Variant report

Variant	nsv1021013
Chromosome Location	chr9:17045105-17072402
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	chr9:17057789-17058149	HepG2	liver:	n/a	n/a
2	BATF	chr9:17057808-17058032	GM12878	blood:	n/a	n/a
3	BHLHE40	chr9:17057793-17058031	HepG2	liver:	n/a	n/a
4	CEBPB	chr9:17057772-17058066	HepG2	liver:	n/a	n/a
5	CTCF	chr9:17063660-17063810	HUVEC	blood vessel:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
6	CTCF	chr9:17066478-17066515	GM10248	blood:	n/a	n/a
7	CTCF	chr9:17072030-17072113	GM13976	blood:	n/a	n/a
8	CTCF	chr9:17063472-17064019	MCF-7	breast:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
9	CTCF	chr9:17063660-17063810	GM12868	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
10	CTCF	chr9:17063373-17064049	A549	lung:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
11	CTCF	chr9:17063580-17063730	RPTEC	kidney:	n/a	n/a
12	CTCF	chr9:17063589-17063914	HUVEC	blood vessel:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
13	CTCF	chr9:17063680-17063830	GM12865	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
14	CTCF	chr9:17063576-17063883	Medullo	brain:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
15	CTCF	chr9:17053960-17054110	HA-sp	spinal cord:	n/a	n/a
16	CTCF	chr9:17063609-17063868	GM12878	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
17	CTCF	chr9:17054020-17054170	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr9:17063680-17063830	GM12867	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
19	CTCF	chr9:17063625-17063855	GM19239	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
20	CTCF	chr9:17063580-17063730	HFF-Myc	foreskin:	n/a	n/a
21	CTCF	chr9:17063656-17063818	MCF-7	breast:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
22	CTCF	chr9:17063660-17063810	NHEK	skin:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
23	CTCF	chr9:17063100-17063250	HPAF	blood vessel:	n/a	n/a
24	CTCF	chr9:17063580-17063730	HL-60	blood:	n/a	n/a
25	CTCF	chr9:17063680-17063830	NHDF-neo	bronchial:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
26	CTCF	chr9:17063680-17063830	GM12872	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
27	CTCF	chr9:17063640-17063790	SAEC	small airway:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
28	CTCF	chr9:17063680-17063830	NB4	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
29	CTCF	chr9:17063446-17063457	Medullo	brain:	n/a	n/a
30	CTCF	chr9:17063700-17063850	NHEK	skin:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
31	CTCF	chr9:17062540-17062690	AG10803	skin:	n/a	n/a
32	CTCF	chr9:17063660-17063810	GM12878	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
33	CTCF	chr9:17063660-17063810	GM12801	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
34	CTCF	chr9:17063576-17063871	SK-N-SH_RA	brain:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
35	CTCF	chr9:17063606-17063827	HepG2	liver:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
36	CTCF	chr9:17063433-17063936	GM12878	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
37	CTCF	chr9:17063660-17063810	GM12872	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
38	CTCF	chr9:17062900-17063050	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr9:17063645-17063816	Lung_OC	lung:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
40	CTCF	chr9:17063700-17063850	HVMF	connective:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
41	CTCF	chr9:17063660-17063810	AoAF	blood vessel:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
42	CTCF	chr9:17063593-17063880	LNCaP	prostate:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
43	CTCF	chr9:17051269-17051282	GM10248	blood:	n/a	n/a
44	CTCF	chr9:17063680-17063830	Hela-S3	cervix:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
45	CTCF	chr9:17063616-17063869	NHEK	skin:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
46	CTCF	chr9:17063660-17063810	GM12874	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
47	CTCF	chr9:17063618-17063857	Spleen_OC	spleen:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
48	CTCF	chr9:17063660-17063810	HRE	kidney:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
49	CTCF	chr9:17063660-17063810	BE2_C	brain:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746
50	CTCF	chr9:17063700-17063850	GM12875	blood:	n/a	chr9:17063734-17063742 chr9:17063729-17063747 chr9:17063731-17063752 chr9:17063730-17063746

