Variant report

Variant	nsv466685
Chromosome Location	chr9:139668443-139674527
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:193)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:193 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr9:139668076-139668471	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF3	chr9:139668130-139668489	GM12878	blood:	n/a	n/a
3	ATF3	chr9:139668158-139668508	K562	blood:	n/a	n/a
4	ATF3	chr9:139668163-139668543	H1-hESC	embryonic stem cell:	n/a	n/a
5	ATF3	chr9:139668215-139668454	HepG2	liver:	n/a	n/a
6	CBX3	chr9:139667695-139668588	HCT-116	colon:	n/a	n/a
7	CBX3	chr9:139667717-139668521	K562	blood:	n/a	n/a
8	CBX3	chr9:139667686-139668554	K562	blood:	n/a	n/a
9	CBX3	chr9:139668883-139669223	K562	blood:	n/a	n/a
10	CHD2	chr9:139668218-139668499	K562	blood:	n/a	n/a
11	CHD2	chr9:139668200-139668514	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr9:139674325-139674597	K562	blood:	n/a	n/a
13	CTCF	chr9:139674421-139674550	MCF-7	breast:	n/a	n/a
14	CTCF	chr9:139674420-139674570	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr9:139674340-139674490	NHEK	skin:	n/a	n/a
16	CTCF	chr9:139674440-139674690	Caco-2	colon:	n/a	n/a
17	CTCF	chr9:139674380-139674530	Caco-2	colon:	n/a	n/a
18	CTCF	chr9:139674400-139674550	HPAF	blood vessel:	n/a	n/a
19	CTCF	chr9:139674420-139674570	K562	blood:	n/a	n/a
20	CTCF	chr9:139674340-139674490	HEEpiC	esophagus:	n/a	n/a
21	CTCF	chr9:139674340-139674490	HMF	breast:	n/a	n/a
22	CTCF	chr9:139674300-139674450	NHDF-neo	bronchial:	n/a	n/a
23	CTCF	chr9:139674378-139674548	MCF-7	breast:	n/a	n/a
24	CTCF	chr9:139674409-139674515	HepG2	liver:	n/a	n/a
25	CTCF	chr9:139674440-139674590	RPTEC	kidney:	n/a	n/a
26	CTCF	chr9:139674360-139674510	HCM	heart:	n/a	n/a
27	CTCF	chr9:139674341-139674540	K562	blood:	n/a	n/a
28	CTCF	chr9:139674380-139674530	AG09309	skin:	n/a	n/a
29	CTCF	chr9:139674373-139674545	HepG2	liver:	n/a	n/a
30	CTCF	chr9:139674400-139674550	AG04450	lung:	n/a	n/a
31	CTCF	chr9:139674480-139674630	MCF-7	breast:	n/a	n/a
32	CTCF	chr9:139674400-139674550	HCPEpiC	choroid plexus:	n/a	n/a
33	CTCF	chr9:139674420-139674570	WERI-Rb-1	eye:	n/a	n/a
34	CTCF	chr9:139674400-139674550	GM12864	blood:	n/a	n/a
35	CTCF	chr9:139674478-139674482	IMR90	lung:	n/a	n/a
36	CTCF	chr9:139674333-139674544	HepG2	liver:	n/a	n/a
37	CTCF	chr9:139674398-139674547	MCF-7	breast:	n/a	n/a
38	CTCF	chr9:139674340-139674490	HRE	kidney:	n/a	n/a
39	CTCF	chr9:139674320-139674470	GM12872	blood:	n/a	n/a
40	CTCF	chr9:139674380-139674530	WERI-Rb-1	eye:	n/a	n/a
41	CTCF	chr9:139674441-139674500	MCF-7	breast:	n/a	n/a
42	CTCF	chr9:139674340-139674490	HPAF	blood vessel:	n/a	n/a
43	CTCF	chr9:139674380-139674530	AoAF	blood vessel:	n/a	n/a
44	CTCF	chr9:139674418-139674512	K562	blood:	n/a	n/a
45	CTCF	chr9:139674420-139674570	AG09319	gingival:	n/a	n/a
46	CTCF	chr9:139674380-139674530	MCF-7	breast:	n/a	n/a
47	CTCF	chr9:139674380-139674530	HAc	cerebellar:	n/a	n/a
48	CTCF	chr9:139674400-139674550	HRPEpiC	eye:	n/a	n/a
49	CTCF	chr9:139674360-139674510	AoAF	blood vessel:	n/a	n/a
50	CTCF	chr9:139674380-139674530	NHDF-neo	bronchial:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:139622733..139626444-chr9:139667758..139670003,3	K562	blood:
2	chr9:139671912..139674656-chr9:140133949..140136932,2	MCF-7	breast:
3	chr9:139662596..139664291-chr9:139666561..139668575,2	K562	blood:
4	chr9:139662206..139666130-chr9:139666450..139670889,6	K562	blood:
5	chr9:139620940..139622667-chr9:139668115..139669659,2	K562	blood:
6	chr9:139671789..139674484-chr9:139759128..139760920,2	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
ENSG00000233016	chromatin interactions
ENSG00000188229	chromatin interactions
ENSG00000107223	chromatin interactions

