Variant report

Variant	nsv961349
Chromosome Location	chr2:123827896-123840926
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	CEBPB	chr2:123831015-123831299	HepG2	liver:	n/a	chr2:123831126-123831137
2	CEBPB	chr2:123830989-123831302	K562	blood:	n/a	chr2:123831126-123831137
3	CHD2	chr2:123837884-123838184	GM12878	blood:	n/a	n/a
4	CTCF	chr2:123831440-123831590	HepG2	liver:	n/a	n/a
5	CUX1	chr2:123839834-123839840	GM12878	blood:	n/a	n/a
6	E2F4	chr2:123830983-123831225	MCF10A-Er-Src	breast:	n/a	n/a
7	EBF1	chr2:123840812-123840987	GM12878	blood:	n/a	n/a
8	EP300	chr2:123837901-123838324	GM12878	blood:	n/a	n/a
9	EP300	chr2:123837920-123838267	GM12878	blood:	n/a	n/a
10	FOS	chr2:123837902-123838279	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr2:123831041-123831270	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr2:123837882-123838243	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr2:123830986-123831329	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr2:123830966-123831292	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr2:123837917-123838277	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr2:123837976-123838246	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr2:123830974-123831341	MCF10A-Er-Src	breast:	n/a	n/a
18	FOXA1	chr2:123834745-123835000	T-47D	breast:	n/a	n/a
19	FOXA1	chr2:123834636-123834953	T-47D	breast:	n/a	n/a
20	GATA3	chr2:123834607-123834993	T-47D	breast:	n/a	n/a
21	GATA3	chr2:123834683-123835049	T-47D	breast:	n/a	n/a
22	GATA3	chr2:123837551-123837631	SH-SY5Y	brain:	n/a	n/a
23	GATA3	chr2:123834756-123835001	MCF-7	breast:	n/a	n/a
24	MAFK	chr2:123832812-123832975	HepG2	liver:	n/a	chr2:123832864-123832879
25	MAFK	chr2:123832816-123832956	HepG2	liver:	n/a	chr2:123832864-123832879
26	MAZ	chr2:123828005-123828046	HepG2	liver:	n/a	n/a
27	MYC	chr2:123831159-123831347	MCF10A-Er-Src	breast:	n/a	n/a
28	MYC	chr2:123839306-123839452	MCF10A-Er-Src	breast:	n/a	n/a
29	NRF1	chr2:123830821-123830930	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr2:123830764-123831258	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr2:123837243-123837396	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr2:123831036-123831288	U87	brain:	n/a	n/a
33	POLR2A	chr2:123839291-123839320	Gliobla	brain:	n/a	n/a
34	POLR2A	chr2:123839241-123839267	MCF-7	breast:	n/a	n/a
35	SIN3A	chr2:123837933-123838052	GM12878	blood:	n/a	n/a
36	SPI1	chr2:123831547-123831967	HL-60	blood:	n/a	n/a
37	SPI1	chr2:123831638-123832034	HL-60	blood:	n/a	n/a
38	STAT3	chr2:123831046-123831246	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr2:123838086-123838175	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr2:123838043-123838233	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:123828454..123831297-chr2:123833230..123835913,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MKI67IP-3	chr2:123827743-123827940	XLOC_002303
2	lnc-MKI67IP-3	chr2:123830728-123831057	XLOC_002303

Variant related genes	Relation type
ENSG00000232740	TF binding region
ENSG00000232740	chromatin interactions

Extended variants
information (count: 494 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:494 , 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	rs17009319	chr2:123827900-123827901	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs559264457	chr2:123827911-123827912	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs299538	chr2:123827926-123827927	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs545072097	chr2:123827946-123827947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs546290542	chr2:123828000-123828001	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs1515164	chr2:123828017-123828018	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs180672690	chr2:123828183-123828184	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs567372296	chr2:123828185-123828186	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs529965865	chr2:123828234-123828235	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs6541878	chr2:123828250-123828251	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs566457991	chr2:123828278-123828279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs191157797	chr2:123828313-123828314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs368438069	chr2:123828368-123828369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs13033813	chr2:123828369-123828370	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs5833971	chr2:123828388-123828389	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs113197455	chr2:123828389-123828390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs558566545	chr2:123828413-123828414	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs185104560	chr2:123828418-123828419	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs299537	chr2:123828431-123828432	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs13033509	chr2:123828452-123828453	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs13033663	chr2:123828463-123828464	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs370946923	chr2:123828468-123828469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs554146633	chr2:123828521-123828522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs13010429	chr2:123828548-123828549	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs534273847	chr2:123828549-123828550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs299536	chr2:123828559-123828560	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs533778223	chr2:123828614-123828615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs13010613	chr2:123828616-123828617	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs115615906	chr2:123828620-123828621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs564549819	chr2:123828625-123828626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs528630202	chr2:123828658-123828659	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs374902002	chr2:123828685-123828686	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs148035929	chr2:123828688-123828689	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs13010816	chr2:123828696-123828697	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs142523047	chr2:123828709-123828710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs191143868	chr2:123828723-123828724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs542042949	chr2:123828747-123828748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs183449402	chr2:123828750-123828751	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs12620936	chr2:123828759-123828760	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs538301012	chr2:123828760-123828761	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs541080061	chr2:123828800-123828801	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs58936843	chr2:123828831-123828832	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs554747284	chr2:123828852-123828853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs13011089	chr2:123828854-123828855	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs35870013	chr2:123828873-123828874	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs369239388	chr2:123828928-123828929	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs114406023	chr2:123828989-123828990	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs577569392	chr2:123828995-123828996	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs546544045	chr2:123829016-123829017	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs116464838	chr2:123829020-123829021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Lung cancer	18438408	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
lymphocytic leukemia	21291569	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Colorectal cancer	16272173	CNVD
myoclonus epilepsy	18472482	CNVD
Benign familial neonatal-infantile seizures	18472482	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
small cell lung cancer	20016488	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Mental retardation	17621639	CNVD
Acute myeloid leukemia	21251322	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Medulloblastoma	16968546	CNVD
Neurocytoma	17123091	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Developmental delay	21147756	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Bladder cancer	21909424	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:123827600-123829200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:123827800-123828800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:123828800-123829800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:123829200-123829800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:123829800-123831800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:123830200-123830800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:123830800-123831000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr2:123831000-123832800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:123831200-123832400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:123831200-123832600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:123831800-123832000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:123836800-123837400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:123838400-123839400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:123839000-123839400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:123839000-123839400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:123839000-123839400	Enhancers	NH-A	brain
17	chr2:123839200-123839800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:123839400-123844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links