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:17063303..17064146-chr9:17462547..17463504,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTLN-1	chr9:17048917-17049039	ENSG00000237153.1
2	lnc-CNTLN-4	chr9:17053899-17054200	NONHSAT130298

Variant related genes	Relation type
RN7SL720P	TF binding region
ENSG00000237153	TF binding region

Extended variants
information (count: 955 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:955 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs416529	chr9:17045105-17045106	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs540170346	chr9:17045155-17045156	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs187809651	chr9:17045217-17045218	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs536987860	chr9:17045226-17045227	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs148282758	chr9:17045275-17045276	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs568911329	chr9:17045288-17045289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs141256235	chr9:17045320-17045321	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs562046278	chr9:17045334-17045335	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs574124905	chr9:17045342-17045343	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs544291078	chr9:17045343-17045344	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs373802398	chr9:17045370-17045371	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs373443744	chr9:17045371-17045372	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs375061302	chr9:17045374-17045375	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs562580706	chr9:17045391-17045392	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs150778458	chr9:17045392-17045393	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs545717094	chr9:17045396-17045397	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs564373402	chr9:17045472-17045473	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs192586307	chr9:17045480-17045481	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs577196555	chr9:17045511-17045512	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs117422595	chr9:17045540-17045541	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs546725171	chr9:17045556-17045557	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs568156425	chr9:17045596-17045597	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs570793480	chr9:17048947-17048948	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs380045	chr9:17048960-17048961	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs534732370	chr9:17048972-17048973	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs548716808	chr9:17048975-17048976	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs552273134	chr9:17048984-17048985	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs10962832	chr9:17048990-17048991	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs530932263	chr9:17048998-17048999	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs568579552	chr9:17049001-17049002	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs552652266	chr9:17049017-17049018	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs138621332	chr9:17049026-17049027	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs558592545	chr9:17049800-17049801	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs540673247	chr9:17049828-17049829	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs558981478	chr9:17049830-17049831	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs189252761	chr9:17049923-17049924	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs541775842	chr9:17049931-17049932	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs149856565	chr9:17049937-17049938	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs188940880	chr9:17051035-17051036	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs192282562	chr9:17051041-17051042	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs557693838	chr9:17051049-17051050	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs112114939	chr9:17051099-17051100	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs381680	chr9:17051103-17051104	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs558370727	chr9:17051123-17051124	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs77916824	chr9:17051135-17051136	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs540743331	chr9:17051145-17051146	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs416421	chr9:17051170-17051171	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs180784778	chr9:17051270-17051271	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs111744960	chr9:17051273-17051274	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs572062224	chr9:17051274-17051275	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	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
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Myelofibrosis	22110671	CNVD
Glycine encephalopathy	21572526	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Glioblastoma multiforme	18628472	CNVD
Breast cancer	21364760	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17044800-17045600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:17052800-17053200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:17053200-17062600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:17057400-17058400	Enhancers	Fetal Intestine Large	intestine
5	chr9:17057600-17058200	Enhancers	Duodenum Mucosa	Duodenum
6	chr9:17057600-17058200	Enhancers	Fetal Intestine Small	intestine
7	chr9:17057600-17058200	Enhancers	HepG2	liver
8	chr9:17058000-17058400	Enhancers	Stomach Mucosa	stomach
9	chr9:17058400-17062200	Weak transcription	Fetal Intestine Large	intestine
10	chr9:17059800-17060400	Enhancers	Adipose Nuclei	Adipose
11	chr9:17060200-17061000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:17062200-17062800	Enhancers	Fetal Intestine Small	intestine
13	chr9:17062200-17063200	Enhancers	Fetal Intestine Large	intestine
14	chr9:17062600-17062800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:17064400-17065200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:17064600-17064800	Enhancers	A549	lung
17	chr9:17064600-17066200	Enhancers	HUVEC	blood vessel
18	chr9:17064800-17065000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:17064800-17065400	Enhancers	Liver	Liver
20	chr9:17065000-17065400	Enhancers	Osteobl	bone
21	chr9:17065000-17078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:17065200-17065400	Enhancers	Fetal Intestine Large	intestine
23	chr9:17068600-17069000	Enhancers	HUES64 Cell Line	embryonic stem cell

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