Variant report

Variant	esv1849738
Chromosome Location	chr9:3389223-3404434
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	ATF2	chr9:3397833-3398676	GM12878	blood:	n/a	n/a
2	ATF2	chr9:3398074-3398747	GM12878	blood:	n/a	n/a
3	BCLAF1	chr9:3397900-3398826	GM12878	blood:	n/a	n/a
4	CREB1	chr9:3397924-3398879	GM12878	blood:	n/a	n/a
5	CUX1	chr9:3397769-3398454	GM12878	blood:	n/a	n/a
6	E2F4	chr9:3400345-3400514	MCF10A-Er-Src	breast:	n/a	n/a
7	EBF1	chr9:3397423-3397840	GM12878	blood:	n/a	n/a
8	EBF1	chr9:3398343-3398442	GM12878	blood:	n/a	n/a
9	EP300	chr9:3398145-3398473	GM12878	blood:	n/a	chr9:3398304-3398318
10	FOS	chr9:3401642-3401838	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr9:3403336-3403650	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr9:3403382-3403627	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr9:3403385-3403648	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr9:3392495-3393021	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr9:3404214-3404297	MCF-7	breast:	n/a	n/a
16	JUN	chr9:3403804-3404004	K562	blood:	n/a	n/a
17	JUND	chr9:3398482-3398669	HepG2	liver:	n/a	chr9:3398644-3398653
18	MAFF	chr9:3395013-3395268	HepG2	liver:	n/a	chr9:3395107-3395125
19	MAFK	chr9:3401602-3401672	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAFK	chr9:3394961-3395273	HepG2	liver:	n/a	chr9:3395109-3395124 chr9:3395109-3395120 chr9:3395108-3395122 chr9:3395109-3395125 chr9:3395110-3395121 chr9:3395109-3395120
21	MAFK	chr9:3394964-3395276	HepG2	liver:	n/a	chr9:3395109-3395124 chr9:3395109-3395120 chr9:3395108-3395122 chr9:3395109-3395125 chr9:3395110-3395121 chr9:3395109-3395120
22	MAFK	chr9:3394988-3395245	IMR90	lung:	n/a	chr9:3395109-3395124 chr9:3395109-3395120 chr9:3395108-3395122 chr9:3395109-3395125 chr9:3395110-3395121 chr9:3395109-3395120
23	MAZ	chr9:3397989-3397996	GM12878	blood:	n/a	n/a
24	NFIC	chr9:3397829-3398860	GM12878	blood:	n/a	n/a
25	NFIC	chr9:3397997-3398730	GM12878	blood:	n/a	n/a
26	PBX3	chr9:3403322-3403667	SK-N-SH	brain:	n/a	n/a
27	PBX3	chr9:3403207-3403684	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr9:3398257-3398773	GM12892	blood:	n/a	n/a
29	POLR2A	chr9:3399838-3399895	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr9:3403723-3403748	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr9:3397546-3397550	MCF10A-Er-Src	breast:	n/a	n/a
32	RCOR1	chr9:3397605-3398744	GM12878	blood:	n/a	n/a
33	RUNX3	chr9:3397914-3398537	GM12878	blood:	n/a	n/a
34	RUNX3	chr9:3397798-3398633	GM12878	blood:	n/a	n/a
35	SMC3	chr9:3398190-3398691	GM12878	blood:	n/a	chr9:3398542-3398549
36	SPI1	chr9:3397817-3398023	GM12878	blood:	n/a	n/a
37	SPI1	chr9:3397666-3398752	HL-60	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
38	SPI1	chr9:3398073-3398666	GM12891	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
39	SPI1	chr9:3397686-3398708	GM12878	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
40	SPI1	chr9:3398113-3398658	GM12878	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
41	SPI1	chr9:3397722-3398030	GM12891	blood:	n/a	n/a
42	SPI1	chr9:3398174-3398389	GM12878	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
43	SPI1	chr9:3397770-3398561	GM12891	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
44	SPI1	chr9:3397775-3398576	HL-60	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
45	STAT1	chr9:3397856-3397887	GM12878	blood:	n/a	n/a
46	STAT3	chr9:3397766-3398640	GM12878	blood:	n/a	chr9:3398357-3398368
47	STAT3	chr9:3395268-3395314	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr9:3394509-3394709	MCF10A-Er-Src	breast:	n/a	n/a
49	YY1	chr9:3398225-3398767	GM12878	blood:	n/a	chr9:3398523-3398545 chr9:3398534-3398542
50	YY1	chr9:3398357-3398657	GM12892	blood:	n/a	chr9:3398523-3398545 chr9:3398534-3398542