Extended variants
information (count: 305 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:305 , 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	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
2	rs546888188	chr9:139668458-139668459	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs560830694	chr9:139668511-139668512	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs532740110	chr9:139668512-139668513	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	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
6	rs114503136	chr9:139668558-139668559	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs117887649	chr9:139668559-139668560	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs373919971	chr9:139668574-139668575	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs184526363	chr9:139668604-139668605	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs188664023	chr9:139668640-139668641	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs532391337	chr9:139668641-139668642	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs192527099	chr9:139668677-139668678	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs370784236	chr9:139668682-139668683	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs144669640	chr9:139668689-139668690	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs558906223	chr9:139668761-139668762	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs111307638	chr9:139668771-139668772	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs544619942	chr9:139668849-139668850	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs570773296	chr9:139668881-139668882	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs375143996	chr9:139668890-139668891	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs138557444	chr9:139669002-139669003	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs141210919	chr9:139669034-139669035	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs560551268	chr9:139669035-139669036	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs532828770	chr9:139669053-139669054	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs1815524	chr9:139669111-139669112	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs150288574	chr9:139669137-139669138	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs530381486	chr9:139669139-139669140	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs550200619	chr9:139669162-139669163	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs137931782	chr9:139669166-139669167	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs200886420	chr9:139669198-139669199	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs79267788	chr9:139669207-139669208	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs546754833	chr9:139669218-139669219	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs566514448	chr9:139669236-139669237	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs372626962	chr9:139669287-139669288	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs567739558	chr9:139669313-139669314	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs372032703	chr9:139669342-139669343	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs149635028	chr9:139669354-139669355	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs575618405	chr9:139669373-139669374	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs538234276	chr9:139669389-139669390	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs112030171	chr9:139669390-139669391	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs555049018	chr9:139669400-139669401	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs7024123	chr9:139669422-139669423	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs2784065	chr9:139669457-139669458	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs555812189	chr9:139669460-139669461	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs34001297	chr9:139669472-139669473	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs2811769	chr9:139669473-139669474	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs575608797	chr9:139669501-139669502	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs2811770	chr9:139669514-139669515	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs77976729	chr9:139669515-139669516	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs147335445	chr9:139669539-139669540	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs531926426	chr9:139669540-139669541	Weak transcription	TF binding region Chromatin interactive region	2 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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:139667600-139669200	ZNF genes & repeats	Fetal Intestine Small	intestine
2	chr9:139667800-139668600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:139667800-139668600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:139667800-139668600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
5	chr9:139668000-139668600	ZNF genes & repeats	Colonic Mucosa	Colon
6	chr9:139668000-139669200	ZNF genes & repeats	K562	blood
7	chr9:139668200-139668600	ZNF genes & repeats	Fetal Thymus	thymus
8	chr9:139668200-139668800	Enhancers	Primary B cells from peripheral blood	blood
9	chr9:139668200-139682400	Weak transcription	Right Atrium	heart
10	chr9:139668400-139668600	Flanking Active TSS	HepG2	liver
11	chr9:139668400-139668800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:139668600-139668800	Enhancers	Fetal Thymus	thymus
13	chr9:139668600-139668800	Enhancers	HepG2	liver
14	chr9:139668600-139671400	Weak transcription	Colonic Mucosa	Colon
15	chr9:139668800-139671200	Weak transcription	HepG2	liver
16	chr9:139669200-139671000	Weak transcription	Fetal Intestine Small	intestine
17	chr9:139669200-139671200	Weak transcription	K562	blood
18	chr9:139670800-139673400	Enhancers	Fetal Intestine Large	intestine
19	chr9:139671000-139671600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr9:139671000-139671800	Enhancers	Fetal Intestine Small	intestine
21	chr9:139671200-139671400	Enhancers	HepG2	liver
22	chr9:139671200-139671800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:139671200-139672600	Enhancers	Duodenum Mucosa	Duodenum
24	chr9:139671200-139672600	Enhancers	K562	blood
25	chr9:139671400-139671800	Enhancers	Colonic Mucosa	Colon
26	chr9:139671400-139671800	Enhancers	Placenta	Placenta
27	chr9:139671400-139672400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr9:139671400-139672400	Flanking Active TSS	HepG2	liver
29	chr9:139671400-139672600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr9:139671600-139671800	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr9:139671600-139672400	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr9:139671600-139672400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr9:139671600-139672600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr9:139671800-139672000	Flanking Active TSS	Placenta	Placenta
35	chr9:139671800-139672000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr9:139671800-139672200	Flanking Active TSS	Colonic Mucosa	Colon
37	chr9:139671800-139672200	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr9:139672000-139672200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr9:139672000-139672600	Enhancers	Placenta	Placenta
40	chr9:139672200-139672400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr9:139672200-139672600	Enhancers	Colonic Mucosa	Colon
42	chr9:139672200-139673400	Enhancers	Fetal Intestine Small	intestine
43	chr9:139672400-139672600	Bivalent/Poised TSS	HSMMtube	muscle
44	chr9:139672400-139672800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr9:139672400-139673000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr9:139672400-139673200	Enhancers	HepG2	liver
47	chr9:139672600-139674000	Weak transcription	K562	blood
48	chr9:139672600-139674200	Weak transcription	Colonic Mucosa	Colon
49	chr9:139672600-139674600	Weak transcription	Placenta	Placenta
50	chr9:139673000-139674400	Weak transcription	Rectal Mucosa Donor 31	rectum

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