Variant report

Variant	esv2761270
Chromosome Location	chr9:115656015-115664299
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	chr9:115661077-115661500	HepG2	liver:	n/a	n/a
2	BATF	chr9:115656385-115656635	GM12878	blood:	n/a	chr9:115656511-115656522
3	CEBPB	chr9:115661124-115661585	HepG2	liver:	n/a	chr9:115661346-115661357 chr9:115661344-115661357 chr9:115661344-115661355 chr9:115661344-115661357
4	CEBPB	chr9:115661033-115661659	MCF-7	breast:	n/a	chr9:115661346-115661357 chr9:115661344-115661357 chr9:115661344-115661355 chr9:115661344-115661357
5	CEBPB	chr9:115657123-115657241	HepG2	liver:	n/a	n/a
6	CEBPB	chr9:115661276-115661500	IMR90	lung:	n/a	chr9:115661346-115661357 chr9:115661344-115661357 chr9:115661344-115661355 chr9:115661344-115661357
7	CEBPB	chr9:115661076-115661521	Hela-S3	cervix:	n/a	chr9:115661346-115661357 chr9:115661344-115661357 chr9:115661344-115661355 chr9:115661344-115661357
8	CEBPB	chr9:115661300-115661520	A549	lung:	n/a	chr9:115661346-115661357 chr9:115661344-115661357 chr9:115661344-115661355 chr9:115661344-115661357
9	CREB1	chr9:115661016-115661446	HepG2	liver:	n/a	n/a
10	EP300	chr9:115661080-115661455	HepG2	liver:	n/a	chr9:115661443-115661450
11	FOS	chr9:115656270-115656660	MCF10A-Er-Src	breast:	n/a	chr9:115656509-115656520
12	FOS	chr9:115656268-115656687	MCF10A-Er-Src	breast:	n/a	chr9:115656509-115656520
13	FOS	chr9:115656266-115656687	MCF10A-Er-Src	breast:	n/a	chr9:115656509-115656520
14	FOS	chr9:115660958-115661028	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr9:115656323-115656638	MCF10A-Er-Src	breast:	n/a	chr9:115656509-115656520
16	FOS	chr9:115656284-115656729	HUVEC	blood vessel:	n/a	chr9:115656509-115656520
17	FOXA1	chr9:115661092-115661564	HepG2	liver:	n/a	n/a
18	GATA2	chr9:115661107-115661479	HUVEC	blood vessel:	n/a	chr9:115661255-115661269
19	GATA3	chr9:115660863-115661645	MCF-7	breast:	n/a	chr9:115661259-115661267 chr9:115661512-115661522
20	GATA3	chr9:115660999-115661397	T-47D	breast:	n/a	chr9:115661259-115661267
21	GATA3	chr9:115660892-115661621	MCF-7	breast:	n/a	chr9:115661259-115661267 chr9:115661512-115661522
22	GATA3	chr9:115660998-115661546	MCF-7	breast:	n/a	chr9:115661259-115661267 chr9:115661512-115661522
23	GATA3	chr9:115661080-115661310	SH-SY5Y	brain:	n/a	chr9:115661259-115661267
24	GATA3	chr9:115661070-115661527	MCF-7	breast:	n/a	chr9:115661259-115661267 chr9:115661512-115661522
25	GATA3	chr9:115663944-115664054	SH-SY5Y	brain:	n/a	n/a
