Variant report

Variant	nsv969761
Chromosome Location	chr9:97254596-97288069
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	chr9:97269975-97270547	HepG2	liver:	n/a	n/a
2	ARID3A	chr9:97273781-97274194	HepG2	liver:	n/a	n/a
3	ATF2	chr9:97254373-97254805	GM12878	blood:	n/a	n/a
4	BATF	chr9:97254351-97254686	GM12878	blood:	n/a	chr9:97254488-97254498
5	BATF	chr9:97254388-97254700	GM12878	blood:	n/a	chr9:97254488-97254498
6	BCL11A	chr9:97254340-97254738	GM12878	blood:	n/a	n/a
7	BCL11A	chr9:97254407-97254725	GM12878	blood:	n/a	n/a
8	BCLAF1	chr9:97254424-97254735	GM12878	blood:	n/a	n/a
9	CEBPB	chr9:97279585-97279790	HepG2	liver:	n/a	n/a
10	CEBPB	chr9:97279633-97279875	K562	blood:	n/a	n/a
11	CEBPB	chr9:97270166-97270600	MCF-7	breast:	n/a	n/a
12	CEBPB	chr9:97270183-97270535	HepG2	liver:	n/a	n/a
13	CEBPB	chr9:97276813-97277321	HepG2	liver:	n/a	n/a
14	CEBPB	chr9:97270146-97270540	HepG2	liver:	n/a	n/a
15	CEBPB	chr9:97279663-97279825	H1-hESC	embryonic stem cell:	n/a	n/a
16	CEBPB	chr9:97270257-97270424	HepG2	liver:	n/a	n/a
17	CTCF	chr9:97276854-97276878	Spleen_OC	spleen:	n/a	n/a
18	CTCF	chr9:97274420-97274570	SK-N-SH_RA	brain:	n/a	n/a
19	CTCF	chr9:97284193-97284209	GM10266	blood:	n/a	n/a
20	E2F4	chr9:97271558-97271856	MCF10A-Er-Src	breast:	n/a	n/a
21	EBF1	chr9:97274022-97274342	GM12878	blood:	n/a	chr9:97274218-97274227 chr9:97274216-97274227
22	EP300	chr9:97254487-97254682	GM12878	blood:	n/a	chr9:97254487-97254496 chr9:97254599-97254613
23	EP300	chr9:97254522-97254731	GM12878	blood:	n/a	chr9:97254599-97254613
24	EP300	chr9:97270090-97270599	HepG2	liver:	n/a	n/a
25	EP300	chr9:97274275-97274490	SK-N-SH_RA	brain:	n/a	n/a
26	EP300	chr9:97270243-97270539	HepG2	liver:	n/a	n/a
27	EP300	chr9:97273771-97274016	HepG2	liver:	n/a	n/a
28	EP300	chr9:97270110-97270573	HepG2	liver:	n/a	n/a
29	EP300	chr9:97274265-97274514	SK-N-SH_RA	brain:	n/a	n/a
30	FOXA1	chr9:97269981-97270629	HepG2	liver:	n/a	chr9:97270331-97270346 chr9:97270292-97270307
31	FOXA1	chr9:97270102-97270644	HepG2	liver:	n/a	chr9:97270331-97270346 chr9:97270292-97270307
