Variant report

Variant	nsv470285
Chromosome Location	chr12:38950082-39007749
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	BATF	chr12:38978937-38979254	GM12878	blood:	n/a	chr12:38978975-38978984 chr12:38979090-38979101
2	BATF	chr12:38978987-38979244	GM12878	blood:	n/a	chr12:38979090-38979101
3	BRCA1	chr12:38980636-38980915	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr12:38951466-38951741	HepG2	liver:	n/a	chr12:38951566-38951577
5	CEBPB	chr12:38950329-38950425	A549	lung:	n/a	n/a
6	CEBPB	chr12:38982562-38983243	Hela-S3	cervix:	n/a	chr12:38982971-38982982
7	CEBPB	chr12:38982762-38983190	ECC-1	luminal epithelium:	n/a	chr12:38982971-38982982
8	CEBPB	chr12:38950379-38950387	HepG2	liver:	n/a	n/a
9	CEBPB	chr12:38982828-38983122	HepG2	liver:	n/a	chr12:38982971-38982982
10	CEBPB	chr12:38951490-38951690	A549	lung:	n/a	chr12:38951566-38951577
11	CEBPB	chr12:38980570-38980873	A549	lung:	n/a	chr12:38980701-38980710 chr12:38980701-38980710 chr12:38980701-38980710 chr12:38980701-38980710 chr12:38980701-38980712
12	CEBPB	chr12:38980443-38981124	Hela-S3	cervix:	n/a	chr12:38980701-38980710 chr12:38980701-38980710 chr12:38980917-38980930 chr12:38980701-38980710 chr12:38980701-38980710 chr12:38980701-38980712
13	CEBPB	chr12:38951464-38951704	IMR90	lung:	n/a	chr12:38951566-38951577
14	CEBPB	chr12:38981442-38981823	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr12:38949928-38950461	Hela-S3	cervix:	n/a	chr12:38950417-38950428
16	CEBPB	chr12:39001091-39001504	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr12:38982717-38983202	ECC-1	luminal epithelium:	n/a	chr12:38982971-38982982
18	CEBPB	chr12:38982837-38983151	H1-hESC	embryonic stem cell:	n/a	chr12:38982971-38982982
19	CEBPB	chr12:38982893-38983133	MCF-7	breast:	n/a	chr12:38982971-38982982
20	CHD2	chr12:38980670-38980954	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr12:38957486-38957542	GM20000	blood:	n/a	n/a
22	CTCF	chr12:38988431-38988556	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr12:38988476-38988548	GM19239	blood:	n/a	n/a
24	CTCF	chr12:38988437-38988541	GM13977	blood:	n/a	n/a
25	CTCF	chr12:38988469-38988544	GM10266	blood:	n/a	n/a
26	CTCF	chr12:38988371-38988674	GM12878	blood:	n/a	n/a
27	CTCF	chr12:38973117-38973139	LNCaP	prostate:	n/a	n/a
28	E2F4	chr12:38984614-38984757	MCF10A-Er-Src	breast:	n/a	n/a
29	E2F4	chr12:38963489-38963533	MCF10A-Er-Src	breast:	n/a	n/a
30	E2F4	chr12:38986469-38986669	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr12:38980654-38981016	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F4	chr12:38981476-38981774	MCF10A-Er-Src	breast:	n/a	n/a
33	EP300	chr12:38978976-38979255	GM12878	blood:	n/a	n/a
34	EP300	chr12:39001111-39001509	Hela-S3	cervix:	n/a	n/a
35	EP300	chr12:39005241-39005253	GM12878	blood:	n/a	n/a
36	EP300	chr12:38980511-38981115	Hela-S3	cervix:	n/a	chr12:38980512-38980526 chr12:38980513-38980527 chr12:38980511-38980525 chr12:38980700-38980714
37	EP300	chr12:38982794-38983207	Hela-S3	cervix:	n/a	chr12:38982968-38982982
38	ESR1	chr12:38995688-38996037	ECC-1	luminal epithelium:	n/a	n/a
39	ESR1	chr12:38995670-38996071	ECC-1	luminal epithelium:	n/a	n/a
40	FOS	chr12:38980634-38981064	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr12:38980529-38981100	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr12:39001211-39001413	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr12:38979006-38979118	MCF10A-Er-Src	breast:	n/a	chr12:38979056-38979064 chr12:38979090-38979098 chr12:38979091-38979102 chr12:38979088-38979100
44	FOS	chr12:38949991-38950328	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr12:38982898-38983098	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr12:38981534-38981734	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr12:38978960-38979219	MCF10A-Er-Src	breast:	n/a	chr12:38979056-38979064 chr12:38979090-38979098 chr12:38979091-38979102 chr12:38979088-38979100
48	FOS	chr12:38949989-38950324	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr12:38978950-38979168	MCF10A-Er-Src	breast:	n/a	chr12:38979056-38979064 chr12:38979090-38979098 chr12:38979091-38979102 chr12:38979088-38979100
50	FOS	chr12:39001134-39001436	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:38984007-38984057	MCF-7	breast:	n/a
2	chr12:38984007-38984057	PANC-1	pancreas:	n/a
3	chr12:38984007-38984057	HCPEpiC	choroid plexus:	n/a
4	chr12:38984007-38984057	HRE	kidney:	n/a
5	chr12:38984007-38984057	Jurkat	blood:	n/a
6	chr12:38984007-38984057	GM06990	blood:	n/a
7	chr12:38984007-38984057	HUVEC	blood vessel:	n/a
8	chr12:38984007-38984057	BJ	skin:	n/a
9	chr12:38984007-38984057	SK-N-SH_RA	brain:	n/a
10	chr12:38984007-38984057	HPAEpiC	pulmonary alveolar:	n/a
11	chr12:38984007-38984057	AoSMC	blood vessel:	n/a
12	chr12:38984007-38984057	HEEpiC	esophagus:	n/a
13	chr12:38984007-38984057	ProgFib	skin:	n/a
