Variant report

Variant	nsv466091
Chromosome Location	chr9:3349487-3389660
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	chr9:3359845-3360042	HepG2	liver:	n/a	n/a
2	ATF1	chr9:3375330-3375528	K562	blood:	n/a	n/a
3	ATF2	chr9:3385879-3386250	GM12878	blood:	n/a	n/a
4	ATF2	chr9:3385810-3386259	GM12878	blood:	n/a	n/a
5	BATF	chr9:3385831-3386250	GM12878	blood:	n/a	n/a
6	BATF	chr9:3385874-3386227	GM12878	blood:	n/a	n/a
7	CEBPB	chr9:3351935-3352044	IMR90	lung:	n/a	n/a
8	CEBPB	chr9:3386846-3387137	A549	lung:	n/a	n/a
9	CEBPB	chr9:3374682-3375091	HepG2	liver:	n/a	chr9:3374764-3374775
10	CEBPB	chr9:3386799-3387117	IMR90	lung:	n/a	n/a
11	CEBPB	chr9:3368003-3368124	A549	lung:	n/a	n/a
12	CEBPB	chr9:3386766-3387164	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr9:3368064-3368180	H1-hESC	embryonic stem cell:	n/a	chr9:3368133-3368146 chr9:3368135-3368146 chr9:3368133-3368146
14	CEBPB	chr9:3386811-3387106	K562	blood:	n/a	n/a
15	CEBPB	chr9:3386798-3387131	HepG2	liver:	n/a	n/a
16	CEBPB	chr9:3386780-3387105	MCF-7	breast:	n/a	n/a
17	CEBPB	chr9:3361965-3362341	H1-hESC	embryonic stem cell:	n/a	n/a
18	CEBPB	chr9:3367948-3368174	HepG2	liver:	n/a	chr9:3368133-3368146 chr9:3368135-3368146 chr9:3368133-3368146
19	CREB1	chr9:3385834-3386287	GM12878	blood:	n/a	n/a
20	CTCF	chr9:3383760-3383910	HMF	breast:	n/a	n/a
21	CUX1	chr9:3381284-3381351	K562	blood:	n/a	chr9:3381302-3381311
22	EBF1	chr9:3371715-3372014	GM12878	blood:	n/a	n/a
23	EBF1	chr9:3367490-3367733	GM12878	blood:	n/a	chr9:3367645-3367654 chr9:3367643-3367654 chr9:3367643-3367656 chr9:3367645-3367654 chr9:3367644-3367654
24	EBF1	chr9:3370818-3370959	GM12878	blood:	n/a	n/a
25	EBF1	chr9:3367513-3367786	GM12878	blood:	n/a	chr9:3367645-3367654 chr9:3367643-3367654 chr9:3367643-3367656 chr9:3367645-3367654 chr9:3367644-3367654
26	EP300	chr9:3386814-3387063	Hela-S3	cervix:	n/a	chr9:3386877-3386891 chr9:3386926-3386935 chr9:3386927-3386936
27	EP300	chr9:3371738-3372046	GM12878	blood:	n/a	chr9:3371837-3371851
28	FOS	chr9:3386753-3387115	MCF10A-Er-Src	breast:	n/a	chr9:3386880-3386889 chr9:3386928-3386935 chr9:3386927-3386935 chr9:3386925-3386937 chr9:3386926-3386936 chr9:3386927-3386936