32	FOXA1	chr9:97270113-97270518	T-47D	breast:	n/a	chr9:97270331-97270346 chr9:97270292-97270307
33	FOXA1	chr9:97272907-97273196	HepG2	liver:	n/a	n/a
34	FOXA1	chr9:97270228-97270549	T-47D	breast:	n/a	chr9:97270331-97270346 chr9:97270292-97270307
35	FOXA1	chr9:97270000-97270630	HepG2	liver:	n/a	chr9:97270331-97270346 chr9:97270292-97270307
36	FOXA1	chr9:97273761-97274170	HepG2	liver:	n/a	n/a
37	FOXA1	chr9:97270066-97270607	HepG2	liver:	n/a	chr9:97270331-97270346 chr9:97270292-97270307
38	FOXA2	chr9:97270102-97270482	A549	lung:	n/a	n/a
39	FOXA2	chr9:97269615-97271081	HepG2	liver:	n/a	n/a
40	FOXA2	chr9:97276746-97276902	HepG2	liver:	n/a	n/a
41	FOXA2	chr9:97270131-97270567	HepG2	liver:	n/a	n/a
42	GATA3	chr9:97280993-97281120	SH-SY5Y	brain:	n/a	n/a
43	GATA3	chr9:97270208-97270480	T-47D	breast:	n/a	n/a
44	GATA3	chr9:97257238-97257438	SH-SY5Y	brain:	n/a	n/a
45	GATA3	chr9:97270185-97270480	T-47D	breast:	n/a	n/a
46	GATA3	chr9:97274386-97274511	SH-SY5Y	brain:	n/a	n/a
47	HDAC2	chr9:97270140-97270541	HepG2	liver:	n/a	n/a
48	HNF4G	chr9:97270226-97270465	HepG2	liver:	n/a	n/a
49	JUND	chr9:97254366-97254636	HepG2	liver:	n/a	chr9:97254486-97254497 chr9:97254487-97254494 chr9:97254487-97254496 chr9:97254485-97254496 chr9:97254485-97254497
50	MYBL2	chr9:97270032-97270624	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97268511..97271349-chr9:97272265..97274587,2	K562	blood:
2	chr9:97270387..97272574-chr9:97275358..97278004,2	MCF-7	breast:
3	chr9:97242816..97244907-chr9:97253508..97257110,3	MCF-7	breast:
4	chr9:97245654..97249341-chr9:97260999..97264040,3	MCF-7	breast:
5	chr9:97270387..97272574-chr9:97275358..97278004,2	MCF-7	breast:
6	chr7:100806149..100807853-chr9:97276402..97278973,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBP2-3	chr9:97273822-97273860	NONHSAT133317
2	lnc-HIATL1-11	chr9:97282721-97283330	NONHSAT133322
3	lnc-HIATL1-9	chr9:97254725-97256383	NONHSAT133319
4	lnc-HIATL1-11	chr9:97281876-97281926	NONHSAT133322
5	lnc-HIATL1-12	chr9:97285819-97288385	NONHSAT133323
6	lnc-HIATL1-12	chr9:97284317-97285679	NONHSAT133323
7	lnc-HIATL1-11	chr9:97280751-97281438	NONHSAT133322

