Variant report

Variant	nsv892276
Chromosome Location	chr9:9778653-9851382
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	chr9:9790306-9790512	HepG2	liver:	n/a	n/a
2	BHLHE40	chr9:9790315-9790593	GM12878	blood:	n/a	n/a
3	BHLHE40	chr9:9847834-9848021	GM12878	blood:	n/a	n/a
4	BRCA1	chr9:9790311-9790476	HepG2	liver:	n/a	n/a
5	CEBPB	chr9:9824877-9825036	HepG2	liver:	n/a	chr9:9824982-9824993
6	CEBPB	chr9:9831770-9832132	A549	lung:	n/a	chr9:9831888-9831899
7	CEBPB	chr9:9831774-9832068	IMR90	lung:	n/a	chr9:9831888-9831899
8	CEBPB	chr9:9831744-9832058	HepG2	liver:	n/a	chr9:9831888-9831899
9	CEBPB	chr9:9781774-9781789	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr9:9790331-9790573	GM13977	blood:	n/a	chr9:9790450-9790458
11	CTCF	chr9:9790360-9790510	HUVEC	blood vessel:	n/a	chr9:9790450-9790458
12	CTCF	chr9:9790400-9790550	GM12864	blood:	n/a	chr9:9790450-9790458
13	CTCF	chr9:9790229-9790573	HepG2	liver:	n/a	chr9:9790450-9790458
14	CTCF	chr9:9790160-9790310	HCT-116	colon:	n/a	n/a
15	CTCF	chr9:9792182-9792193	GM10248	blood:	n/a	n/a
16	CTCF	chr9:9790360-9790510	MCF-7	breast:	n/a	chr9:9790450-9790458
17	CTCF	chr9:9790400-9790550	NHEK	skin:	n/a	chr9:9790450-9790458
18	CTCF	chr9:9790324-9790587	Spleen_OC	spleen:	n/a	chr9:9790450-9790458
19	CTCF	chr9:9790380-9790530	HFF-Myc	foreskin:	n/a	chr9:9790450-9790458
20	CTCF	chr9:9791620-9791770	GM06990	blood:	n/a	n/a
21	CTCF	chr9:9790320-9790470	AG04450	lung:	n/a	chr9:9790450-9790458
22	CTCF	chr9:9791780-9791930	RPTEC	kidney:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
23	CTCF	chr9:9790480-9790630	A549	lung:	n/a	n/a
24	CTCF	chr9:9791623-9792177	SK-N-SH	brain:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
25	CTCF	chr9:9790380-9790530	GM06990	blood:	n/a	chr9:9790450-9790458
26	CTCF	chr9:9790358-9790459	Fibrobl	skin:	n/a	chr9:9790450-9790458
27	CTCF	chr9:9791760-9791910	GM06990	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
28	CTCF	chr9:9790372-9790450	NHEK	skin:	n/a	n/a
29	CTCF	chr9:9790340-9790490	GM12878	blood:	n/a	chr9:9790450-9790458
30	CTCF	chr9:9790380-9790530	AoAF	blood vessel:	n/a	chr9:9790450-9790458
31	CTCF	chr9:9791740-9791890	HPF	lung:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
32	CTCF	chr9:9791720-9791870	HUVEC	blood vessel:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
33	CTCF	chr9:9791380-9791530	RPTEC	kidney:	n/a	n/a
34	CTCF	chr9:9790330-9790461	GM19238	blood:	n/a	chr9:9790450-9790458
35	CTCF	chr9:9791827-9791882	GM10248	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
36	CTCF	chr9:9791760-9791910	AG09319	gingival:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
37	CTCF	chr9:9790420-9790570	HEEpiC	esophagus:	n/a	chr9:9790450-9790458
38	CTCF	chr9:9791840-9791990	GM12865	blood:	n/a	chr9:9791844-9791862
39	CTCF	chr9:9790320-9790470	K562	blood:	n/a	chr9:9790450-9790458
40	CTCF	chr9:9790380-9790530	BE2_C	brain:	n/a	chr9:9790450-9790458
41	CTCF	chr9:9790360-9790510	Caco-2	colon:	n/a	chr9:9790450-9790458
42	CTCF	chr9:9790420-9790570	HPAF	blood vessel:	n/a	chr9:9790450-9790458
43	CTCF	chr9:9790360-9790510	NHLF	lung:	n/a	chr9:9790450-9790458
44	CTCF	chr9:9791800-9791950	HVMF	connective:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
45	CTCF	chr9:9791775-9791884	HepG2	liver:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
46	CTCF	chr9:9790321-9790567	GM12878	blood:	n/a	chr9:9790450-9790458
47	CTCF	chr9:9778994-9779135	GM10248	blood:	n/a	n/a
48	CTCF	chr9:9791640-9791790	HVMF	connective:	n/a	n/a
49	CTCF	chr9:9790400-9790550	HA-sp	spinal cord:	n/a	chr9:9790450-9790458
50	CTCF	chr9:9790340-9790490	GM12869	blood:	n/a	chr9:9790450-9790458