26	MAFK	chr9:115656381-115656687	IMR90	lung:	n/a	chr9:115656531-115656542 chr9:115656494-115656505 chr9:115656531-115656542 chr9:115656494-115656514 chr9:115656496-115656512 chr9:115656494-115656505
27	MAFK	chr9:115659391-115659499	HepG2	liver:	n/a	n/a
28	MYC	chr9:115657046-115657325	NB4	blood:	n/a	n/a
29	MYC	chr9:115656332-115656593	MCF10A-Er-Src	breast:	n/a	n/a
30	NR2F2	chr9:115660900-115661574	MCF-7	breast:	n/a	n/a
31	NR2F2	chr9:115660913-115661526	MCF-7	breast:	n/a	n/a
32	POLR2A	chr9:115661206-115661618	HL-60	blood:	n/a	n/a
33	POLR2A	chr9:115656701-115656789	Gliobla	brain:	n/a	n/a
34	POLR2A	chr9:115656943-115657427	HL-60	blood:	n/a	n/a
35	RUNX3	chr9:115656383-115656691	GM12878	blood:	n/a	n/a
36	RUNX3	chr9:115658443-115658742	GM12878	blood:	n/a	n/a
37	SIN3AK20	chr9:115660817-115661662	MCF-7	breast:	n/a	n/a
38	SPI1	chr9:115661292-115661661	HL-60	blood:	n/a	n/a
39	SPI1	chr9:115661370-115661611	GM12891	blood:	n/a	n/a
40	SPI1	chr9:115661258-115661748	HL-60	blood:	n/a	n/a
41	STAT3	chr9:115656360-115656629	MCF10A-Er-Src	breast:	n/a	chr9:115656511-115656520
42	STAT3	chr9:115656330-115656631	MCF10A-Er-Src	breast:	n/a	chr9:115656511-115656520
43	USF1	chr9:115663202-115663522	SK-N-SH	brain:	n/a	chr9:115663378-115663389
44	USF1	chr9:115663259-115663456	HepG2	liver:	n/a	chr9:115663378-115663389
45	USF1	chr9:115663237-115663488	SK-N-SH_RA	brain:	n/a	chr9:115663378-115663389
46	USF2	chr9:115663247-115663460	HepG2	liver:	n/a	chr9:115663378-115663389
47	USF2	chr9:115663275-115663444	Hela-S3	cervix:	n/a	chr9:115663378-115663389
48	ZNF217	chr9:115661101-115661423	MCF-7	breast:	n/a	n/a
49	ZNF263	chr9:115661039-115661580	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:115653409..115654935-chr9:115663870..115665546,2	MCF-7	breast:
2	chr9:115663052..115664958-chr9:115669316..115671393,2	K562	blood:
3	chr9:115605115..115608085-chr9:115663970..115666331,4	MCF-7	breast:
4	chr9:115659389..115661774-chr9:115663212..115665423,2	MCF-7	breast:
5	chr9:115511803..115513775-chr9:115660401..115662010,2	MCF-7	breast:
6	chr9:115658787..115660468-chr9:115666043..115668753,2	K562	blood:
7	chr9:115653737..115657233-chr9:115662868..115665778,3	K562	blood:
8	chr9:115653499..115655772-chr9:115659487..115662405,2	MCF-7	breast:
9	chr9:115609355..115610986-chr9:115659802..115661844,2	MCF-7	breast:
10	chr9:115659389..115661774-chr9:115663212..115665423,2	MCF-7	breast:
11	chr9:115661009..115663181-chr9:115664939..115667779,3	MCF-7	breast:
12	chr9:115653737..115657233-chr9:115662868..115665778,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC46A2-2	chr9:115661341-115661886	XLOC_007831

