Variant report

Variant	esv3483320
Chromosome Location	chr9:139667109-139677386
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:289)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:289 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr9:139668130-139668489	GM12878	blood:	n/a	n/a
2	ATF3	chr9:139668269-139668395	GM12878	blood:	n/a	n/a
3	ATF3	chr9:139668163-139668543	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF3	chr9:139668215-139668454	HepG2	liver:	n/a	n/a
5	ATF3	chr9:139668158-139668508	K562	blood:	n/a	n/a
6	ATF3	chr9:139668076-139668471	H1-hESC	embryonic stem cell:	n/a	n/a
7	CBX3	chr9:139667695-139668588	HCT-116	colon:	n/a	n/a
8	CBX3	chr9:139667717-139668521	K562	blood:	n/a	n/a
9	CBX3	chr9:139668883-139669223	K562	blood:	n/a	n/a
10	CBX3	chr9:139667686-139668554	K562	blood:	n/a	n/a
11	CEBPB	chr9:139676958-139677311	A549	lung:	n/a	chr9:139677133-139677144
12	CEBPB	chr9:139676964-139677310	IMR90	lung:	n/a	chr9:139677133-139677144
13	CEBPB	chr9:139677017-139677281	H1-hESC	embryonic stem cell:	n/a	chr9:139677133-139677144
14	CEBPB	chr9:139676955-139677301	K562	blood:	n/a	chr9:139677133-139677144
15	CEBPB	chr9:139676958-139677313	HepG2	liver:	n/a	chr9:139677133-139677144
16	CEBPB	chr9:139676969-139677304	Hela-S3	cervix:	n/a	chr9:139677133-139677144
17	CHD2	chr9:139668218-139668499	K562	blood:	n/a	n/a
18	CHD2	chr9:139668200-139668514	H1-hESC	embryonic stem cell:	n/a	n/a
19	CHD2	chr9:139668334-139668429	GM12878	blood:	n/a	n/a
20	CTCF	chr9:139674380-139674530	WERI-Rb-1	eye:	n/a	n/a
21	CTCF	chr9:139674400-139674550	HRPEpiC	eye:	n/a	n/a
22	CTCF	chr9:139674340-139674490	HRE	kidney:	n/a	n/a
23	CTCF	chr9:139676277-139676308	GM13976	blood:	n/a	n/a
24	CTCF	chr9:139674480-139674630	MCF-7	breast:	n/a	n/a
25	CTCF	chr9:139674400-139674550	K562	blood:	n/a	n/a
26	CTCF	chr9:139668180-139668330	HepG2	liver:	n/a	n/a
27	CTCF	chr9:139674380-139674530	GM12873	blood:	n/a	n/a
28	CTCF	chr9:139674380-139674530	A549	lung:	n/a	n/a
29	CTCF	chr9:139674380-139674530	AG10803	skin:	n/a	n/a
30	CTCF	chr9:139674440-139674590	RPTEC	kidney:	n/a	n/a
31	CTCF	chr9:139674341-139674540	K562	blood:	n/a	n/a
32	CTCF	chr9:139674480-139674630	HFF-Myc	foreskin:	n/a	n/a
33	CTCF	chr9:139674380-139674530	AoAF	blood vessel:	n/a	n/a
34	CTCF	chr9:139674340-139674490	NHEK	skin:	n/a	n/a
35	CTCF	chr9:139668260-139668410	BE2_C	brain:	n/a	n/a
36	CTCF	chr9:139674420-139674570	HPF	lung:	n/a	n/a
37	CTCF	chr9:139674440-139674690	Caco-2	colon:	n/a	n/a
38	CTCF	chr9:139674400-139674550	HVMF	connective:	n/a	n/a
39	CTCF	chr9:139674420-139674570	AG09319	gingival:	n/a	n/a
40	CTCF	chr9:139674380-139674530	Caco-2	colon:	n/a	n/a
41	CTCF	chr9:139674420-139674570	HEEpiC	esophagus:	n/a	n/a
42	CTCF	chr9:139674400-139674550	HBMEC	blood vessel:	n/a	n/a
43	CTCF	chr9:139674420-139674650	HCFaa	heart:	n/a	n/a
44	CTCF	chr9:139674420-139674570	WERI-Rb-1	eye:	n/a	n/a
45	CTCF	chr9:139674320-139674470	AG04449	skin:	n/a	n/a
46	CTCF	chr9:139674420-139674570	AG10803	skin:	n/a	n/a
47	CTCF	chr9:139674413-139674522	A549	lung:	n/a	n/a
48	CTCF	chr9:139674409-139674515	HepG2	liver:	n/a	n/a
49	CTCF	chr9:139674420-139674570	HEK293	kidney:	n/a	n/a
50	CTCF	chr9:139674380-139674530	AG04450	lung:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:139677108..139679215-chr9:139738761..139741423,2	K562	blood:
2	chr9:139662596..139664291-chr9:139666561..139668575,2	K562	blood:
3	chr9:139671789..139674484-chr9:139759128..139760920,2	MCF-7	breast:
4	chr9:139662206..139666130-chr9:139666450..139670889,6	K562	blood:
5	chr9:139677027..139679580-chr9:139683653..139686548,4	K562	blood:
6	chr9:139620940..139622667-chr9:139668115..139669659,2	K562	blood:
7	chr9:139622733..139626444-chr9:139667758..139670003,3	K562	blood:
8	chr9:139666515..139668281-chr9:139676251..139678403,3	MCF-7	breast:
9	chr9:139666515..139668281-chr9:139676251..139678403,3	MCF-7	breast:
10	chr9:139617845..139623838-chr9:139660350..139667246,10	K562	blood:
11	chr9:139671912..139674656-chr9:140133949..140136932,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM141-1	chr9:139674391-139674670	NONHSAT135598

