Variant report

Variant	nsv539937
Chromosome Location	chr9:2904217-2932528
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	CEBPB	chr9:2910804-2910901	K562	blood:	n/a	chr9:2910843-2910854
2	CEBPB	chr9:2910755-2910992	HepG2	liver:	n/a	chr9:2910843-2910854
3	CEBPB	chr9:2909981-2910245	HepG2	liver:	n/a	chr9:2910102-2910113
4	CTCF	chr9:2918657-2918697	ProgFib	skin:	n/a	n/a
5	CTCF	chr9:2915809-2915846	GM13976	blood:	n/a	n/a
6	CUX1	chr9:2912638-2912701	GM12878	blood:	n/a	n/a
7	E2F4	chr9:2905425-2905557	MCF10A-Er-Src	breast:	n/a	n/a
8	E2F4	chr9:2910727-2911115	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr9:2916771-2916811	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr9:2916652-2916900	MCF10A-Er-Src	breast:	n/a	chr9:2916858-2916867
11	FOS	chr9:2916737-2916822	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr9:2920020-2920155	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr9:2919424-2919632	MCF10A-Er-Src	breast:	n/a	chr9:2919618-2919626 chr9:2919618-2919625 chr9:2919618-2919626
14	FOS	chr9:2919300-2919661	MCF10A-Er-Src	breast:	n/a	chr9:2919618-2919626 chr9:2919618-2919625 chr9:2919618-2919626 chr9:2919335-2919344
15	GATA3	chr9:2931838-2931923	SH-SY5Y	brain:	n/a	n/a
16	IRF3	chr9:2920526-2920535	GM12878	blood:	n/a	n/a
17	JUN	chr9:2921273-2921377	HepG2	liver:	n/a	n/a
18	JUND	chr9:2930238-2930345	HepG2	liver:	n/a	n/a
19	KAP1	chr9:2923916-2924552	U2OS	brain:	n/a	n/a
20	MAX	chr9:2923891-2924198	H1-hESC	embryonic stem cell:	n/a	chr9:2923944-2923953
21	MAX	chr9:2931166-2931431	NB4	blood:	n/a	n/a
22	MAX	chr9:2917618-2917808	NB4	blood:	n/a	chr9:2917751-2917758 chr9:2917749-2917758 chr9:2917748-2917759 chr9:2917750-2917759 chr9:2917747-2917760 chr9:2917747-2917760 chr9:2917744-2917763 chr9:2917747-2917760
23	MXI1	chr9:2923783-2924062	H1-hESC	embryonic stem cell:	n/a	n/a
24	MYC	chr9:2919471-2919697	MCF10A-Er-Src	breast:	n/a	chr9:2919618-2919627
25	MYC	chr9:2919334-2919510	MCF10A-Er-Src	breast:	n/a	n/a
26	NRF1	chr9:2905814-2905816	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr9:2912333-2912365	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr9:2927803-2927885	MCF10A-Er-Src	breast:	n/a	n/a
29	REST	chr9:2923656-2924172	H1-hESC	embryonic stem cell:	n/a	n/a
30	REST	chr9:2923765-2924042	A549	lung:	n/a	n/a
31	REST	chr9:2923755-2924118	PFSK-1	brain:	n/a	n/a
32	REST	chr9:2924690-2924871	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr9:2916453-2916654	Hela-S3	cervix:	n/a	n/a
34	REST	chr9:2923830-2923988	HepG2	liver:	n/a	n/a
35	REST	chr9:2916460-2916711	ECC-1	luminal epithelium:	n/a	n/a
36	REST	chr9:2916336-2916825	HL-60	blood:	n/a	n/a
37	REST	chr9:2923735-2924144	PFSK-1	brain:	n/a	n/a
38	REST	chr9:2923810-2923991	GM12878	blood:	n/a	n/a
39	REST	chr9:2923843-2923992	GM12878	blood:	n/a	n/a
40	REST	chr9:2923762-2924151	A549	lung:	n/a	n/a
41	REST	chr9:2923789-2924094	SK-N-SH	brain:	n/a	n/a
42	REST	chr9:2916372-2916803	HL-60	blood:	n/a	n/a
43	REST	chr9:2916381-2916793	H1-hESC	embryonic stem cell:	n/a	n/a
44	REST	chr9:2923757-2924317	HL-60	blood:	n/a	n/a
45	REST	chr9:2923750-2924110	HCT-116	colon:	n/a	n/a
46	REST	chr9:2916415-2916678	K562	blood:	n/a	n/a
47	REST	chr9:2923815-2924005	GM12878	blood:	n/a	n/a
48	REST	chr9:2923715-2924158	HL-60	blood:	n/a	n/a
49	REST	chr9:2923816-2924172	MCF-7	breast:	n/a	n/a
50	REST	chr9:2916474-2916705	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:2910352..2912486-chr9:2913384..2916184,2	MCF-7	breast:
2	chr9:2910352..2912486-chr9:2913384..2916184,2	MCF-7	breast:
3	chr9:2889601..2892216-chr9:2916356..2918847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229184	TF binding region
ENSG00000221450	TF binding region

