Variant report

Variant	nsv1032098
Chromosome Location	chr9:12163322-12411586
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:493)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:493 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr9:12328968-12329168	HepG2	liver:	n/a	n/a
2	BACH1	chr9:12292536-12292567	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr9:12170667-12170713	H1-hESC	embryonic stem cell:	n/a	n/a
4	BATF	chr9:12230772-12231081	GM12878	blood:	n/a	n/a
5	BATF	chr9:12329455-12329670	GM12878	blood:	n/a	n/a
6	BCLAF1	chr9:12329426-12329668	GM12878	blood:	n/a	n/a
7	BHLHE40	chr9:12329021-12329257	GM12878	blood:	n/a	n/a
8	BHLHE40	chr9:12328884-12329725	HepG2	liver:	n/a	n/a
9	BHLHE40	chr9:12328995-12329158	K562	blood:	n/a	n/a
10	BRCA1	chr9:12368889-12368916	GM12878	blood:	n/a	n/a
11	CEBPB	chr9:12195470-12195708	H1-hESC	embryonic stem cell:	n/a	chr9:12195611-12195622
12	CEBPB	chr9:12180768-12180970	IMR90	lung:	n/a	n/a
13	CEBPB	chr9:12367335-12367535	HepG2	liver:	n/a	chr9:12367443-12367454
14	CEBPB	chr9:12193945-12194181	A549	lung:	n/a	chr9:12194071-12194082 chr9:12194071-12194084
15	CEBPB	chr9:12195471-12195788	IMR90	lung:	n/a	chr9:12195611-12195622
16	CEBPB	chr9:12208833-12209071	HepG2	liver:	n/a	chr9:12208898-12208909 chr9:12208899-12208908 chr9:12208897-12208910
17	CEBPB	chr9:12288039-12288167	HepG2	liver:	n/a	n/a
18	CEBPB	chr9:12195456-12195797	HepG2	liver:	n/a	chr9:12195611-12195622
19	CEBPB	chr9:12195488-12195695	K562	blood:	n/a	chr9:12195611-12195622
20	CHD1	chr9:12314638-12314797	GM12878	blood:	n/a	n/a
21	CHD2	chr9:12314733-12314838	GM12878	blood:	n/a	n/a
22	CHD2	chr9:12319226-12319370	GM12878	blood:	n/a	n/a
23	CTCF	chr9:12329480-12329630	GM12872	blood:	n/a	n/a
24	CTCF	chr9:12329337-12329779	GM12878	blood:	n/a	n/a
25	CTCF	chr9:12329500-12329650	HEK293	kidney:	n/a	n/a
26	CTCF	chr9:12329520-12329670	BJ	skin:	n/a	n/a
27	CTCF	chr9:12329500-12329650	K562	blood:	n/a	n/a
28	CTCF	chr9:12329180-12329330	HRE	kidney:	n/a	n/a
29	CTCF	chr9:12329500-12329650	Caco-2	colon:	n/a	n/a
30	CTCF	chr9:12328920-12329070	WERI-Rb-1	eye:	n/a	n/a
31	CTCF	chr9:12317058-12317076	GM10248	blood:	n/a	n/a
32	CTCF	chr9:12329373-12329660	A549	lung:	n/a	n/a
33	CTCF	chr9:12329500-12329650	HCPEpiC	choroid plexus:	n/a	n/a
34	CTCF	chr9:12329500-12329650	GM12875	blood:	n/a	n/a
35	CTCF	chr9:12329500-12329650	GM12868	blood:	n/a	n/a
36	CTCF	chr9:12329500-12329650	GM12873	blood:	n/a	n/a
37	CTCF	chr9:12210677-12210803	Kidney_OC	kidney:	n/a	n/a
38	CTCF	chr9:12329362-12329672	HepG2	liver:	n/a	n/a
39	CTCF	chr9:12329280-12329352	GM12892	blood:	n/a	n/a
40	CTCF	chr9:12329520-12329670	GM12869	blood:	n/a	n/a
41	CTCF	chr9:12329520-12329670	GM12870	blood:	n/a	n/a
42	CTCF	chr9:12329451-12329695	Lung_OC	lung:	n/a	n/a
43	CTCF	chr9:12353504-12353555	Lung_OC	lung:	n/a	n/a
44	CTCF	chr9:12264400-12264550	HFF	foreskin:	n/a	n/a
45	CTCF	chr9:12329500-12329650	HUVEC	blood vessel:	n/a	n/a
46	CTCF	chr9:12329460-12329610	HAc	cerebellar:	n/a	n/a
47	CTCF	chr9:12329439-12329720	GM13977	blood:	n/a	n/a
48	CTCF	chr9:12329480-12329630	AG09309	skin:	n/a	n/a
49	CTCF	chr9:12195600-12195750	NHEK	skin:	n/a	n/a
50	CTCF	chr9:12329390-12329697	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:10365979..10366914-chr9:12329143..12329893,2	MCF-7	breast:
2	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
3	chr16:89002000..89004763-chr9:12244429..12246932,2	MCF-7	breast:
4	chr9:10855828..10856443-chr9:12329128..12329639,2	MCF-7	breast:
5	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:
6	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
7	chr6:116381055..116381867-chr9:12405688..12406208,2	Hela-S3	cervix:
8	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TYRP1-4	chr9:12287320-12288238	NONHSAT130222

