Variant report

Variant	esv2422381
Chromosome Location	chr9:9647540-9887820
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	chr9:9752784-9753086	HepG2	liver:	n/a	n/a
2	ARID3A	chr9:9790306-9790512	HepG2	liver:	n/a	n/a
3	BCL11A	chr9:9730250-9730402	GM12878	blood:	n/a	chr9:9730337-9730346
4	BCL11A	chr9:9730200-9730443	GM12878	blood:	n/a	chr9:9730337-9730346
5	BHLHE40	chr9:9847834-9848021	GM12878	blood:	n/a	n/a
6	BHLHE40	chr9:9790315-9790593	GM12878	blood:	n/a	n/a
7	BHLHE40	chr9:9730272-9730481	GM12878	blood:	n/a	n/a
8	BRCA1	chr9:9790311-9790476	HepG2	liver:	n/a	n/a
9	CEBPB	chr9:9824877-9825036	HepG2	liver:	n/a	chr9:9824982-9824993
10	CEBPB	chr9:9726424-9726758	HepG2	liver:	n/a	chr9:9726569-9726580 chr9:9726570-9726581 chr9:9726571-9726580
11	CEBPB	chr9:9750771-9751082	A549	lung:	n/a	chr9:9750940-9750951
12	CEBPB	chr9:9752779-9753043	HepG2	liver:	n/a	chr9:9752948-9752959 chr9:9752948-9752959 chr9:9752837-9752849
13	CEBPB	chr9:9672972-9673266	IMR90	lung:	n/a	chr9:9673125-9673136 chr9:9673127-9673136 chr9:9673127-9673136 chr9:9673125-9673136 chr9:9673127-9673136 chr9:9673125-9673138 chr9:9673126-9673137 chr9:9673127-9673136 chr9:9673125-9673138 chr9:9673125-9673138
14	CEBPB	chr9:9722810-9723118	HepG2	liver:	n/a	chr9:9722955-9722966
15	CEBPB	chr9:9655795-9656027	H1-hESC	embryonic stem cell:	n/a	n/a
16	CEBPB	chr9:9750792-9751088	ECC-1	luminal epithelium:	n/a	chr9:9750940-9750951
17	CEBPB	chr9:9726463-9726753	IMR90	lung:	n/a	chr9:9726569-9726580 chr9:9726570-9726581 chr9:9726571-9726580
18	CEBPB	chr9:9781774-9781789	H1-hESC	embryonic stem cell:	n/a	n/a
19	CEBPB	chr9:9750805-9751120	H1-hESC	embryonic stem cell:	n/a	chr9:9750940-9750951
20	CEBPB	chr9:9673021-9673231	A549	lung:	n/a	chr9:9673125-9673136 chr9:9673127-9673136 chr9:9673127-9673136 chr9:9673125-9673136 chr9:9673127-9673136 chr9:9673125-9673138 chr9:9673126-9673137 chr9:9673127-9673136 chr9:9673125-9673138 chr9:9673125-9673138
21	CEBPB	chr9:9750781-9751123	IMR90	lung:	n/a	chr9:9750940-9750951
22	CEBPB	chr9:9750778-9751121	HepG2	liver:	n/a	chr9:9750940-9750951
23	CEBPB	chr9:9705353-9705504	HepG2	liver:	n/a	chr9:9705374-9705387
24	CEBPB	chr9:9726550-9726603	K562	blood:	n/a	chr9:9726569-9726580 chr9:9726570-9726581 chr9:9726571-9726580
25	CEBPB	chr9:9860177-9860680	HepG2	liver:	n/a	chr9:9860493-9860504 chr9:9860492-9860503 chr9:9860492-9860505
26	CEBPB	chr9:9860120-9860628	IMR90	lung:	n/a	chr9:9860493-9860504 chr9:9860133-9860145 chr9:9860492-9860503 chr9:9860492-9860505
27	CEBPB	chr9:9878262-9878354	A549	lung:	n/a	n/a
28	CEBPB	chr9:9831774-9832068	IMR90	lung:	n/a	chr9:9831888-9831899
29	CEBPB	chr9:9831770-9832132	A549	lung:	n/a	chr9:9831888-9831899
30	CEBPB	chr9:9704465-9704788	A549	lung:	n/a	chr9:9704620-9704631
31	CEBPB	chr9:9704471-9704800	HepG2	liver:	n/a	chr9:9704620-9704631
32	CEBPB	chr9:9726482-9726765	A549	lung:	n/a	chr9:9726569-9726580 chr9:9726570-9726581 chr9:9726571-9726580
33	CEBPB	chr9:9672953-9673253	HepG2	liver:	n/a	chr9:9673125-9673136 chr9:9673127-9673136 chr9:9673127-9673136 chr9:9673125-9673136 chr9:9673127-9673136 chr9:9673125-9673138 chr9:9673126-9673137 chr9:9673127-9673136 chr9:9673125-9673138 chr9:9673125-9673138
34	CEBPB	chr9:9863586-9863715	A549	lung:	n/a	n/a
35	CEBPB	chr9:9754428-9754673	A549	lung:	n/a	chr9:9754580-9754589 chr9:9754578-9754591 chr9:9754580-9754591
36	CEBPB	chr9:9831744-9832058	HepG2	liver:	n/a	chr9:9831888-9831899
37	CEBPB	chr9:9860376-9860648	A549	lung:	n/a	chr9:9860493-9860504 chr9:9860492-9860503 chr9:9860492-9860505
38	CHD2	chr9:9757890-9758032	HepG2	liver:	n/a	n/a
39	CTCF	chr9:9790346-9790563	Lung_OC	lung:	n/a	chr9:9790450-9790458
40	CTCF	chr9:9790365-9790542	K562	blood:	n/a	chr9:9790450-9790458
41	CTCF	chr9:9790340-9790490	HEK293	kidney:	n/a	chr9:9790450-9790458
42	CTCF	chr9:9790340-9790490	NB4	blood:	n/a	chr9:9790450-9790458
43	CTCF	chr9:9847600-9847750	GM06990	blood:	n/a	n/a
44	CTCF	chr9:9791800-9791950	RPTEC	kidney:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
45	CTCF	chr9:9791827-9791882	GM10248	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
46	CTCF	chr9:9790480-9790630	A549	lung:	n/a	n/a
47	CTCF	chr9:9790285-9790614	K562	blood:	n/a	chr9:9790450-9790458
48	CTCF	chr9:9791740-9791890	GM12873	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
49	CTCF	chr9:9790340-9790490	GM12869	blood:	n/a	chr9:9790450-9790458
50	CTCF	chr9:9791740-9791890	BE2_C	brain:	n/a	chr9:9791839-9791860 chr9:9791844-9791862