Variant related genes	Relation type
RFX3	TF binding region

Extended variants
information (count: 730 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:730 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17659225	chr9:3389223-3389224	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs547758304	chr9:3389245-3389246	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs375849017	chr9:3389255-3389256	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs536484699	chr9:3389298-3389299	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs535082451	chr9:3389316-3389317	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs182632562	chr9:3389334-3389335	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs575713691	chr9:3389337-3389338	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs537916624	chr9:3389353-3389354	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs12348958	chr9:3389354-3389355	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs577569200	chr9:3389358-3389359	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs117252225	chr9:3389362-3389363	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs552907963	chr9:3389377-3389378	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs566362157	chr9:3389389-3389390	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs72699079	chr9:3389392-3389393	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs538714524	chr9:3389400-3389401	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs573981434	chr9:3389417-3389418	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs543236034	chr9:3389429-3389430	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs562915364	chr9:3389451-3389452	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs531453234	chr9:3389472-3389473	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs145741498	chr9:3389534-3389535	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs148959942	chr9:3389535-3389536	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs564384170	chr9:3389627-3389628	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs185949567	chr9:3389657-3389658	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs558260987	chr9:3389658-3389659	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs13283163	chr9:3389660-3389661	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs538086725	chr9:3389724-3389725	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs554750161	chr9:3389728-3389729	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs143642075	chr9:3389733-3389734	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs116863961	chr9:3389750-3389751	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs191594414	chr9:3389751-3389752	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs138245313	chr9:3389811-3389812	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs538340239	chr9:3389889-3389890	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs558016155	chr9:3389898-3389899	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs577706849	chr9:3389928-3389929	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs533969182	chr9:3389940-3389941	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs372090194	chr9:3389975-3389976	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs553730818	chr9:3389978-3389979	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs141835353	chr9:3390036-3390037	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs542918740	chr9:3390040-3390041	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs540590097	chr9:3390041-3390042	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs533307837	chr9:3390043-3390044	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs560503440	chr9:3390093-3390094	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs576603403	chr9:3390113-3390114	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545571222	chr9:3390126-3390127	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs182924656	chr9:3390140-3390141	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs527359034	chr9:3390141-3390142	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs187478179	chr9:3390159-3390160	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs376022754	chr9:3390187-3390188	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs368650971	chr9:3390211-3390212	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs371488874	chr9:3390212-3390213	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:104)

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
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:370 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
3	chr9:3364200-3397200	Weak transcription	Left Ventricle	heart
4	chr9:3364800-3393800	Weak transcription	Adipose Nuclei	Adipose
5	chr9:3369400-3398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:3375800-3390200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:3377200-3390000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr9:3377400-3390400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:3377600-3401400	Weak transcription	HMEC	breast
10	chr9:3377800-3401600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:3379800-3390400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:3380400-3390400	Weak transcription	Thymus	Thymus
13	chr9:3380600-3391400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:3381000-3397000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:3382200-3425000	Weak transcription	Aorta	Aorta
16	chr9:3382400-3397000	Weak transcription	Fetal Intestine Large	intestine
17	chr9:3382400-3401400	Weak transcription	Brain Anterior Caudate	brain
18	chr9:3382800-3401000	Weak transcription	Brain Germinal Matrix	brain
19	chr9:3383200-3410000	Weak transcription	Fetal Brain Male	brain
20	chr9:3383400-3401400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:3384000-3390000	Strong transcription	Primary B cells from cord blood	blood
22	chr9:3384600-3390600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:3384800-3389800	Weak transcription	Primary T cells from cord blood	blood
24	chr9:3385000-3389800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:3385200-3395800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:3386000-3392600	Weak transcription	Dnd41	blood
27	chr9:3386000-3398000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:3386200-3390200	Weak transcription	Ovary	ovary
29	chr9:3386200-3409600	Weak transcription	Psoas Muscle	Psoas
30	chr9:3386400-3390600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:3386400-3391800	Weak transcription	NH-A	brain
32	chr9:3387000-3397200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:3387200-3389600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:3387200-3390400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:3387200-3390600	Weak transcription	Fetal Lung	lung
36	chr9:3387200-3393400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:3387200-3394600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:3387200-3397000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:3387200-3397000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr9:3387200-3401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr9:3387200-3433800	Weak transcription	Pancreas	Pancrea
42	chr9:3387400-3390000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:3387400-3390200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr9:3387600-3390200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr9:3387600-3397600	Weak transcription	HepG2	liver
46	chr9:3387800-3401400	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:3388000-3389600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:3388000-3401400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr9:3388200-3401400	Weak transcription	Brain Substantia Nigra	brain
50	chr9:3388600-3390200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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