No data

Variant related genes	Relation type
ATP6V1G1P3	TF binding region
ENSG00000188229	chromatin interactions
ENSG00000272896	chromatin interactions
ENSG00000233016	chromatin interactions
ENSG00000232434	chromatin interactions
ENSG00000107223	chromatin interactions
ENSG00000244187	chromatin interactions

Extended variants
information (count: 502 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:502 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs555740010	chr9:139667112-139667113	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs575763424	chr9:139667127-139667128	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs140950318	chr9:139667161-139667162	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs561165698	chr9:139667172-139667173	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs577675100	chr9:139667200-139667201	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs372676879	chr9:139667300-139667301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs573258235	chr9:139667301-139667302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs12552459	chr9:139667317-139667318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs144705502	chr9:139667340-139667341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs573579685	chr9:139667356-139667357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs542549328	chr9:139667396-139667397	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs147914357	chr9:139667405-139667406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs550625723	chr9:139667430-139667431	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs528438201	chr9:139667433-139667434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs35988889	chr9:139667476-139667477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs11304434	chr9:139667497-139667498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs567756774	chr9:139667498-139667499	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs545080935	chr9:139667571-139667572	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs187772408	chr9:139667656-139667657	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs192448218	chr9:139667692-139667693	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs117188394	chr9:139667699-139667700	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs567892314	chr9:139667734-139667735	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs35916472	chr9:139667832-139667833	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs560879924	chr9:139667833-139667834	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs139981341	chr9:139667850-139667851	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs149972788	chr9:139667870-139667871	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs542164390	chr9:139667880-139667881	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs567057044	chr9:139667899-139667900	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs145201949	chr9:139667917-139667918	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs557509188	chr9:139668002-139668003	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs112955529	chr9:139668061-139668062	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs571006721	chr9:139668104-139668105	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs73556049	chr9:139668122-139668123	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs148895314	chr9:139668136-139668137	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs62584361	chr9:139668164-139668165	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs114785910	chr9:139668195-139668196	ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs72772799	chr9:139668202-139668203	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs573093934	chr9:139668206-139668207	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs569258590	chr9:139668220-139668221	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs143616703	chr9:139668260-139668261	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs146481397	chr9:139668261-139668262	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs531858162	chr9:139668389-139668390	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs72772800	chr9:139668400-139668401	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs2811768	chr9:139668443-139668444	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs546888188	chr9:139668458-139668459	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs560830694	chr9:139668511-139668512	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs532740110	chr9:139668512-139668513	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs11145879	chr9:139668527-139668528	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs114503136	chr9:139668558-139668559	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs117887649	chr9:139668559-139668560	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:83)

