Variant report

Variant	nsv875250
Chromosome Location	chr2:142540240-142614345
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	BHLHE40	chr2:142556827-142557091	GM12878	blood:	n/a	n/a
2	CEBPB	chr2:142549199-142549267	A549	lung:	n/a	n/a
3	CEBPB	chr2:142608734-142608994	HepG2	liver:	n/a	chr2:142608735-142608746 chr2:142608837-142608850 chr2:142608838-142608849
4	CEBPB	chr2:142586356-142586630	HepG2	liver:	n/a	chr2:142586587-142586598
5	CEBPB	chr2:142599194-142599452	HepG2	liver:	n/a	chr2:142599226-142599239
6	CEBPB	chr2:142601809-142602160	Hela-S3	cervix:	n/a	chr2:142601997-142602008
7	CEBPB	chr2:142564329-142564530	HepG2	liver:	n/a	chr2:142564423-142564436 chr2:142564423-142564434
8	CEBPB	chr2:142549134-142549357	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr2:142549080-142549369	HepG2	liver:	n/a	chr2:142549089-142549101
10	CEBPB	chr2:142614190-142614416	A549	lung:	n/a	chr2:142614281-142614290
11	CEBPB	chr2:142601830-142602173	HepG2	liver:	n/a	chr2:142601997-142602008
12	CTCF	chr2:142574060-142574210	HepG2	liver:	n/a	n/a
13	CTCF	chr2:142582460-142582719	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr2:142549353-142549358	LNCaP	prostate:	n/a	n/a
15	CTCF	chr2:142574100-142574250	HEK293	kidney:	n/a	n/a
16	CTCF	chr2:142576695-142576788	Fibrobl	skin:	n/a	n/a
17	CTCF	chr2:142549302-142549350	LNCaP	prostate:	n/a	n/a
18	E2F4	chr2:142606193-142606555	MCF10A-Er-Src	breast:	n/a	n/a
19	E2F4	chr2:142596018-142596191	MCF10A-Er-Src	breast:	n/a	n/a
20	E2F4	chr2:142587489-142587689	MCF10A-Er-Src	breast:	n/a	n/a
21	EBF1	chr2:142555247-142555282	GM12878	blood:	n/a	n/a
22	EP300	chr2:142575490-142575753	MCF-7	breast:	n/a	n/a
23	EP300	chr2:142556839-142557090	GM12878	blood:	n/a	n/a
24	FAM48A	chr2:142607754-142607833	GM12878	blood:	n/a	n/a
25	FOS	chr2:142542107-142542300	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr2:142591094-142591294	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr2:142591169-142591250	MCF10A-Er-Src	breast:	n/a	n/a
28	FOSL2	chr2:142575398-142575862	MCF-7	breast:	n/a	n/a
29	FOXM1	chr2:142556743-142557066	GM12878	blood:	n/a	n/a
30	GATA3	chr2:142592419-142593132	MCF-7	breast:	n/a	n/a
31	GATA3	chr2:142575217-142575879	MCF-7	breast:	n/a	n/a
32	GATA3	chr2:142575352-142575799	MCF-7	breast:	n/a	n/a
33	GATA3	chr2:142569893-142570223	SK-N-SH	brain:	n/a	chr2:142570103-142570113 chr2:142570024-142570034 chr2:142570084-142570093
34	GATA3	chr2:142590133-142590229	SH-SY5Y	brain:	n/a	n/a
35	GATA3	chr2:142575487-142575710	MCF-7	breast:	n/a	n/a
36	GATA3	chr2:142592419-142593131	MCF-7	breast:	n/a	n/a
37	IRF3	chr2:142560418-142560430	GM12878	blood:	n/a	n/a
38	JUND	chr2:142563435-142563660	HepG2	liver:	n/a	chr2:142563497-142563508 chr2:142563500-142563507 chr2:142563498-142563508 chr2:142563497-142563509 chr2:142563499-142563507 chr2:142563499-142563508
39	JUND	chr2:142591200-142591208	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAFF	chr2:142554060-142554381	HepG2	liver:	n/a	chr2:142554201-142554219 chr2:142554200-142554214
41	MAFF	chr2:142603631-142603808	HepG2	liver:	n/a	n/a
42	MAFF	chr2:142540161-142540517	HepG2	liver:	n/a	n/a
43	MAFF	chr2:142554068-142554318	K562	blood:	n/a	chr2:142554201-142554219 chr2:142554200-142554214
44	MAFF	chr2:142592628-142592788	HepG2	liver:	n/a	n/a
45	MAFF	chr2:142572923-142573221	HepG2	liver:	n/a	n/a
46	MAFF	chr2:142540216-142540482	K562	blood:	n/a	n/a
47	MAFK	chr2:142554063-142554378	IMR90	lung:	n/a	chr2:142554197-142554217 chr2:142554199-142554215 chr2:142554201-142554211 chr2:142554200-142554214 chr2:142554202-142554217
48	MAFK	chr2:142554103-142554371	H1-hESC	embryonic stem cell:	n/a	chr2:142554197-142554217 chr2:142554199-142554215 chr2:142554201-142554211 chr2:142554200-142554214 chr2:142554202-142554217
49	MAFK	chr2:142540186-142540474	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAFK	chr2:142572911-142573210	HepG2	liver:	n/a	chr2:142572972-142572987 chr2:142573050-142573065

