Variant report

Variant	nsv875943
Chromosome Location	chr2:230960946-231027162
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	ARID3A	chr2:230993862-230994516	HepG2	liver:	n/a	n/a
2	ATF2	chr2:230999124-230999554	GM12878	blood:	n/a	n/a
3	BACH1	chr2:230973690-230973935	H1-hESC	embryonic stem cell:	n/a	n/a
4	BHLHE40	chr2:231023362-231023446	K562	blood:	n/a	n/a
5	BHLHE40	chr2:231024958-231025134	GM12878	blood:	n/a	n/a
6	BRCA1	chr2:230994334-230994425	HepG2	liver:	n/a	n/a
7	CBX3	chr2:230999053-230999513	K562	blood:	n/a	n/a
8	CBX3	chr2:230999140-230999390	K562	blood:	n/a	n/a
9	CBX3	chr2:230999037-230999598	HCT-116	colon:	n/a	n/a
10	CBX3	chr2:231023179-231023471	K562	blood:	n/a	n/a
11	CBX3	chr2:231017056-231017388	HCT-116	colon:	n/a	n/a
12	CBX3	chr2:231017065-231017382	K562	blood:	n/a	n/a
13	CBX3	chr2:231023152-231023575	K562	blood:	n/a	n/a
14	CEBPB	chr2:231025956-231026282	HepG2	liver:	n/a	n/a
15	CEBPB	chr2:231024952-231025302	H1-hESC	embryonic stem cell:	n/a	n/a
16	CEBPB	chr2:231025941-231026290	IMR90	lung:	n/a	n/a
17	CEBPB	chr2:230971620-230971657	H1-hESC	embryonic stem cell:	n/a	n/a
18	CEBPB	chr2:231007797-231007880	K562	blood:	n/a	n/a
19	CEBPB	chr2:231007748-231008023	HepG2	liver:	n/a	chr2:231007896-231007907
20	CEBPB	chr2:231025982-231026182	A549	lung:	n/a	n/a
21	CEBPB	chr2:230989549-230989881	K562	blood:	n/a	n/a
22	CEBPB	chr2:230993992-230994469	HepG2	liver:	n/a	chr2:230994175-230994188
23	CEBPB	chr2:231003468-231003585	HepG2	liver:	n/a	chr2:231003476-231003487
24	CEBPB	chr2:230999122-230999429	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr2:231025993-231026267	Hela-S3	cervix:	n/a	n/a
26	CEBPZ	chr2:231020341-231020415	HepG2	liver:	n/a	n/a
27	CHD1	chr2:231024649-231025276	IMR90	lung:	n/a	n/a
28	CHD2	chr2:231025939-231026063	Hela-S3	cervix:	n/a	n/a
29	CHD2	chr2:230995548-230995552	GM12878	blood:	n/a	n/a
30	CHD2	chr2:231024774-231025146	H1-hESC	embryonic stem cell:	n/a	n/a
31	CREB1	chr2:230994107-230994540	HepG2	liver:	n/a	n/a
32	CTCF	chr2:231024978-231025191	MCF-7	breast:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
33	CTCF	chr2:231026080-231026230	HCFaa	heart:	n/a	n/a
34	CTCF	chr2:231024960-231025110	GM12871	blood:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
35	CTCF	chr2:231025400-231025550	GM12875	blood:	n/a	n/a
36	CTCF	chr2:231025000-231025150	GM06990	blood:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
37	CTCF	chr2:231024947-231025221	A549	lung:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
38	CTCF	chr2:231024598-231025297	A549	lung:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231024646-231024659 chr2:231025059-231025069 chr2:231025051-231025072
39	CTCF	chr2:231024960-231025110	GM12869	blood:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
40	CTCF	chr2:231024925-231025172	HUVEC	blood vessel:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
41	CTCF	chr2:231003066-231003116	MCF-7	breast:	n/a	n/a
42	CTCF	chr2:231025440-231025590	WI-38	lung:	n/a	n/a
43	CTCF	chr2:231025000-231025150	GM12872	blood:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
44	CTCF	chr2:231024941-231025131	A549	lung:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
45	CTCF	chr2:231024960-231025110	HAc	cerebellar:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
46	CTCF	chr2:231024946-231025205	GM10266	blood:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
47	CTCF	chr2:231025700-231025850	HRPEpiC	eye:	n/a	n/a
48	CTCF	chr2:231024929-231025178	SK-N-SH_RA	brain:	n/a	chr2:231025062-231025071 chr2:231025057-231025073 chr2:231025058-231025071 chr2:231025056-231025074 chr2:231025059-231025069 chr2:231025051-231025072
49	CTCF	chr2:231018220-231018370	HRPEpiC	eye:	n/a	n/a
50	CTCF	chr2:231026080-231026230	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:231018019..231019836-chr2:231022699..231024449,2	MCF-7	breast:
2	chr2:230931515..230932312-chr2:231024624..231025691,3	MCF-7	breast:
3	chr2:231018019..231019836-chr2:231022699..231024449,2	MCF-7	breast:
4	chr2:230994161..230996459-chr2:230999501..231001005,2	K562	blood:
5	chr2:230872559..230873386-chr2:231024550..231025144,4	K562	blood:
6	chr2:230786411..230788705-chr2:231002066..231004543,2	MCF-7	breast:
7	chr2:231017697..231020252-chr2:231024181..231026351,2	K562	blood:
8	chr2:230872589..230873492-chr2:231024488..231025490,5	MCF-7	breast:
9	chr2:231016438..231018368-chr2:231018976..231021680,2	K562	blood:
10	chr2:231018752..231022838-chr2:231023461..231026351,3	K562	blood:
11	chr2:231020225..231023004-chr2:231144034..231146526,2	K562	blood:
12	chr2:230994161..230996459-chr2:230999501..231001005,2	K562	blood:
13	chr2:231016438..231018368-chr2:231018976..231021680,2	K562	blood:
14	chr2:230931398..230932313-chr2:231024797..231025421,3	MCF-7	breast:
15	chr2:231007633..231009577-chr2:231010416..231014547,3	K562	blood:
16	chr2:231018752..231022838-chr2:231023461..231026351,3	K562	blood:
17	chr2:231017697..231020252-chr2:231024181..231026351,2	K562	blood:
18	chr2:231007633..231009577-chr2:231010416..231014547,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP140-3	chr2:230989750-230990265	XLOC_001894
2	lnc-SP140-3	chr2:230989749-230990390	NONHSAT077258
3	lnc-SP140-3	chr2:230993699-230993728	XLOC_001894
4	lnc-SP140-3	chr2:230993698-230993728	NONHSAT077258
5	lnc-SP110-3	chr2:230983659-230985488	ncRnaDb_ncrna_FR295603_1
6	lnc-SP140-3	chr2:230990026-230990265	XLOC_001894
7	lnc-SP140-3	chr2:231004784-231004862	XLOC_001894

