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs182352382	chr9:7889269-7889270	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs529815898	chr9:7889279-7889280	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs550053906	chr9:7889310-7889311	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs552183325	chr9:7889313-7889314	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs571640564	chr9:7889320-7889321	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs116314468	chr9:7889380-7889381	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs186681034	chr9:7889421-7889422	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs191335622	chr9:7889458-7889459	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs79674789	chr9:7889461-7889462	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs141203541	chr9:7889503-7889504	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs35952115	chr9:7889514-7889515	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs145111341	chr9:7889525-7889526	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs147624898	chr9:7889529-7889530	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs17630650	chr9:7891408-7891409	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs114829434	chr9:7891421-7891422	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs553216690	chr9:7891429-7891430	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs577825510	chr9:7891430-7891431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs188786123	chr9:7891447-7891448	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs13283580	chr9:7891448-7891449	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs13283581	chr9:7891449-7891450	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs369011006	chr9:7891469-7891470	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs79744348	chr9:7891504-7891505	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs537578081	chr9:7891511-7891512	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs556065303	chr9:7891520-7891521	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs554328948	chr9:7891552-7891553	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs372102696	chr9:7891568-7891569	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs574275134	chr9:7891583-7891584	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs193210364	chr9:7891608-7891609	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs185223672	chr9:7891618-7891619	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs147360421	chr9:7891645-7891646	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs573881370	chr9:7891672-7891673	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs187269401	chr9:7891680-7891681	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs560019197	chr9:7891690-7891691	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs574338402	chr9:7891714-7891715	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs533414200	chr9:7891726-7891727	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs191991996	chr9:7891730-7891731	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs563262262	chr9:7891731-7891732	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs530668165	chr9:7891742-7891743	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs184138323	chr9:7891776-7891777	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs567502845	chr9:7891798-7891799	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs534827920	chr9:7891818-7891819	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs139441634	chr9:7891821-7891822	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs540090959	chr9:7891831-7891832	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs559498849	chr9:7891847-7891848	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:105)

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
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Renal cell carcinoma	21215367	CNVD
Chordoma	21215367	CNVD

Chromatin state (count:940 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7891400-7893200	Enhancers	Stomach Mucosa	stomach
2	chr9:7892800-7893600	Enhancers	NH-A	brain
3	chr9:7893200-7896000	Enhancers	Brain Germinal Matrix	brain
4	chr9:7895800-7896000	Enhancers	Fetal Lung	lung
5	chr9:7895800-7896200	Enhancers	Adipose Nuclei	Adipose
6	chr9:7896000-7897600	Weak transcription	Fetal Lung	lung
7	chr9:7897600-7898400	Enhancers	Fetal Lung	lung
8	chr9:7898400-7906800	Weak transcription	Fetal Lung	lung
9	chr9:7900000-7900800	Enhancers	Fetal Heart	heart
10	chr9:7900800-7901000	Weak transcription	NH-A	brain
11	chr9:7900800-7901400	Weak transcription	Fetal Heart	heart
12	chr9:7901000-7901200	Enhancers	NH-A	brain
13	chr9:7901000-7902400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:7901200-7902000	Weak transcription	NH-A	brain
15	chr9:7901400-7902400	Enhancers	Fetal Heart	heart
16	chr9:7901600-7902400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:7902000-7902800	Enhancers	NH-A	brain
18	chr9:7902400-7907400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:7902400-7908000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:7902800-7906800	Weak transcription	NH-A	brain
21	chr9:7904400-7906800	Weak transcription	Brain Angular Gyrus	brain
22	chr9:7905200-7905400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr9:7905200-7905600	Enhancers	Brain Hippocampus Middle	brain
24	chr9:7905200-7905600	Enhancers	Brain Substantia Nigra	brain
25	chr9:7905200-7908400	Enhancers	Fetal Thymus	thymus
26	chr9:7905600-7905800	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:7905600-7905800	Weak transcription	Brain Substantia Nigra	brain
28	chr9:7905800-7906200	Enhancers	Brain Hippocampus Middle	brain
29	chr9:7905800-7906200	Enhancers	Brain Substantia Nigra	brain
30	chr9:7906000-7906200	Enhancers	Thymus	Thymus
31	chr9:7906000-7908800	Enhancers	Brain Cingulate Gyrus	brain
32	chr9:7906200-7906800	Weak transcription	Thymus	Thymus
33	chr9:7906200-7907000	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:7906200-7907000	Weak transcription	Brain Substantia Nigra	brain
35	chr9:7906600-7907200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr9:7906600-7907800	Enhancers	Fetal Muscle Leg	muscle
37	chr9:7906800-7907800	Enhancers	Brain Angular Gyrus	brain
38	chr9:7906800-7907800	Enhancers	Fetal Lung	lung
39	chr9:7906800-7908400	Enhancers	NH-A	brain
40	chr9:7906800-7908600	Enhancers	Brain Anterior Caudate	brain
41	chr9:7906800-7908600	Enhancers	Thymus	Thymus
42	chr9:7907000-7907800	Enhancers	Fetal Brain Male	brain
43	chr9:7907000-7908400	Enhancers	Brain Substantia Nigra	brain
44	chr9:7907000-7908600	Enhancers	Brain Hippocampus Middle	brain
45	chr9:7907000-7908600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr9:7907400-7908000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:7907600-7908400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:7907800-7908200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:7907800-7910400	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:7908000-7908400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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