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
Urothelial carcinoma	21177765	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	20435627	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
Breast cancer	17603634	CNVD
Oral cancer	21386901	CNVD
Cardiac fibroma	18329553	CNVD
Lung cancer	19147751	CNVD
Melanoma	18172304	CNVD
Cervical cancer	16585170	CNVD
Ependymoma	19289631	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Cervical cancer	17311676	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Breast cancer	16608533	CNVD
Metanephric adenoma	20802469	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Chordoma	18071362	CNVD
small cell lung cancer	20016488	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Kleefstra Syndrome	21538692	CNVD
Disorders of sex development	22290220	CNVD
Cancer	21183584	CNVD
Chronic myelomonocytic leukemia	16760666	CNVD
Abnormal phenotypes	18644119	CNVD
Ovarian cancer	21720365	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Sudden cardiac death	19188705	CNVD
Myoepithelioma	18604193	CNVD
Tuberous sclerosis	19566914	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Hepatocellular carcinoma	22174799	CNVD
Idiopathic chronic pancreatitis	21572526	CNVD
Kleefstra syndrome	22670141	CNVD
Schizophrenia	22241247	CNVD
9q deletion syndrome	16826528	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Non-small cell lung cancer	21829676	CNVD
Non-syndromic sensorineural hearing loss	19293338	CNVD
Neurodevelopmental disorder	22521361	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Mantle cell lymphoma	19029149	CNVD
Autism	20808228	CNVD
Epilepsy	22083797	CNVD
Cancer	20164920	CNVD
Breast cancer	21509527	CNVD
Developmental delay	20877625	CNVD
Hypoplastic	20877625	CNVD
Mental retardation	20877625	CNVD
Microcephaly	20877625	CNVD
Palpebral fissures	20877625	CNVD
Melanoma	20877625	CNVD
Medulloblastoma	21163964	CNVD

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:139657800-139667800	Weak transcription	Right Atrium	heart
2	chr9:139659200-139667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:139664600-139667600	Weak transcription	Fetal Intestine Small	intestine
4	chr9:139664600-139667800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:139664600-139668000	Weak transcription	Colonic Mucosa	Colon
6	chr9:139667400-139667600	Weak transcription	Ovary	ovary
7	chr9:139667600-139669200	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr9:139667800-139668200	ZNF genes & repeats	Right Atrium	heart
9	chr9:139667800-139668400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:139667800-139668600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:139667800-139668600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:139667800-139668600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
13	chr9:139668000-139668600	ZNF genes & repeats	Colonic Mucosa	Colon
14	chr9:139668000-139669200	ZNF genes & repeats	K562	blood
15	chr9:139668200-139668600	ZNF genes & repeats	Fetal Thymus	thymus
16	chr9:139668200-139668800	Enhancers	Primary B cells from peripheral blood	blood
17	chr9:139668200-139682400	Weak transcription	Right Atrium	heart
18	chr9:139668400-139668600	Flanking Active TSS	HepG2	liver
19	chr9:139668400-139668800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:139668600-139668800	Enhancers	Fetal Thymus	thymus
21	chr9:139668600-139668800	Enhancers	HepG2	liver
22	chr9:139668600-139671400	Weak transcription	Colonic Mucosa	Colon
23	chr9:139668800-139671200	Weak transcription	HepG2	liver
24	chr9:139669200-139671000	Weak transcription	Fetal Intestine Small	intestine
25	chr9:139669200-139671200	Weak transcription	K562	blood
26	chr9:139670800-139673400	Enhancers	Fetal Intestine Large	intestine
27	chr9:139671000-139671600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr9:139671000-139671800	Enhancers	Fetal Intestine Small	intestine
29	chr9:139671200-139671400	Enhancers	HepG2	liver
30	chr9:139671200-139671800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:139671200-139672600	Enhancers	Duodenum Mucosa	Duodenum
32	chr9:139671200-139672600	Enhancers	K562	blood
33	chr9:139671400-139671800	Enhancers	Colonic Mucosa	Colon
34	chr9:139671400-139671800	Enhancers	Placenta	Placenta
35	chr9:139671400-139672400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr9:139671400-139672400	Flanking Active TSS	HepG2	liver
37	chr9:139671400-139672600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr9:139671600-139671800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr9:139671600-139672400	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr9:139671600-139672400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr9:139671600-139672600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr9:139671800-139672000	Flanking Active TSS	Placenta	Placenta
43	chr9:139671800-139672000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr9:139671800-139672200	Flanking Active TSS	Colonic Mucosa	Colon
45	chr9:139671800-139672200	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr9:139672000-139672200	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr9:139672000-139672600	Enhancers	Placenta	Placenta
48	chr9:139672200-139672400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr9:139672200-139672600	Enhancers	Colonic Mucosa	Colon
50	chr9:139672200-139673400	Enhancers	Fetal Intestine Small	intestine

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