Variant report

Variant	nsv892288
Chromosome Location	chr9:9794545-9882950
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	chr9:9847834-9848021	GM12878	blood:	n/a	n/a
2	CEBPB	chr9:9878262-9878354	A549	lung:	n/a	n/a
3	CEBPB	chr9:9860177-9860680	HepG2	liver:	n/a	chr9:9860493-9860504 chr9:9860492-9860503 chr9:9860492-9860505
4	CEBPB	chr9:9860120-9860628	IMR90	lung:	n/a	chr9:9860493-9860504 chr9:9860133-9860145 chr9:9860492-9860503 chr9:9860492-9860505
5	CEBPB	chr9:9831770-9832132	A549	lung:	n/a	chr9:9831888-9831899
6	CEBPB	chr9:9860376-9860648	A549	lung:	n/a	chr9:9860493-9860504 chr9:9860492-9860503 chr9:9860492-9860505
7	CEBPB	chr9:9824877-9825036	HepG2	liver:	n/a	chr9:9824982-9824993
8	CEBPB	chr9:9831744-9832058	HepG2	liver:	n/a	chr9:9831888-9831899
9	CEBPB	chr9:9831774-9832068	IMR90	lung:	n/a	chr9:9831888-9831899
10	CEBPB	chr9:9863586-9863715	A549	lung:	n/a	n/a
11	CTCF	chr9:9847600-9847750	GM06990	blood:	n/a	n/a
12	CTCF	chr9:9833966-9834024	GM10248	blood:	n/a	n/a
13	CTCF	chr9:9865400-9865550	GM12864	blood:	n/a	n/a
14	CTCF	chr9:9855680-9855830	GM06990	blood:	n/a	n/a
15	E2F4	chr9:9806090-9806169	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr9:9796904-9797116	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr9:9798861-9798880	Hela-S3	cervix:	n/a	n/a
18	FOS	chr9:9831836-9831957	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr9:9836518-9836580	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr9:9831831-9831953	MCF10A-Er-Src	breast:	n/a	n/a
21	GATA2	chr9:9862293-9862864	SH-SY5Y	brain:	n/a	chr9:9862598-9862608 chr9:9862600-9862607 chr9:9862593-9862614 chr9:9862600-9862607 chr9:9862600-9862610 chr9:9862600-9862607 chr9:9862595-9862611
22	GATA2	chr9:9849655-9850161	SH-SY5Y	brain:	n/a	n/a
23	GATA3	chr9:9862365-9862660	T-47D	breast:	n/a	chr9:9862598-9862608 chr9:9862600-9862607 chr9:9862593-9862614 chr9:9862600-9862607 chr9:9862599-9862607 chr9:9862600-9862610 chr9:9862600-9862607 chr9:9862595-9862611
24	GATA3	chr9:9862074-9862849	SH-SY5Y	brain:	n/a	chr9:9862598-9862608 chr9:9862600-9862607 chr9:9862593-9862614 chr9:9862600-9862607 chr9:9862599-9862607 chr9:9862600-9862610 chr9:9862600-9862607 chr9:9862595-9862611
25	GATA3	chr9:9879636-9879898	SH-SY5Y	brain:	n/a	chr9:9879727-9879734 chr9:9879750-9879757 chr9:9879860-9879867 chr9:9879860-9879867 chr9:9879727-9879734 chr9:9879858-9879867 chr9:9879750-9879757 chr9:9879748-9879758 chr9:9879860-9879867 chr9:9879858-9879868 chr9:9879750-9879757 chr9:9879727-9879734 chr9:9879855-9879871
26	GATA3	chr9:9849607-9850126	SH-SY5Y	brain:	n/a	n/a
27	GATA3	chr9:9804049-9804244	SH-SY5Y	brain:	n/a	n/a
28	GTF2F1	chr9:9795671-9795745	H1-hESC	embryonic stem cell:	n/a	n/a
29	IRF1	chr9:9803600-9803610	K562	blood:	n/a	n/a
30	JUN	chr9:9831820-9831933	HepG2	liver:	n/a	chr9:9831885-9831898
31	JUN	chr9:9796761-9797028	HepG2	liver:	n/a	chr9:9796897-9796910
32	JUN	chr9:9849493-9849582	H1-hESC	embryonic stem cell:	n/a	n/a
33	JUND	chr9:9831058-9831201	HepG2	liver:	n/a	n/a
34	JUND	chr9:9807729-9807992	HepG2	liver:	n/a	chr9:9807861-9807872
35	JUND	chr9:9877172-9877249	HepG2	liver:	n/a	chr9:9877189-9877199 chr9:9877188-9877199 chr9:9877191-9877198 chr9:9877189-9877198
36	JUND	chr9:9796725-9797083	HepG2	liver:	n/a	n/a
37	MAFF	chr9:9845222-9845444	HepG2	liver:	n/a	n/a
38	MAFF	chr9:9860824-9860933	HepG2	liver:	n/a	n/a
39	MAFF	chr9:9843707-9843869	HepG2	liver:	n/a	chr9:9843754-9843772
40	MAFF	chr9:9873039-9873207	HepG2	liver:	n/a	chr9:9873096-9873114
41	MAFK	chr9:9836766-9836822	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAFK	chr9:9860771-9861007	HepG2	liver:	n/a	n/a
43	MAFK	chr9:9872971-9873261	HepG2	liver:	n/a	chr9:9873097-9873113 chr9:9873102-9873113 chr9:9873100-9873114 chr9:9873097-9873112 chr9:9873101-9873112 chr9:9873102-9873113
44	MAFK	chr9:9845209-9845502	HepG2	liver:	n/a	chr9:9845315-9845329
45	MAFK	chr9:9843619-9843855	HepG2	liver:	n/a	chr9:9843757-9843768 chr9:9843756-9843767 chr9:9843756-9843767 chr9:9843755-9843769 chr9:9843756-9843772 chr9:9843757-9843768
46	MAFK	chr9:9807749-9807946	HepG2	liver:	n/a	n/a
47	MAFK	chr9:9881274-9881302	HepG2	liver:	n/a	n/a
48	MAFK	chr9:9862968-9863178	HepG2	liver:	n/a	n/a
49	MAFK	chr9:9860871-9860959	HepG2	liver:	n/a	n/a
50	MAFK	chr9:9872960-9873244	HepG2	liver:	n/a	chr9:9873097-9873113 chr9:9873102-9873113 chr9:9873100-9873114 chr9:9873097-9873112 chr9:9873101-9873112 chr9:9873102-9873113

