Variant report

Variant	nsv892342
Chromosome Location	chr9:11262118-11326457
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	BRCA1	chr9:11319527-11319802	H1-hESC	embryonic stem cell:	n/a	n/a
2	BRCA1	chr9:11272473-11272479	Hela-S3	cervix:	n/a	n/a
3	CBX3	chr9:11269115-11269340	K562	blood:	n/a	n/a
4	CEBPB	chr9:11294410-11294610	HepG2	liver:	n/a	n/a
5	CEBPB	chr9:11267004-11267299	HepG2	liver:	n/a	chr9:11267135-11267146
6	CEBPB	chr9:11267017-11267301	K562	blood:	n/a	chr9:11267135-11267146
7	CEBPB	chr9:11266996-11267317	IMR90	lung:	n/a	chr9:11267135-11267146
8	CTCF	chr9:11293809-11293811	Kidney_OC	kidney:	n/a	n/a
9	CTCF	chr9:11319860-11320010	NHEK	skin:	n/a	n/a
10	CTCF	chr9:11319580-11319730	HMF	breast:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
11	CTCF	chr9:11319580-11319730	HEK293	kidney:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
12	CTCF	chr9:11319580-11319730	WERI-Rb-1	eye:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
13	CTCF	chr9:11319540-11319690	HPF	lung:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
14	CTCF	chr9:11319540-11319690	HAc	cerebellar:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
15	CTCF	chr9:11319540-11319721	SK-N-SH_RA	brain:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
16	CTCF	chr9:11319597-11319703	K562	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
17	CTCF	chr9:11319620-11319770	NHDF-neo	bronchial:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
18	CTCF	chr9:11319622-11319733	GM19238	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
19	CTCF	chr9:11292504-11292560	GM13976	blood:	n/a	n/a
20	CTCF	chr9:11319505-11319791	Medullo	brain:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
21	CTCF	chr9:11319524-11319760	HUVEC	blood vessel:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
22	CTCF	chr9:11313320-11313470	GM12874	blood:	n/a	n/a
23	CTCF	chr9:11266027-11266077	LNCaP	prostate:	n/a	n/a
24	CTCF	chr9:11319580-11319730	HEEpiC	esophagus:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
25	CTCF	chr9:11319560-11319710	GM12869	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
26	CTCF	chr9:11319580-11319730	HepG2	liver:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
27	CTCF	chr9:11319590-11319696	Lung_OC	lung:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
28	CTCF	chr9:11319500-11319650	HL-60	blood:	n/a	n/a
29	CTCF	chr9:11319560-11319710	HPAF	blood vessel:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
30	CTCF	chr9:11319500-11319650	HCM	heart:	n/a	n/a
31	CTCF	chr9:11319560-11319710	GM12864	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
32	CTCF	chr9:11319580-11319730	NB4	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
33	CTCF	chr9:11319540-11319690	HPAF	blood vessel:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
34	CTCF	chr9:11319560-11319710	GM12868	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
35	CTCF	chr9:11319520-11319670	GM12801	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
36	CTCF	chr9:11291462-11291489	GM10248	blood:	n/a	n/a
37	CTCF	chr9:11319579-11319733	GM10248	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
38	CTCF	chr9:11319560-11319710	GM12870	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
39	CTCF	chr9:11266011-11266069	Kidney_OC	kidney:	n/a	n/a
40	CTCF	chr9:11319520-11319670	GM12865	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
41	CTCF	chr9:11319580-11319730	HCPEpiC	choroid plexus:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
42	CTCF	chr9:11319542-11319759	GM12878	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
43	CTCF	chr9:11319540-11319690	SAEC	small airway:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
44	CTCF	chr9:11319456-11319819	H1-hESC	embryonic stem cell:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
45	CTCF	chr9:11293769-11293802	Kidney_OC	kidney:	n/a	n/a
46	CTCF	chr9:11319615-11319718	GM19240	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
47	CTCF	chr9:11319540-11319690	GM12869	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
48	CTCF	chr9:11319620-11319770	Caco-2	colon:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658
49	CTCF	chr9:11273460-11273610	GM12866	blood:	n/a	n/a
50	CTCF	chr9:11319520-11319670	GM12873	blood:	n/a	chr9:11319641-11319657 chr9:11319635-11319656 chr9:11319640-11319658