No.	Distal block	Cell Line	Cell type
1	chr9:9606153..9607209-chr9:9791346..9792141,4	MCF-7	breast:
2	chr9:9606507..9607603-chr9:9789935..9790958,7	MCF-7	breast:
3	chr9:9606480..9607195-chr9:9789919..9790916,3	MCF-7	breast:
4	chr9:9606591..9607143-chr9:9791328..9791942,2	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000230920	TF binding region

Extended variants
information (count: 1257 )
Associated
traits (count: 115 )

Variant overlapped rSNPs/rCNVs (count:1257 , 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	rs2761723	chr9:9778653-9778654	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs552857029	chr9:9778702-9778703	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs144304908	chr9:9778708-9778709	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs544996445	chr9:9778714-9778715	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs558566310	chr9:9778715-9778716	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs369863355	chr9:9778734-9778735	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs183615018	chr9:9778783-9778784	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs532601664	chr9:9778808-9778809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs527945798	chr9:9778826-9778827	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs377650023	chr9:9778827-9778828	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs367865934	chr9:9778828-9778829	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs2761724	chr9:9778837-9778838	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs561500885	chr9:9778840-9778841	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs2821470	chr9:9778858-9778859	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs540875970	chr9:9778859-9778860	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs10977974	chr9:9778861-9778862	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs376089847	chr9:9779012-9779013	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs560766064	chr9:9779019-9779020	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs572764968	chr9:9779053-9779054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs532897252	chr9:9779074-9779075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs201942223	chr9:9779077-9779078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs112566238	chr9:9779079-9779080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs76575148	chr9:9779104-9779105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs370933053	chr9:9779105-9779106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs551381577	chr9:9779110-9779111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs552701488	chr9:9779167-9779168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs76588836	chr9:9779189-9779190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs530600262	chr9:9779279-9779280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs146380284	chr9:9779285-9779286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs2476587	chr9:9779291-9779292	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs534392153	chr9:9779310-9779311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs375337407	chr9:9779314-9779315	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs72710118	chr9:9779347-9779348	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs2476588	chr9:9779358-9779359	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs191980435	chr9:9779361-9779362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs538578184	chr9:9779383-9779384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs2494403	chr9:9779386-9779387	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs2476589	chr9:9779412-9779413	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs544654559	chr9:9779413-9779414	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs554771584	chr9:9779414-9779415	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs574924169	chr9:9779418-9779419	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs540822293	chr9:9779444-9779445	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs566419816	chr9:9779448-9779449	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs560702696	chr9:9779473-9779474	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs139763598	chr9:9779475-9779476	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs541623688	chr9:9779531-9779532	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs182653249	chr9:9779535-9779536	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs564840801	chr9:9779536-9779537	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs144367005	chr9:9779540-9779541	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs372234522	chr9:9779608-9779609	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:115)

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
Schizophrenia	23813976	CNVD
Nasopharyngeal cancer	20548289	CNVD
Breast cancer	21611746	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9765000-9778800	Weak transcription	Aorta	Aorta
2	chr9:9776600-9779000	Enhancers	HUVEC	blood vessel
3	chr9:9778400-9778800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:9778400-9778800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:9779000-9782000	Weak transcription	HUVEC	blood vessel
6	chr9:9779400-9780000	Enhancers	NH-A	brain
7	chr9:9782000-9784000	Enhancers	HUVEC	blood vessel
8	chr9:9782600-9784000	Enhancers	Brain Angular Gyrus	brain
9	chr9:9782800-9783400	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr9:9783400-9783800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr9:9783600-9784000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr9:9783800-9784600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr9:9784600-9786000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr9:9786000-9786200	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr9:9789200-9789400	Enhancers	Liver	Liver
16	chr9:9790000-9790400	Enhancers	Dnd41	blood
17	chr9:9790200-9790400	Enhancers	Liver	Liver
18	chr9:9791400-9793000	Enhancers	Primary B cells from cord blood	blood
19	chr9:9792000-9792600	Enhancers	Primary hematopoietic stem cells	blood
20	chr9:9792000-9792600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:9792000-9792600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:9792200-9792800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:9799400-9799800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr9:9799400-9799800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr9:9799400-9800800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr9:9799400-9801400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr9:9799600-9799800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr9:9799800-9800600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:9799800-9800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:9799800-9801000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:9800600-9801600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr9:9800800-9801600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr9:9801000-9801600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr9:9805200-9806000	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr9:9807800-9808000	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr9:9820000-9821000	Enhancers	NH-A	brain
37	chr9:9825200-9825400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:9825400-9825600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:9832800-9834600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr9:9834200-9834600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:9845200-9845800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:9845400-9846200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:9845400-9846200	Enhancers	Dnd41	blood
44	chr9:9845800-9846800	Enhancers	Primary hematopoietic stem cells	blood
45	chr9:9845800-9847000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:9845800-9847800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:9846200-9847000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:9846200-9847000	Flanking Active TSS	Dnd41	blood
49	chr9:9846600-9847000	Active TSS	GM12878-XiMat	blood
50	chr9:9846800-9847200	Weak transcription	Primary hematopoietic stem cells	blood

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