No.	Distal block	Cell Line	Cell type
1	chr2:142596259..142599085-chr2:142603241..142604892,2	K562	blood:
2	chr2:142538922..142540737-chr2:142542566..142546321,3	MCF-7	breast:
3	chr2:142600461..142603381-chr2:142603710..142605716,2	MCF-7	breast:
4	chr2:142600461..142603381-chr2:142603710..142605716,2	MCF-7	breast:
5	chr2:142538922..142540737-chr2:142542566..142546321,3	MCF-7	breast:
6	chr2:142596259..142599085-chr2:142603241..142604892,2	K562	blood:
7	chr2:142601107..142603350-chr2:142610818..142614066,3	MCF-7	breast:
8	chr2:142536364..142538824-chr2:142574055..142576511,2	K562	blood:
9	chr2:142579723..142582513-chr2:142586057..142589014,2	MCF-7	breast:
10	chr2:142601107..142603350-chr2:142610818..142614066,3	MCF-7	breast:
11	chr2:142588077..142589694-chr2:142590092..142592138,2	MCF-7	breast:
12	chr18:37319878..37320632-chr2:142591665..142592650,2	MCF-7	breast:
13	chr2:142579723..142582513-chr2:142586057..142589014,2	MCF-7	breast:
14	chr2:142567189..142569498-chr2:142579008..142581669,2	MCF-7	breast:
15	chr2:142588077..142589694-chr2:142590092..142592138,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTDC1-26	chr2:142562933-142563323	NONHSAT074708
2	lnc-GTDC1-26	chr2:142567848-142567970	NONHSAT074708

Variant related genes	Relation type
LRP1B	TF binding region
ENSG00000168702	chromatin interactions

Extended variants
information (count: 795 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:795 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs555849234	chr2:142554210-142554211	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs578222404	chr2:142554261-142554262	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs533989817	chr2:142554276-142554277	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs1898425	chr2:142554281-142554282	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs554328088	chr2:142554332-142554333	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs191932821	chr2:142554356-142554357	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs542090257	chr2:142554384-142554385	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs74552345	chr2:142554390-142554391	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs57938540	chr2:142554397-142554398	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs186616501	chr2:142554402-142554403	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs531674728	chr2:142554544-142554545	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs6749148	chr2:142554550-142554551	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs142026128	chr2:142554559-142554560	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs7583921	chr2:142554562-142554563	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs547056627	chr2:142554581-142554582	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs573344797	chr2:142558818-142558819	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs542441126	chr2:142558824-142558825	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs555578545	chr2:142558860-142558861	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs184447353	chr2:142558869-142558870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs572406131	chr2:142558870-142558871	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs574707829	chr2:142558880-142558881	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs564424101	chr2:142558912-142558913	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs533383403	chr2:142558921-142558922	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs542952125	chr2:142558952-142558953	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs370024230	chr2:142558963-142558964	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs540496809	chr2:142558976-142558977	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs561102559	chr2:142559044-142559045	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs187679501	chr2:142559054-142559055	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs192689674	chr2:142559063-142559064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs183588380	chr2:142559064-142559065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs143435822	chr2:142559067-142559068	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs531933280	chr2:142559072-142559073	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs531390934	chr2:142559074-142559075	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs138148356	chr2:142559080-142559081	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs373873185	chr2:142559131-142559132	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs570876001	chr2:142559164-142559165	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs12612242	chr2:142559190-142559191	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs553231711	chr2:142559214-142559215	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs141081173	chr2:142559239-142559240	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs535663578	chr2:142559262-142559263	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs555890736	chr2:142559284-142559285	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs575749820	chr2:142559306-142559307	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs544687678	chr2:142559356-142559357	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs114955246	chr2:142559366-142559367	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs60606290	chr2:142559370-142559371	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs4352182	chr2:142559408-142559409	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs1567305	chr2:142559429-142559430	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs144787988	chr2:142559477-142559478	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs138633542	chr2:142559505-142559506	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs370723690	chr2:142559584-142559585	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

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
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	16272173	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	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
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Mental retardation	22214275	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma	21080181	CNVD
Cancer	22183965	CNVD
Melanoma	22183965	CNVD
Autism	22543975	CNVD
Cancer	20164920	CNVD
Hypertension	22686481	CNVD
Hypospadia	22686481	CNVD
Intellectual disability	22686481	CNVD
Omphalocele	22686481	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Prostate cancer	22341455	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142554200-142554600	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr2:142558800-142559200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr2:142559000-142559800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:142559600-142560000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:142562000-142566400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:142567600-142568200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:142574400-142574600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:142578400-142579000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr2:142578400-142579000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr2:142578400-142579000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:142578400-142579000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:142578400-142579200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:142578600-142579000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:142579000-142582400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:142582400-142583000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:142582400-142583200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr2:142584600-142585000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:142599000-142599400	Enhancers	Brain Hippocampus Middle	brain
19	chr2:142599000-142599400	Enhancers	Brain Substantia Nigra	brain
20	chr2:142599000-142599600	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:142601400-142601600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr2:142608400-142609000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:142609000-142613800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:142613600-142614800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:142613800-142614200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:142613800-142614400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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