No.	Distal block	Cell Line	Cell type
1	chr9:9751206..9753342-chr9:9765211..9766880,2	MCF-7	breast:
2	chr9:9751206..9753342-chr9:9765211..9766880,2	MCF-7	breast:
3	chr9:9606507..9607603-chr9:9789935..9790958,7	MCF-7	breast:
4	chr9:9606153..9607209-chr9:9791346..9792141,4	MCF-7	breast:
5	chr9:9606480..9607195-chr9:9789919..9790916,3	MCF-7	breast:
6	chr9:9606591..9607143-chr9:9791328..9791942,2	MCF-7	breast:
7	chr1:11968121..11968918-chr9:9730851..9731851,3	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-10	chr9:9799423-9799608	ENSG00000230920
2	lnc-KDM4C-10	chr9:9800546-9800674	ENSG00000230920
3	lnc-KDM4C-10	chr9:9803717-9803784	ENSG00000230920

Variant related genes	Relation type
ENSG00000230920	TF binding region
ENSG00000199347	chromatin interactions

Extended variants
information (count: 4889 )
Associated
traits (count: 117 )

Variant overlapped rSNPs/rCNVs (count:4889 , 50 per page) page: 1 2 3 4 5 6 7 ... 98

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs187241245	chr9:9647574-9647575	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs191900517	chr9:9647587-9647588	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs575550725	chr9:9647638-9647639	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs184511799	chr9:9647657-9647658	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs570337775	chr9:9647676-9647677	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs147396269	chr9:9647696-9647697	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs556288493	chr9:9647736-9647737	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs568072832	chr9:9647739-9647740	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs190391383	chr9:9647744-9647745	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs561403939	chr9:9647764-9647765	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs553848569	chr9:9647782-9647783	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs572057051	chr9:9647852-9647853	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs113257372	chr9:9647856-9647857	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs559365802	chr9:9647864-9647865	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs559314591	chr9:9647883-9647884	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs368598800	chr9:9647885-9647886	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs528700737	chr9:9647915-9647916	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs10759083	chr9:9647916-9647917	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs563053875	chr9:9647944-9647945	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs142632041	chr9:9647958-9647959	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs369381028	chr9:9647992-9647993	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs560146582	chr9:9648010-9648011	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs555676340	chr9:9648018-9648019	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs151270237	chr9:9648035-9648036	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs572286256	chr9:9648053-9648054	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs570429096	chr9:9648055-9648056	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs559121964	chr9:9648069-9648070	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs113202123	chr9:9648083-9648084	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs541288908	chr9:9648086-9648087	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs181939227	chr9:9648136-9648137	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs185692056	chr9:9648139-9648140	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs369067775	chr9:9648162-9648163	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs535232546	chr9:9648176-9648177	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs34293416	chr9:9648181-9648182	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs189054745	chr9:9648189-9648190	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs149982433	chr9:9648196-9648197	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs180893768	chr9:9648209-9648210	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs557748667	chr9:9648212-9648213	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs146547929	chr9:9648213-9648214	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs564500932	chr9:9648221-9648222	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs544889002	chr9:9648222-9648223	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs556522927	chr9:9648226-9648227	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs574958297	chr9:9648234-9648235	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs185203666	chr9:9648264-9648265	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs548753588	chr9:9648277-9648278	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs527743038	chr9:9648301-9648302	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs545801164	chr9:9648318-9648319	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs564456748	chr9:9648348-9648349	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs531553477	chr9:9648379-9648380	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs141384026	chr9:9648408-9648409	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:117)