14	chr12:38984007-38984057	SKMC	muscle:	n/a
15	chr12:38984007-38984057	AG04450	lung:	fetal
16	chr12:38984007-38984057	AG09319	gingival:	n/a
17	chr12:38984007-38984057	BE2_C	brain:	n/a
18	chr12:38984007-38984057	NT2-D1	testis:	n/a
19	chr12:38984007-38984057	AG04449	skin:	fetal
20	chr12:38984007-38984057	MCF10A-Er-Src	breast:	n/a
21	chr12:38984007-38984057	GM19239	blood:	n/a
22	chr12:38984007-38984057	HepG2	liver:	n/a
23	chr12:38984007-38984057	ECC-1	luminal epithelium:	n/a
24	chr12:38984007-38984057	CMK	blood:	n/a
25	chr12:38984007-38984057	HCT-116	colon:	n/a
26	chr12:38984007-38984057	T-47D	breast:	n/a
27	chr12:38984007-38984057	NHDF-neo	bronchial:	n/a
28	chr12:38984007-38984057	HCF	heart:	n/a
29	chr12:38984007-38984057	GM12892	blood:	n/a
30	chr12:38984007-38984057	NHBE	bronchial:	n/a
31	chr12:38984007-38984057	Caco-2	colon:	n/a
32	chr12:38984007-38984057	AG09309	skin:	n/a
33	chr12:38984007-38984057	ovcar-3	ovarian:	n/a
34	chr12:38984007-38984057	HIPEpiC	eye:	n/a
35	chr12:38984007-38984057	RPTEC	kidney:	n/a
36	chr12:38984007-38984057	NB4	blood:	n/a
37	chr12:38984007-38984057	AG10803	skin:	n/a
38	chr12:38984007-38984057	HRPEpiC	eye:	n/a
39	chr12:38984007-38984057	PFSK-1	brain:	n/a
40	chr12:38984007-38984057	GM12878	blood:	n/a
41	chr12:38984007-38984057	PrEC	prostate:	n/a
42	chr12:38984007-38984057	HAEpiC	amniotic membrane:	n/a
43	chr12:38984007-38984057	HMEC	breast:	n/a
44	chr12:38984007-38984057	NH-A	brain:	n/a
45	chr12:38984007-38984057	SK-N-MC	brain:	n/a
46	chr12:38984007-38984057	HNPCEpiC	eye:	n/a
47	chr12:38984007-38984057	LNCaP	prostate:	n/a
48	chr12:38984007-38984057	HRCEpiC	kidney:	n/a
49	chr12:38984007-38984057	HCM	heart:	n/a
50	chr12:38984007-38984057	HEK293	kidney:	embryo

No.	Distal block	Cell Line	Cell type
1	chr12:38990179..38991129-chr4:2331691..2332483,2	Hela-S3	cervix:
2	chr12:38954957..38957532-chr12:38958850..38960983,2	K562	blood:
3	chr12:38954957..38957532-chr12:38958850..38960983,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE8-1	chr12:38983132-38983232	XLOC_010050
2	lnc-CPNE8-1	chr12:38983517-38983614	ENSG00000258119
3	lnc-CPNE8-1	chr12:38983517-38983614	XLOC_010050
4	lnc-CPNE8-1	chr12:38983132-38983232	ENSG00000258119

Variant related genes	Relation type
ENSG00000258119	TF binding region
ENSG00000258119	CpG island
SLC39A14	miRNA target sites
C1D	miRNA target sites
SLC39A11	miRNA target sites

Extended variants
information (count: 484 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:484 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2653777	chr12:38950082-38950083	Flanking Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs573263599	chr12:38950088-38950089	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs573525761	chr12:38950095-38950096	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs186050518	chr12:38950157-38950158	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs190327505	chr12:38950158-38950159	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs201274334	chr12:38950172-38950173	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs183282969	chr12:38950201-38950202	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs544295560	chr12:38950206-38950207	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs375007627	chr12:38950239-38950240	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs533605684	chr12:38950249-38950250	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs11168552	chr12:38950261-38950262	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs560810958	chr12:38950284-38950285	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs533034884	chr12:38950305-38950306	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs187250403	chr12:38950322-38950323	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs142288320	chr12:38950364-38950365	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs79843964	chr12:38950386-38950387	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs140414850	chr12:38950426-38950427	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs549656141	chr12:38950451-38950452	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs144148207	chr12:38950466-38950467	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs143698884	chr12:38950513-38950514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs80014679	chr12:38950536-38950537	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs551077529	chr12:38950633-38950634	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs12322362	chr12:38950695-38950696	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs1995419	chr12:38950726-38950727	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs553744100	chr12:38950727-38950728	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs550276916	chr12:38950780-38950781	