No data

Variant related genes	Relation type
ENSG00000231491	TF binding region
ENSG00000224935	TF binding region
RNU2-47P	TF binding region
ENSG00000261226	chromatin interactions

Extended variants
information (count: 3841 )
Associated
traits (count: 107 )

Variant overlapped rSNPs/rCNVs (count:3841 , 50 per page) page: 1 2 3 4 5 6 7 ... 77

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558621005	chr9:12163339-12163340	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs182370910	chr9:12163341-12163342	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs188349201	chr9:12163344-12163345	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs554374195	chr9:12163373-12163374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs538904693	chr9:12163413-12163414	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs550630189	chr9:12163465-12163466	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs574378086	chr9:12163477-12163478	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs6474686	chr9:12163506-12163507	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs192584012	chr9:12163537-12163538	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs565348362	chr9:12163574-12163575	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs10115948	chr9:12163583-12163584	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs545133048	chr9:12163624-12163625	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs549304280	chr9:12163711-12163712	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs566273535	chr9:12163716-12163717	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs183804776	chr9:12163725-12163726	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs147911193	chr9:12163746-12163747	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs551172926	chr9:12163767-12163768	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs567892263	chr9:12163816-12163817	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs140497023	chr9:12163832-12163833	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs368730719	chr9:12163833-12163834	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs2166424	chr9:12163844-12163845	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs533004608	chr9:12163866-12163867	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs371325072	chr9:12163875-12163876	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs149994136	chr9:12163911-12163912	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs538635379	chr9:12163914-12163915	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs34405443	chr9:12163987-12163988	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs558306385	chr9:12164042-12164043	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs540403365	chr9:12164057-12164058	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs113669855	chr9:12164059-12164060	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs560225471	chr9:12164081-12164082	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs534963082	chr9:12164113-12164114	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs529190658	chr9:12164127-12164128	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs372658338	chr9:12164162-12164163	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs145195916	chr9:12164172-12164173	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs375569986	chr9:12164173-12164174	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs540091362	chr9:12164175-12164176	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs149130779	chr9:12164177-12164178	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs577104331	chr9:12164187-12164188	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs545383058	chr9:12164196-12164197	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs369623633	chr9:12164272-12164273	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs571639001	chr9:12164279-12164280	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs565163436	chr9:12164326-12164327	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs575676909	chr9:12164335-12164336	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs34021111	chr9:12164340-12164341	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs34474068	chr9:12164378-12164379	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs544732694	chr9:12164386-12164387	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs561437337	chr9:12164388-12164389	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs537024111	chr9:12164406-12164407	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs530318467	chr9:12164408-12164409	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs547273042	chr9:12164412-12164413	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:107)

Disease	PMID	Source
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
abnormal development	18461090	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
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	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
low-grade B-cell lymphoma tumor	18367492	CNVD
Type 2 diabetes	21526130	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Chordoma	21215367	CNVD

Chromatin state (count:179 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12161400-12167200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:12161600-12164800	Enhancers	Brain Germinal Matrix	brain
3	chr9:12162600-12163400	Enhancers	Fetal Brain Male	brain
4	chr9:12162800-12166400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:12162800-12166600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:12163200-12164000	Weak transcription	Fetal Brain Female	brain
7	chr9:12164000-12164200	Enhancers	Fetal Brain Female	brain
8	chr9:12164200-12166200	Weak transcription	Fetal Brain Female	brain
9	chr9:12165800-12166400	Enhancers	Brain Substantia Nigra	brain
10	chr9:12166200-12166400	Enhancers	Fetal Brain Female	brain
11	chr9:12166400-12167000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr9:12166600-12167000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:12191600-12192000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr9:12191600-12192000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:12191800-12192000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:12192000-12200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:12200400-12200600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:12200400-12200800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr9:12200400-12202000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:12200600-12201000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr9:12200800-12201200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:12201200-12204400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:12204400-12204800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:12212600-12213000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:12212600-12213600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:12212800-12214000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:12213000-12213400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:12213000-12213800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:12213400-12214200	Enhancers	Brain Germinal Matrix	brain
30	chr9:12213400-12214400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:12213800-12214200	Enhancers	Brain Hippocampus Middle	brain
32	chr9:12221800-12222000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:12222000-12224400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:12224200-12224600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:12224200-12225000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr9:12224200-12225000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr9:12224400-12224800	Enhancers	H9 Cell Line	embryonic stem cell
38	chr9:12224400-12224800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:12231000-12231400	Enhancers	Liver	Liver
40	chr9:12231200-12231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:12231400-12233400	Weak transcription	Liver	Liver
42	chr9:12231600-12232000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:12233400-12233800	Enhancers	Liver	Liver
44	chr9:12235200-12235600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:12241200-12242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr9:12241400-12243200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr9:12241600-12242000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:12241600-12242000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr9:12241600-12242000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr9:12241600-12242000	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links