Disease	PMID	Source
abnormal development	18461090	CNVD
Disorders of sex development	21048976	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
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21080181	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
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
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
Myelofibrosis	22110671	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Lung cancer	20668451	CNVD
Schizophrenia	20838587	CNVD
Glioblastoma	18772890	CNVD
Glioblastoma multiforme	21390271	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	21764851	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Gastric cancer	16891809	CNVD
Mental retardation	17847001	CNVD
Cutaneous squamous cell carcinomas	17420988	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Acute myeloid leukemia	21251322	CNVD
Lung adenocarcinoma	17982442	CNVD
Gastric cancer	22315472	CNVD
Chordoma	21215367	CNVD
Schizophrenia	23813976	CNVD
Nasopharyngeal cancer	20548289	CNVD
Breast cancer	21611746	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:173 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9643400-9647600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:9646200-9648000	Enhancers	NH-A	brain
3	chr9:9646800-9648200	Enhancers	HUVEC	blood vessel
4	chr9:9646800-9648600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr9:9647600-9648200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr9:9647600-9648600	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr9:9647800-9648200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:9648200-9648600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:9648600-9649400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr9:9655200-9656000	Enhancers	Placenta	Placenta
11	chr9:9667600-9668000	Enhancers	Aorta	Aorta
12	chr9:9670600-9670800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:9679000-9680200	Enhancers	Liver	Liver
14	chr9:9680200-9681200	Weak transcription	Liver	Liver
15	chr9:9681200-9681400	Enhancers	Liver	Liver
16	chr9:9714000-9714800	Enhancers	Fetal Kidney	kidney
17	chr9:9718200-9718400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:9718400-9719200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:9718600-9720000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:9719000-9719800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
21	chr9:9729200-9731200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:9730200-9730600	Enhancers	GM12878-XiMat	blood
23	chr9:9745200-9750800	Enhancers	HUVEC	blood vessel
24	chr9:9747800-9748600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr9:9748600-9752600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr9:9749600-9751000	Enhancers	Fetal Kidney	kidney
27	chr9:9750600-9751200	Enhancers	Liver	Liver
28	chr9:9751200-9751400	Flanking Active TSS	Liver	Liver
29	chr9:9751400-9751600	Enhancers	Liver	Liver
30	chr9:9751600-9751800	Flanking Active TSS	Liver	Liver
31	chr9:9751800-9753600	Enhancers	Liver	Liver
32	chr9:9752200-9754200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:9752200-9754800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:9752400-9752800	Enhancers	Rectal Smooth Muscle	rectum
35	chr9:9752400-9753600	Enhancers	HepG2	liver
36	chr9:9752600-9753400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr9:9752600-9754000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:9752800-9753400	Enhancers	Adipose Nuclei	Adipose
39	chr9:9752800-9753400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr9:9752800-9753600	Enhancers	Brain Hippocampus Middle	brain
41	chr9:9753400-9754400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:9754200-9754600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:9754200-9755200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr9:9754400-9754600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr9:9754400-9755000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr9:9756000-9756600	Enhancers	Fetal Heart	heart
47	chr9:9764800-9765000	Enhancers	Aorta	Aorta
48	chr9:9765000-9778800	Weak transcription	Aorta	Aorta
49	chr9:9775400-9776200	Enhancers	HUVEC	blood vessel
50	chr9:9776200-9776600	Flanking Active TSS	HUVEC	blood vessel

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