Variant report

Variant	nsv892641
Chromosome Location	chr9:16218659-16242088
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	BHLHE40	chr9:16221777-16222097	GM12878	blood:	n/a	n/a
2	CEBPB	chr9:16236214-16236699	IMR90	lung:	n/a	n/a
3	CEBPB	chr9:16236327-16236675	A549	lung:	n/a	n/a
4	CEBPB	chr9:16236346-16236654	HepG2	liver:	n/a	n/a
5	CEBPB	chr9:16236229-16236824	A549	lung:	n/a	n/a
6	CEBPB	chr9:16236289-16236673	A549	lung:	n/a	n/a
7	CEBPB	chr9:16236307-16236698	Hela-S3	cervix:	n/a	n/a
8	CHD2	chr9:16233684-16233721	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr9:16236180-16236330	AG09309	skin:	n/a	chr9:16236230-16236237
10	CTCF	chr9:16236140-16236290	NHDF-neo	bronchial:	n/a	chr9:16236230-16236237
11	CTCF	chr9:16236280-16236430	AG10803	skin:	n/a	n/a
12	CTCF	chr9:16236180-16236330	AoAF	blood vessel:	n/a	chr9:16236230-16236237
13	CTCF	chr9:16236276-16236283	Kidney_OC	kidney:	n/a	n/a
14	CTCF	chr9:16235280-16235430	A549	lung:	n/a	n/a
15	CTCF	chr9:16236420-16236570	HRE	kidney:	n/a	n/a
16	CTCF	chr9:16234424-16234486	Kidney_OC	kidney:	n/a	n/a
17	CTCF	chr9:16226872-16226945	Kidney_OC	kidney:	n/a	n/a
18	CTCF	chr9:16236140-16236290	HMF	breast:	n/a	chr9:16236230-16236237
19	CTCF	chr9:16236040-16236190	NHDF-neo	bronchial:	n/a	n/a
20	CTCF	chr9:16236100-16236250	HPF	lung:	n/a	chr9:16236230-16236237
21	CUX1	chr9:16221738-16222038	GM12878	blood:	n/a	n/a
22	EBF1	chr9:16221388-16222346	GM12878	blood:	n/a	n/a
23	EP300	chr9:16221729-16222041	GM12878	blood:	n/a	n/a
24	EP300	chr9:16236387-16236644	Hela-S3	cervix:	n/a	n/a
25	EP300	chr9:16221681-16222032	GM12878	blood:	n/a	n/a
26	FOS	chr9:16241267-16241660	HUVEC	blood vessel:	n/a	chr9:16241458-16241468 chr9:16241458-16241468 chr9:16241457-16241468
27	FOS	chr9:16222055-16222209	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr9:16241394-16241531	MCF10A-Er-Src	breast:	n/a	chr9:16241458-16241468 chr9:16241458-16241468 chr9:16241457-16241468
29	FOS	chr9:16236415-16236614	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr9:16222123-16222232	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr9:16236425-16236641	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr9:16241332-16241531	MCF10A-Er-Src	breast:	n/a	chr9:16241458-16241468 chr9:16241458-16241468 chr9:16241457-16241468
33	FOS	chr9:16236455-16236514	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr9:16222103-16222229	MCF10A-Er-Src	breast:	n/a	n/a
35	FOSL2	chr9:16241189-16241708	A549	lung:	n/a	chr9:16241458-16241468 chr9:16241458-16241468
36	FOSL2	chr9:16236303-16236815	A549	lung:	n/a	n/a
37	FOSL2	chr9:16241227-16241724	SK-N-SH	brain:	n/a	chr9:16241458-16241468 chr9:16241458-16241468
38	FOXA1	chr9:16223629-16223851	HepG2	liver:	n/a	n/a
39	FOXA1	chr9:16223573-16223924	HepG2	liver:	n/a	n/a
40	FOXA1	chr9:16223587-16223861	HepG2	liver:	n/a	n/a
41	FOXA1	chr9:16223622-16223848	HepG2	liver:	n/a	n/a
42	FOXA2	chr9:16223404-16224021	A549	lung:	n/a	n/a
43	FOXA2	chr9:16223459-16224088	A549	lung:	n/a	n/a
44	FOXA2	chr9:16223559-16223817	HepG2	liver:	n/a	n/a
45	GATA2	chr9:16241245-16241600	HUVEC	blood vessel:	n/a	n/a
46	GATA3	chr9:16221850-16222564	SK-N-SH	brain:	n/a	n/a
47	GATA3	chr9:16241064-16241807	SK-N-SH	brain:	n/a	n/a
48	GATA3	chr9:16221805-16222545	SK-N-SH	brain:	n/a	n/a
49	GATA3	chr9:16221694-16221741	SH-SY5Y	brain:	n/a	n/a
50	IKZF1	chr9:16221878-16222177	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:16233531..16235152-chr9:16236701..16238739,2	MCF-7	breast:
2	chr9:16233531..16235152-chr9:16236701..16238739,2	MCF-7	breast:
3	chr9:16201134..16203881-chr9:16231710..16234448,2	MCF-7	breast:
4	chr9:16207216..16210158-chr9:16217890..16219835,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf93-8	chr9:16216806-16219226	NONHSAT130285