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

Variant related genes	Relation type
ENSG00000230920	TF binding region

Extended variants
information (count: 2058 )
Associated
traits (count: 114 )

Variant overlapped rSNPs/rCNVs (count:2058 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs574171756	chr9:9794689-9794690	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs368514527	chr9:9794695-9794696	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs542890072	chr9:9794716-9794717	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs144577294	chr9:9794718-9794719	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs59583349	chr9:9794720-9794721	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs541000423	chr9:9794758-9794759	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs113657703	chr9:9794761-9794762	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs371475151	chr9:9794793-9794794	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs370278040	chr9:9794799-9794800	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs191729377	chr9:9794800-9794801	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs559066296	chr9:9795680-9795681	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs572690729	chr9:9795733-9795734	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs573313572	chr9:9795742-9795743	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs10114232	chr9:9795743-9795744	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs376480304	chr9:9795744-9795745	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs538296221	chr9:9796726-9796727	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs143204881	chr9:9796735-9796736	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs568968322	chr9:9796761-9796762	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs556631328	chr9:9796791-9796792	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs138820666	chr9:9796794-9796795	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs554772985	chr9:9796795-9796796	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs142841324	chr9:9796813-9796814	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs147260766	chr9:9796821-9796822	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs554156255	chr9:9796823-9796824	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs567071963	chr9:9796889-9796890	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs535821722	chr9:9796892-9796893	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs76553457	chr9:9796898-9796899	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs140830787	chr9:9796993-9796994	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs377278419	chr9:9797004-9797005	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs141398171	chr9:9797011-9797012	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs542022066	chr9:9797015-9797016	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs10977986	chr9:9797029-9797030	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs561956096	chr9:9797041-9797042	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs10977987	chr9:9797049-9797050	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs527934405	chr9:9797063-9797064	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs547685452	chr9:9797098-9797099	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs547341219	chr9:9797107-9797108	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs141214159	chr9:9797112-9797113	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs189768587	chr9:9799417-9799418	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs371250465	chr9:9799424-9799425	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs567796661	chr9:9799438-9799439	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs113460807	chr9:9799439-9799440	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs181604476	chr9:9799451-9799452	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs561165813	chr9:9799461-9799462	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs2296171	chr9:9799476-9799477	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs146153795	chr9:9799489-9799490	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs546682230	chr9:9799520-9799521	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs567135849	chr9:9799532-9799533	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs548752046	chr9:9799548-9799549	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs369292440	chr9:9799565-9799566	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:114)

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
Breast cancer	21611746	CNVD
Schizophrenia	23813976	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9799400-9799800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr9:9799400-9799800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:9799400-9800800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr9:9799400-9801400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:9799600-9799800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:9799800-9800600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:9799800-9800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:9799800-9801000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:9800600-9801600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:9800800-9801600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr9:9801000-9801600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr9:9805200-9806000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr9:9807800-9808000	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr9:9820000-9821000	Enhancers	NH-A	brain
15	chr9:9825200-9825400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:9825400-9825600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:9832800-9834600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr9:9834200-9834600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr9:9845200-9845800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:9845400-9846200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:9845400-9846200	Enhancers	Dnd41	blood
22	chr9:9845800-9846800	Enhancers	Primary hematopoietic stem cells	blood
23	chr9:9845800-9847000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:9845800-9847800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr9:9846200-9847000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:9846200-9847000	Flanking Active TSS	Dnd41	blood
27	chr9:9846600-9847000	Active TSS	GM12878-XiMat	blood
28	chr9:9846800-9847200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:9847000-9848200	Enhancers	Dnd41	blood
30	chr9:9847000-9848400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:9847000-9848600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:9847200-9848400	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:9847600-9847800	Enhancers	GM12878-XiMat	blood
34	chr9:9847600-9848200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:9847600-9848200	Enhancers	Placenta	Placenta
36	chr9:9848200-9855000	Weak transcription	Placenta	Placenta
37	chr9:9848600-9855400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:9853600-9853800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:9854000-9855600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:9855000-9855200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr9:9855000-9855600	Enhancers	Dnd41	blood
42	chr9:9855000-9856200	Enhancers	Fetal Thymus	thymus
43	chr9:9855000-9856400	Enhancers	Placenta	Placenta
44	chr9:9855200-9855400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:9855200-9855600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr9:9855400-9855600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:9855400-9855800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr9:9855400-9855800	Enhancers	Primary T cells from cord blood	blood
49	chr9:9855400-9855800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:9855400-9856000	Active TSS	HUES6 Cell Line	embryonic stem cell

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