Extended variants
information (count: 789 )
Associated
traits (count: 99 )

Variant overlapped rSNPs/rCNVs (count:789 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs559967404	chr9:2904219-2904220	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs201701946	chr9:2904250-2904251	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs190777798	chr9:2904273-2904274	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs12347833	chr9:2904296-2904297	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs574744550	chr9:2904310-2904311	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs60171854	chr9:2904363-2904364	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs180789822	chr9:2904393-2904394	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs551289257	chr9:2904421-2904422	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs183968252	chr9:2904428-2904429	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs552830092	chr9:2904430-2904431	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs559713804	chr9:2904471-2904472	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs76338751	chr9:2904500-2904501	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs548606146	chr9:2904508-2904509	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs188650171	chr9:2904530-2904531	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs144981083	chr9:2904609-2904610	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs550145684	chr9:2904651-2904652	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs181126456	chr9:2904655-2904656	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs117658682	chr9:2904661-2904662	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs552614355	chr9:2904667-2904668	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs186553992	chr9:2904747-2904748	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs73381721	chr9:2904771-2904772	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs182028306	chr9:2904781-2904782	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs575482933	chr9:2904783-2904784	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs543869493	chr9:2904790-2904791	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs1501572	chr9:2904794-2904795	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs148666169	chr9:2904822-2904823	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs548922029	chr9:2904852-2904853	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs62533910	chr9:2904869-2904870	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs187125030	chr9:2904901-2904902	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs190995134	chr9:2904910-2904911	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs542400338	chr9:2904913-2904914	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs2376415	chr9:2904934-2904935	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs531088561	chr9:2904945-2904946	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs56815843	chr9:2904960-2904961	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs570127773	chr9:2904968-2904969	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs182190861	chr9:2904972-2904973	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs2062675	chr9:2905016-2905017	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs566558649	chr9:2905030-2905031	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs144254991	chr9:2905080-2905081	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs535328171	chr9:2905081-2905082	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs7861184	chr9:2905109-2905110	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs569083269	chr9:2905159-2905160	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs565201615	chr9:2905160-2905161	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs7875486	chr9:2905167-2905168	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs372071351	chr9:2905240-2905241	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs565899744	chr9:2905370-2905371	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs73381728	chr9:2905373-2905374	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs573272816	chr9:2905397-2905398	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs371348460	chr9:2905425-2905426	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs542085812	chr9:2905438-2905439	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:99)

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

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2903800-2904400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:2904000-2904400	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr9:2904000-2904800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr9:2904000-2906000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:2904200-2904800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:2904200-2905600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr9:2904200-2906000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:2904400-2904600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:2904400-2905400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:2904400-2905600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:2904400-2906200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:2904800-2905800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:2905600-2905800	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr9:2905800-2906000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr9:2906800-2907400	Enhancers	NHDF-Ad	bronchial
16	chr9:2907000-2907600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:2909000-2911800	Enhancers	Fetal Brain Male	brain
18	chr9:2911800-2912600	Weak transcription	Fetal Brain Male	brain
19	chr9:2912400-2913600	Enhancers	Fetal Brain Female	brain
20	chr9:2912600-2912800	Enhancers	Fetal Brain Male	brain
21	chr9:2912800-2913200	Weak transcription	Fetal Brain Male	brain
22	chr9:2913200-2913600	Enhancers	Fetal Brain Male	brain
23	chr9:2918400-2920800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:2918600-2921000	Enhancers	NHDF-Ad	bronchial
25	chr9:2919000-2919800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:2919400-2920200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:2919600-2920000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr9:2919800-2920000	Enhancers	Osteobl	bone
29	chr9:2920800-2922200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:2922200-2922400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:2922400-2922800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:2922800-2924000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:2923000-2923400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:2924000-2924200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:2924000-2924200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:2924000-2924400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:2924000-2924600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:2924000-2924600	Enhancers	Stomach Mucosa	stomach
39	chr9:2927800-2928400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr9:2927800-2928400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:2927800-2928800	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr9:2928000-2928400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr9:2928200-2929000	Enhancers	Fetal Brain Male	brain

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