Variant related genes	Relation type
RNU6-669P	TF binding region
ENSG00000224245	TF binding region
ENSG00000202445	chromatin interactions

Extended variants
information (count: 1442 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:1442 , 50 per page) page: 1 2 3 4 5 6 7 ... 29

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs146076440	chr9:97254643-97254644	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs75043712	chr9:97254651-97254652	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs34618707	chr9:97254655-97254656	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs79805338	chr9:97254656-97254657	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs77545199	chr9:97254657-97254658	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs377383240	chr9:97254668-97254669	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs370422208	chr9:97254669-97254670	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs79236054	chr9:97254678-97254679	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs560989351	chr9:97254689-97254690	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs147782299	chr9:97254709-97254710	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs181869026	chr9:97254714-97254715	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs141121940	chr9:97254718-97254719	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs544259090	chr9:97254719-97254720	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs562893942	chr9:97254728-97254729	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs76608751	chr9:97254749-97254750	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs74754308	chr9:97254750-97254751	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs74575629	chr9:97254763-97254764	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs75644366	chr9:97254771-97254772	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs76184065	chr9:97254773-97254774	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs76225027	chr9:97254802-97254803	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs76148903	chr9:97254814-97254815	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs551915188	chr9:97254838-97254839	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs567023835	chr9:97254850-97254851	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs527876984	chr9:97254908-97254909	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs190516024	chr9:97254932-97254933	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs567847117	chr9:97254938-97254939	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs376754009	chr9:97254949-97254950	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs571344421	chr9:97254980-97254981	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs538970896	chr9:97254984-97254985	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs7042434	chr9:97254997-97254998	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs555709570	chr9:97255046-97255047	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs7042468	chr9:97255083-97255084	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs536260668	chr9:97255090-97255091	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs7022386	chr9:97255100-97255101	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs553450247	chr9:97255141-97255142	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs572149623	chr9:97255206-97255207	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs573001172	chr9:97255225-97255226	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs561196602	chr9:97255251-97255252	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs150331351	chr9:97255271-97255272	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs554779887	chr9:97255277-97255278	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs533986433	chr9:97255279-97255280	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs371550998	chr9:97255305-97255306	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs182724009	chr9:97255310-97255311	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs375027637	chr9:97255345-97255346	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs533368923	chr9:97255349-97255350	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs79450473	chr9:97255350-97255351	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs372602052	chr9:97255360-97255361	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs560559235	chr9:97255396-97255397	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs187007067	chr9:97255399-97255400	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs549287973	chr9:97255432-97255433	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Bipolar disorder	18458673	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Biliary cancer	19435499	CNVD
small cell lung cancer	20016488	CNVD
Intracranial aneurysm	16715129	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Basal cell nevus syndrome	21572526	CNVD
Mental retardation	19951919	CNVD
Retinoblastoma	22278416	CNVD
9q22.3 microdeletion syndrome	22283845	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Microcephaly	18830227	CNVD
overgrowth syndrome	16570072	CNVD
Effusion lymphoma	18079361	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
Breast cancer	22522925	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97241800-97262800	Weak transcription	Liver	Liver
2	chr9:97254000-97255400	Enhancers	GM12878-XiMat	blood
3	chr9:97261000-97261200	Enhancers	Pancreas	Pancrea
4	chr9:97261000-97261400	Enhancers	Fetal Lung	lung
5	chr9:97261200-97272600	Weak transcription	Pancreas	Pancrea
6	chr9:97261400-97262200	Enhancers	Duodenum Mucosa	Duodenum
7	chr9:97263000-97265600	Weak transcription	Hela-S3	cervix
8	chr9:97269800-97271200	Enhancers	HepG2	liver
9	chr9:97270400-97270600	Enhancers	Gastric	stomach
10	chr9:97270600-97272800	Weak transcription	Gastric	stomach
11	chr9:97271200-97272800	Weak transcription	HepG2	liver
12	chr9:97272600-97272800	Enhancers	Pancreas	Pancrea
13	chr9:97272800-97273200	Weak transcription	Pancreas	Pancrea
14	chr9:97272800-97273800	Enhancers	Gastric	stomach
15	chr9:97272800-97274800	Enhancers	HepG2	liver
16	chr9:97273200-97273800	Enhancers	Pancreas	Pancrea
17	chr9:97273400-97274600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:97273400-97275200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr9:97273800-97274000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:97273800-97274600	Enhancers	Liver	Liver
21	chr9:97274600-97276600	Weak transcription	Liver	Liver
22	chr9:97274800-97276200	Weak transcription	HepG2	liver
23	chr9:97275200-97276000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr9:97275600-97276000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:97275600-97276200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr9:97275600-97276400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr9:97275800-97276200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr9:97275800-97276400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:97276200-97278000	Enhancers	HepG2	liver
30	chr9:97276400-97277400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:97276600-97277200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:97276600-97278000	Enhancers	Liver	Liver
33	chr9:97277200-97277800	Enhancers	Fetal Kidney	kidney
34	chr9:97277400-97277600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr9:97278000-97279800	Weak transcription	HepG2	liver
36	chr9:97278000-97295200	Weak transcription	Liver	Liver
37	chr9:97279800-97281200	Enhancers	HepG2	liver

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