29	FOS	chr9:3386769-3387120	MCF10A-Er-Src	breast:	n/a	chr9:3386880-3386889 chr9:3386928-3386935 chr9:3386927-3386935 chr9:3386925-3386937 chr9:3386926-3386936 chr9:3386927-3386936
30	FOS	chr9:3385923-3386153	MCF10A-Er-Src	breast:	n/a	chr9:3386140-3386149 chr9:3386084-3386092 chr9:3386004-3386016
31	FOS	chr9:3386755-3387117	MCF10A-Er-Src	breast:	n/a	chr9:3386880-3386889 chr9:3386928-3386935 chr9:3386927-3386935 chr9:3386925-3386937 chr9:3386926-3386936 chr9:3386927-3386936
32	FOS	chr9:3386763-3387126	MCF10A-Er-Src	breast:	n/a	chr9:3386880-3386889 chr9:3386928-3386935 chr9:3386927-3386935 chr9:3386925-3386937 chr9:3386926-3386936 chr9:3386927-3386936
33	GATA3	chr9:3365682-3365817	SH-SY5Y	brain:	n/a	n/a
34	GATA3	chr9:3387852-3388008	SH-SY5Y	brain:	n/a	n/a
35	GATA3	chr9:3350642-3350741	SH-SY5Y	brain:	n/a	n/a
36	GATA3	chr9:3383258-3383318	SH-SY5Y	brain:	n/a	n/a
37	GATA3	chr9:3360089-3360485	SH-SY5Y	brain:	n/a	n/a
38	GTF2F1	chr9:3386836-3387072	Hela-S3	cervix:	n/a	n/a
39	IKZF1	chr9:3371743-3372033	GM12878	blood:	n/a	n/a
40	IKZF1	chr9:3385882-3386220	GM12878	blood:	n/a	n/a
41	IRF1	chr9:3388095-3388110	K562	blood:	n/a	n/a
42	IRF3	chr9:3367226-3367362	GM12878	blood:	n/a	n/a
43	IRF4	chr9:3385933-3386175	GM12878	blood:	n/a	n/a
44	JUND	chr9:3386748-3387114	Hela-S3	cervix:	n/a	chr9:3386880-3386889 chr9:3386928-3386935 chr9:3386927-3386935 chr9:3386925-3386936 chr9:3386925-3386937 chr9:3386926-3386936 chr9:3386927-3386936
45	JUND	chr9:3386791-3387048	HepG2	liver:	n/a	chr9:3386880-3386889 chr9:3386928-3386935 chr9:3386927-3386935 chr9:3386925-3386936 chr9:3386925-3386937 chr9:3386926-3386936 chr9:3386927-3386936
46	MAFK	chr9:3352174-3352301	HepG2	liver:	n/a	n/a
47	MAFK	chr9:3360729-3360730	HepG2	liver:	n/a	n/a
48	MAZ	chr9:3349443-3349595	HepG2	liver:	n/a	n/a
49	MEF2A	chr9:3385846-3386283	GM12878	blood:	n/a	chr9:3386084-3386092 chr9:3386259-3386274 chr9:3386162-3386176 chr9:3386164-3386175
50	MEF2A	chr9:3385855-3386224	GM12878	blood:	n/a	chr9:3386084-3386092 chr9:3386162-3386176 chr9:3386164-3386175