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs573435902	chr12:38950785-38950786	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs535675295	chr12:38950794-38950795	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs190873143	chr12:38950844-38950845	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs571635557	chr12:38950899-38950900	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs539660539	chr12:38950935-38950936	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs544719906	chr12:38950978-38950979	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs182955456	chr12:38950981-38950982	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs187541845	chr12:38950993-38950994	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs185380764	chr12:38957008-38957009	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs576471653	chr12:38957037-38957038	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs557697745	chr12:38957042-38957043	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs577468575	chr12:38957065-38957066	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs543942507	chr12:38957091-38957092	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs144080014	chr12:38957102-38957103	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs187912841	chr12:38957133-38957134	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs573243899	chr12:38957135-38957136	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs1502630	chr12:38957140-38957141	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs562115994	chr12:38957191-38957192	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs561934573	chr12:38957226-38957227	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs146856362	chr12:38957235-38957236	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs1502631	chr12:38957302-38957303	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs191155216	chr12:38957309-38957310	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs78821124	chr12:38957310-38957311	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs546460580	chr12:38957323-38957324	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38949600-38950400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:38949600-38950400	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:38949600-38950600	Enhancers	Hela-S3	cervix
4	chr12:38949600-38951000	Enhancers	Colon Smooth Muscle	Colon
5	chr12:38949800-38950200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:38950000-38950400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr12:38950000-38950400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:38950000-38950800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:38950200-38950600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:38950600-38951000	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr12:38957000-38957200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:38957000-38957800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr12:38957000-38957800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:38957800-38958000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr12:38965000-38966600	Enhancers	Placenta	Placenta
16	chr12:38978600-38983200	Enhancers	Hela-S3	cervix
17	chr12:38979200-38979400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:38979200-38983200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:38979400-38980400	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr12:38979400-38981200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:38980400-38981400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:38980400-38982200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:38980600-38982800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:38981000-38981800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:38981200-38981600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:38981200-38981600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:38981200-38981600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:38981400-38982600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:38981600-38982600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:38982200-38983200	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:38982600-38982800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:38982600-38982800	Enhancers	Fetal Lung	lung
33	chr12:38982600-38983200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:38982800-38983200	Enhancers	Fetal Kidney	kidney
35	chr12:38995600-38996800	Enhancers	Hela-S3	cervix
36	chr12:39004600-39005200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr12:39004800-39005200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr12:39005200-39007800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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