No.	Distal block	Cell Line	Cell type
1	chr9:10855589..10857004-chr9:11319142..11320476,6	MCF-7	breast:
2	chr11:13082457..13083259-chr9:11319197..11319700,2	MCF-7	breast:
3	chr9:10366359..10367238-chr9:11319480..11320059,2	MCF-7	breast:
4	chr9:10855837..10856356-chr9:11319207..11319905,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPRD-9	chr9:11266253-11266314	NONHSAT130211
2	lnc-PTPRD-9	chr9:11265314-11265536	NONHSAT130211
3	lnc-PTPRD-4	chr9:11275314-11275536	XLOC_007646
4	lnc-TYRP1-1	chr9:11325743-11325750	XLOC_007282
5	lnc-TYRP1-1	chr9:11313363-11313595	XLOC_007282
6	lnc-TYRP1-2	chr9:11277589-11277655	XLOC_007281
7	lnc-TYRP1-2	chr9:11277792-11277964	XLOC_007281
8	lnc-PTPRD-4	chr9:11276253-11276314	XLOC_007646

Variant related genes	Relation type
ENSG00000230365	TF binding region

Extended variants
information (count: 731 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:731 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs139580500	chr9:11265336-11265337	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs545778949	chr9:11265354-11265355	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs193176271	chr9:11265357-11265358	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs1352521	chr9:11265404-11265405	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs184395703	chr9:11265444-11265445	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs189006947	chr9:11265474-11265475	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs527866453	chr9:11265492-11265493	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs373214877	chr9:11265518-11265519	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs538176796	chr9:11265521-11265522	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs376939630	chr9:11265523-11265524	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs575991089	chr9:11266302-11266303	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs112513186	chr9:11266309-11266310	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs553250704	chr9:11268812-11268813	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs567060901	chr9:11268852-11268853	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs191033194	chr9:11268871-11268872	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs559273937	chr9:11268918-11268919	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs575742564	chr9:11268926-11268927	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs560974070	chr9:11268949-11268950	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs544246449	chr9:11268958-11268959	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs182456635	chr9:11268968-11268969	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs115390366	chr9:11268989-11268990	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs60073929	chr9:11268997-11268998	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs376613110	chr9:11269002-11269003	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs114962483	chr9:11269028-11269029	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs150412559	chr9:11269078-11269079	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs539549759	chr9:11269111-11269112	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs544938858	chr9:11269112-11269113	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs7852406	chr9:11269117-11269118	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs546938544	chr9:11269132-11269133	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs550263629	chr9:11269147-11269148	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs567364729	chr9:11269154-11269155	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs188325014	chr9:11269163-11269164	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs374419394	chr9:11269166-11269167	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs546715889	chr9:11269193-11269194	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs145175828	chr9:11269274-11269275	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs539219216	chr9:11269275-11269276	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs141473607	chr9:11269286-11269287	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs569542779	chr9:11269303-11269304	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs538241780	chr9:11269307-11269308	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs554623203	chr9:11269318-11269319	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs7852565	chr9:11269319-11269320	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs370864494	chr9:11269335-11269336	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs540415643	chr9:11269344-11269345	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs532791068	chr9:11269405-11269406	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs34855741	chr9:11269412-11269413	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs373371558	chr9:11269473-11269474	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs76540689	chr9:11269514-11269515	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs13288265	chr9:11269531-11269532	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs78030853	chr9:11269562-11269563	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs574557116	chr9:11269574-11269575	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:102)

Disease	PMID	Source
abnormal development	18461090	CNVD
Disorders of sex development	21048976	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
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21080181	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
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Cancer	20164920	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	21764851	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Gastric cancer	16891809	CNVD
Mental retardation	17847001	CNVD
Cutaneous squamous cell carcinomas	17420988	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21611746	CNVD
Melanoma	22183965	CNVD
Barrett''s syndrome	19417022	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Bipolar disorder	19114987	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:11268800-11269600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr9:11280400-11281000	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr9:11280600-11281000	Enhancers	Fetal Brain Female	brain
4	chr9:11280800-11281200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:11295400-11297000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:11296400-11296600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:11296600-11300800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:11297000-11297400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:11300800-11301000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:11312800-11313600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:11312800-11313600	Enhancers	Brain Hippocampus Middle	brain
12	chr9:11313000-11313400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:11313000-11313400	Enhancers	Brain Cingulate Gyrus	brain
14	chr9:11313000-11313600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:11313000-11313600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr9:11313000-11313800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:11313600-11314600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:11318000-11321800	Enhancers	Fetal Brain Male	brain
19	chr9:11318200-11319200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:11318200-11319800	Enhancers	Fetal Brain Female	brain
21	chr9:11318800-11320000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr9:11318800-11320200	Enhancers	Brain Germinal Matrix	brain
23	chr9:11319200-11320200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr9:11319600-11320400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:11319600-11320400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:11319800-11320800	Weak transcription	Fetal Brain Female	brain
27	chr9:11320800-11321600	Enhancers	Fetal Brain Female	brain
28	chr9:11321800-11322600	Weak transcription	Fetal Brain Male	brain
29	chr9:11322600-11322800	Enhancers	Fetal Brain Male	brain
30	chr9:11326000-11326400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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