Variant related genes	Relation type
C9orf92	TF binding region

Extended variants
information (count: 1291 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:1291 , 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	rs16934274	chr9:16218659-16218660	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs150787396	chr9:16218666-16218667	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs533155663	chr9:16218673-16218674	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs552254576	chr9:16218715-16218716	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs114849233	chr9:16218723-16218724	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs185575694	chr9:16218733-16218734	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs116671546	chr9:16218778-16218779	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs188476032	chr9:16218884-16218885	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs139040839	chr9:16218915-16218916	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs10962335	chr9:16218929-16218930	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs537542397	chr9:16218958-16218959	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs143961283	chr9:16218980-16218981	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs571706549	chr9:16218998-16218999	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs539234357	chr9:16218999-16219000	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs554144687	chr9:16219004-16219005	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs116866914	chr9:16219021-16219022	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs77734309	chr9:16219022-16219023	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs554995549	chr9:16219029-16219030	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs576553548	chr9:16219030-16219031	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs377043668	chr9:16219052-16219053	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs117323632	chr9:16219058-16219059	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs371844619	chr9:16219082-16219083	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs565387950	chr9:16219099-16219100	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs140387635	chr9:16219102-16219103	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs545166400	chr9:16219126-16219127	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs181081704	chr9:16219145-16219146	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs116341743	chr9:16219148-16219149	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs527572783	chr9:16219183-16219184	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs79331230	chr9:16219189-16219190	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs548911340	chr9:16219191-16219192	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs56920562	chr9:16219193-16219194	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs190607044	chr9:16219258-16219259	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs549428261	chr9:16219285-16219286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs145588077	chr9:16219309-16219310	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs538386420	chr9:16219321-16219322	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs554329646	chr9:16219332-16219333	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs76207457	chr9:16219337-16219338	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs147719394	chr9:16219363-16219364	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs184098955	chr9:16219407-16219408	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs386733076	chr9:16219430-16219431	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs112551877	chr9:16219432-16219433	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs537458214	chr9:16219437-16219438	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs376920738	chr9:16219441-16219442	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs558708941	chr9:16219453-16219454	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs553282675	chr9:16219466-16219467	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs142663244	chr9:16219473-16219474	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs142460887	chr9:16219479-16219480	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs560290236	chr9:16219483-16219484	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs369676896	chr9:16219486-16219487	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs538914701	chr9:16219487-16219488	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

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
Intellectual disability	22102821	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
Breast cancer	21364760	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	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
Pancreatic ductal adenocarcinoma	19077451	CNVD
early-passage human iPS cells	21368824	CNVD
Breast cancer	21611746	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:230 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16215000-16223400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:16215400-16220800	Weak transcription	Adipose Nuclei	Adipose
3	chr9:16215400-16222000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:16215600-16221200	Weak transcription	Fetal Kidney	kidney
5	chr9:16215800-16221400	Weak transcription	Right Atrium	heart
6	chr9:16217000-16221200	Weak transcription	Fetal Lung	lung
7	chr9:16217000-16221200	Weak transcription	Ovary	ovary
8	chr9:16217200-16221400	Weak transcription	A549	lung
9	chr9:16217600-16218800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:16217800-16218800	Enhancers	HSMM	muscle
11	chr9:16217800-16219200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:16217800-16219200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr9:16217800-16219200	Enhancers	NH-A	brain
14	chr9:16217800-16219200	Enhancers	Osteobl	bone
15	chr9:16218000-16218800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:16218000-16219000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:16218000-16221400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:16218000-16222600	Enhancers	NHDF-Ad	bronchial
19	chr9:16218200-16219000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:16218200-16219000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr9:16218400-16219000	Enhancers	HSMMtube	muscle
22	chr9:16218400-16219000	Enhancers	NHLF	lung
23	chr9:16218400-16219800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:16218400-16221200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:16218600-16218800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:16218600-16223400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:16218600-16233600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:16218800-16219600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:16218800-16221400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:16218800-16221400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:16219000-16219800	Enhancers	HMEC	breast
32	chr9:16219000-16221200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:16219000-16221400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:16219000-16221400	Weak transcription	NHLF	lung
35	chr9:16219000-16223600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:16219200-16221200	Weak transcription	Osteobl	bone
37	chr9:16219200-16221600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr9:16219600-16220000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:16219800-16221200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:16220400-16220800	Enhancers	GM12878-XiMat	blood
41	chr9:16220800-16221200	Weak transcription	GM12878-XiMat	blood
42	chr9:16220800-16222400	Enhancers	Adipose Nuclei	Adipose
43	chr9:16221200-16221400	Bivalent Enhancer	Fetal Heart	heart
44	chr9:16221200-16221400	Active TSS	GM12878-XiMat	blood
45	chr9:16221200-16221800	Enhancers	Brain Substantia Nigra	brain
46	chr9:16221200-16221800	Enhancers	Fetal Muscle Leg	muscle
47	chr9:16221200-16222000	Enhancers	Ovary	ovary
48	chr9:16221200-16222200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:16221200-16222400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:16221200-16222400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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