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:3362011..3363818-chr9:3525245..3528041,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL365202.1-1	chr9:3364329-3364792	NONHSAT130019

Variant related genes	Relation type
RFX3	TF binding region
ENSG00000215297	TF binding region
ENSG00000232104	chromatin interactions
ENSG00000080298	chromatin interactions

Extended variants
information (count: 1807 )
Associated
traits (count: 105 )

Variant overlapped rSNPs/rCNVs (count:1807 , 50 per page) page: 1 2 3 4 5 6 7 ... 37

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3012675	chr9:3349487-3349488	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs116602246	chr9:3349515-3349516	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs151022950	chr9:3349524-3349525	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs570991289	chr9:3349528-3349529	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs139566048	chr9:3349542-3349543	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs111349335	chr9:3349559-3349560	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs536138451	chr9:3349581-3349582	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs181275551	chr9:3349582-3349583	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs186257406	chr9:3349583-3349584	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs114541353	chr9:3349584-3349585	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs28723588	chr9:3349585-3349586	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs201001342	chr9:3349593-3349594	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs190581384	chr9:3349602-3349603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs527739516	chr9:3349606-3349607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs80015762	chr9:3349623-3349624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs577393439	chr9:3349638-3349639	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs182013985	chr9:3349649-3349650	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs187089132	chr9:3349652-3349653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs528608584	chr9:3349660-3349661	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs2991324	chr9:3349667-3349668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs562074512	chr9:3349671-3349672	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs10971491	chr9:3349684-3349685	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs376787710	chr9:3349708-3349709	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs571089314	chr9:3349726-3349727	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs191101331	chr9:3349734-3349735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs540026158	chr9:3349840-3349841	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs182373725	chr9:3349858-3349859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs188264149	chr9:3349870-3349871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs80174002	chr9:3349922-3349923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs190283792	chr9:3349937-3349938	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs117539107	chr9:3349942-3349943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs537469226	chr9:3349975-3349976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs566636479	chr9:3349985-3349986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs10813972	chr9:3349997-3349998	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs10971494	chr9:3350023-3350024	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs182485598	chr9:3350086-3350087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs145575343	chr9:3350112-3350113	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs140268984	chr9:3350119-3350120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs371719764	chr9:3350167-3350168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs146415836	chr9:3350196-3350197	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs115472813	chr9:3350204-3350205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs562064363	chr9:3350213-3350214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs140847919	chr9:3350270-3350271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs145157623	chr9:3350306-3350307	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs371632514	chr9:3350336-3350337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs187486126	chr9:3350361-3350362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs533719895	chr9:3350387-3350388	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs574790809	chr9:3350394-3350395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs547323258	chr9:3350424-3350425	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs553122338	chr9:3350426-3350427	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:105)

Disease	PMID	Source
Gastric cancer	16715143	CNVD
Glioblastoma multiforme	22286061	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	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
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
Developmental delay	21147756	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	20531469	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21373258	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Ovarian cancer	22355333	CNVD
Autism	20808228	CNVD
Pancreatic cancer	17952125	CNVD
T-cell lymphomas	22341440	CNVD
Breast cancer	22522925	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD

Chromatin state (count:312 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:3309400-3350400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:3313400-3352400	Weak transcription	Primary T cells from cord blood	blood
5	chr9:3319800-3353800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:3330400-3354200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:3333000-3352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:3337800-3352600	Weak transcription	Primary B cells from cord blood	blood
9	chr9:3337800-3388800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:3344400-3350800	Weak transcription	Fetal Intestine Small	intestine
12	chr9:3345400-3352600	Weak transcription	Fetal Lung	lung
13	chr9:3346000-3352600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:3350400-3351400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:3350600-3360800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:3350800-3351000	ZNF genes & repeats	Fetal Intestine Small	intestine
17	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
18	chr9:3351400-3361400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:3351800-3353400	Weak transcription	Dnd41	blood
20	chr9:3352000-3354600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:3352400-3352800	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr9:3352600-3352800	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:3352600-3352800	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr9:3352600-3352800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr9:3352600-3352800	ZNF genes & repeats	Fetal Lung	lung
26	chr9:3352600-3353600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:3352800-3353400	Weak transcription	Primary B cells from cord blood	blood
28	chr9:3353400-3353800	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr9:3353800-3354600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
30	chr9:3353800-3359200	Weak transcription	Primary B cells from cord blood	blood
31	chr9:3354000-3354400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr9:3354600-3354800	Weak transcription	Primary T cells from cord blood	blood
33	chr9:3354600-3355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:3354600-3364600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:3355000-3383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:3355400-3365600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:3356200-3358600	Weak transcription	Primary T cells from cord blood	blood
38	chr9:3356400-3360400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:3358600-3359000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:3358600-3359400	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr9:3358800-3359200	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr9:3358800-3359200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:3358800-3359600	Enhancers	Pancreas	Pancrea
44	chr9:3359000-3359200	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr9:3359000-3359600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:3359000-3359600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr9:3359000-3359600	Enhancers	Primary B cells from peripheral blood	blood
48	chr9:3359200-3359400	Active TSS	Primary B cells from cord blood	blood
49	chr9:3359200-3359400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:3359200-3359400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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