Variant related genes	Relation type
SLC46A2	TF binding region
ENSG00000148158	chromatin interactions
ENSG00000226609	chromatin interactions
ZBTB4	miRNA target sites

Extended variants
information (count: 348 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:348 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10759609	chr9:115656015-115656016	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs541087102	chr9:115656048-115656049	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs564568598	chr9:115656080-115656081	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs573125361	chr9:115656089-115656090	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs199832035	chr9:115656096-115656097	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs35933967	chr9:115656103-115656104	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs201625023	chr9:115656106-115656107	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs386415938	chr9:115656110-115656111	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs373375877	chr9:115656115-115656116	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs111311665	chr9:115656160-115656161	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs540378405	chr9:115656212-115656213	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs545936797	chr9:115656250-115656251	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs558831054	chr9:115656254-115656255	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs536429678	chr9:115656275-115656276	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs367573382	chr9:115656277-115656278	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs140748447	chr9:115656318-115656319	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs531627198	chr9:115656353-115656354	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs548538494	chr9:115656354-115656355	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs12004418	chr9:115656463-115656464	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs183722960	chr9:115656465-115656466	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs570489110	chr9:115656466-115656467	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs78257352	chr9:115656467-115656468	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs187798806	chr9:115656526-115656527	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs556717418	chr9:115656531-115656532	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs569946861	chr9:115656553-115656554	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs539891294	chr9:115656564-115656565	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs535723602	chr9:115656565-115656566	Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs555610603	chr9:115656614-115656615	Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs372274020	chr9:115656649-115656650	Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs10123432	chr9:115656671-115656672	Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs145880486	chr9:115656677-115656678	Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs10117269	chr9:115656697-115656698	Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs372773058	chr9:115656795-115656796	Bivalent Enhancer Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs190332358	chr9:115656796-115656797	Bivalent Enhancer Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs375705582	chr9:115656797-115656798	Bivalent Enhancer Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs531564889	chr9:115656835-115656836	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs182148771	chr9:115656850-115656851	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs10123517	chr9:115656863-115656864	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs527602321	chr9:115656893-115656894	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs186736776	chr9:115656895-115656896	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs540058346	chr9:115656905-115656906	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs7036845	chr9:115656923-115656924	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs558786809	chr9:115656974-115656975	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs533039641	chr9:115656989-115656990	Enhancers Flanking Active TSS Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs10123530	chr9:115657046-115657047	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs191602675	chr9:115657049-115657050	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs376230599	chr9:115657084-115657085	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs117977334	chr9:115657085-115657086	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs10114585	chr9:115657091-115657092	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs77636942	chr9:115657110-115657111	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:52)

Disease	PMID	Source
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
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	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
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
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Lung cancer	19147751	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16272173	CNVD

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115653200-115659000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr9:115654000-115656600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr9:115654800-115657600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:115655000-115657600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:115655600-115656800	Enhancers	Osteobl	bone
6	chr9:115655800-115656600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
7	chr9:115655800-115657600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr9:115655800-115658200	Enhancers	GM12878-XiMat	blood
9	chr9:115656000-115657000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:115656200-115656400	Bivalent Enhancer	Primary B cells from cord blood	blood
11	chr9:115656200-115656400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:115656200-115656800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:115656200-115656800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr9:115656200-115656800	Enhancers	HSMM	muscle
15	chr9:115656200-115656800	Enhancers	HUVEC	blood vessel
16	chr9:115656200-115657000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr9:115656200-115657000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:115656400-115656600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:115656400-115656800	Enhancers	Primary hematopoietic stem cells	blood
20	chr9:115656400-115659400	Enhancers	Primary B cells from cord blood	blood
21	chr9:115656600-115656800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:115656600-115656800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:115656600-115657000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr9:115656600-115658000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr9:115656800-115658200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:115657000-115663400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr9:115657200-115659400	Enhancers	Primary B cells from peripheral blood	blood
28	chr9:115657600-115660600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:115658200-115658600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:115658200-115658800	Flanking Active TSS	GM12878-XiMat	blood
31	chr9:115658400-115658600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
32	chr9:115658600-115658800	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:115658800-115659400	Enhancers	GM12878-XiMat	blood
34	chr9:115659000-115659800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr9:115659400-115659600	Bivalent Enhancer	Primary B cells from cord blood	blood
36	chr9:115659800-115661600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr9:115660400-115662000	Enhancers	HepG2	liver
38	chr9:115660600-115661600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr9:115660800-115661400	Bivalent Enhancer	Primary B cells from cord blood	blood
40	chr9:115660800-115661600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
41	chr9:115661000-115661400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr9:115661000-115661600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:115661000-115661600	Enhancers	Fetal Thymus	thymus
44	chr9:115661200-115661600	Enhancers	Fetal Kidney	kidney
45	chr9:115661400-115661600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:115661600-115663000	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr9:115661600-115665000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:115661600-115667000	Weak transcription	Fetal Kidney	kidney
49	chr9:115662800-115663000	Enhancers	Osteobl	bone
50	chr9:115663000-115664800	Weak transcription	Monocytes-CD14+_RO01746	blood

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