Variant related genes	Relation type
ENSG00000225963	TF binding region
ENSG00000153832	chromatin interactions
ENSG00000153827	chromatin interactions
C2orf42	miRNA target sites
BCL2L11	miRNA target sites

Extended variants
information (count: 1486 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:1486 , 50 per page) page: 1 2 3 4 5 6 7 ... 30

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7586233	chr2:230961632-230961633	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs75903243	chr2:230961648-230961649	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs72537696	chr2:230961678-230961679	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs36100639	chr2:230961679-230961680	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs149756198	chr2:230961680-230961681	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs374020272	chr2:230961681-230961682	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs11893862	chr2:230961724-230961725	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs76541816	chr2:230961741-230961742	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs397735427	chr2:230961742-230961743	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs549607669	chr2:230961773-230961774	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs7589000	chr2:230961778-230961779	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs537684750	chr2:230961801-230961802	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs554335340	chr2:230961806-230961807	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs570984393	chr2:230961867-230961868	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs191928026	chr2:230961872-230961873	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs12694824	chr2:230961878-230961879	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs536306960	chr2:230961897-230961898	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs12694825	chr2:230961915-230961916	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs142307600	chr2:230961919-230961920	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs150126895	chr2:230961930-230961931	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs12694826	chr2:230961933-230961934	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs78665982	chr2:230961939-230961940	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs558822327	chr2:230961947-230961948	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs75581847	chr2:230961950-230961951	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs12694827	chr2:230961970-230961971	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs149306904	chr2:230961975-230961976	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs12694828	chr2:230961984-230961985	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs55982019	chr2:230962026-230962027	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs528807009	chr2:230962035-230962036	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs546772141	chr2:230962041-230962042	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs144536569	chr2:230962063-230962064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs532587668	chr2:230962081-230962082	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs374218260	chr2:230962105-230962106	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs550213061	chr2:230962127-230962128	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs6740011	chr2:230962197-230962198	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs529682173	chr2:230962218-230962219	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs184306579	chr2:230962223-230962224	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs368786522	chr2:230962278-230962279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs566743896	chr2:230962296-230962297	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs138088811	chr2:230962303-230962304	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs576844700	chr2:230962305-230962306	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs11904634	chr2:230962306-230962307	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs11899718	chr2:230962309-230962310	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs370179723	chr2:230962409-230962410	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs557483633	chr2:230962437-230962438	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs143748147	chr2:230962501-230962502	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs11899803	chr2:230962511-230962512	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs554697911	chr2:230962548-230962549	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs573203432	chr2:230962576-230962577	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs540495320	chr2:230962626-230962627	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16272173	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
Colorectal cancer	16272173	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cervical cancer	21062161	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Chordoma	18071362	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Cancer	22429812	CNVD
Bladder cancer	21909424	CNVD
Renal cell carcinoma	21668985	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Wilms tumour	21544195	CNVD
Esophageal adenocarcinoma	18519675	CNVD
prenatal diagnosis	22389664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Myelofibrosis	22110671	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Mental retardation	20152051	CNVD
Cancer	21183584	CNVD
Albright''s disease	22277900	CNVD
Brachydactyly-Mental Retardation Syndrome	22470819	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Colorectal cancer	19359472	CNVD
Autism	18414403	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:471 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:230961600-230962800	Enhancers	Liver	Liver
2	chr2:230973000-230973800	Enhancers	Esophagus	oesophagus
3	chr2:230973800-230974200	Enhancers	Brain Hippocampus Middle	brain
4	chr2:230974000-230975000	Enhancers	Brain Substantia Nigra	brain
5	chr2:230987600-230990200	Weak transcription	Brain Substantia Nigra	brain
6	chr2:230988600-230989200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:230988800-230989000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:230988800-230989000	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:230988800-230989000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:230988800-230989200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:230988800-230989200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:230988800-230989200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:230988800-230989600	Active TSS	Primary B cells from cord blood	blood
14	chr2:230989000-230989400	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:230989000-230989400	Enhancers	Fetal Brain Male	brain
16	chr2:230989000-230990000	Enhancers	Placenta	Placenta
17	chr2:230989000-230990200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:230989000-230990400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr2:230989000-230990600	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr2:230989000-230990800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr2:230989000-230992200	Enhancers	Spleen	Spleen
22	chr2:230989200-230989400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:230989200-230989800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr2:230989200-230990000	Enhancers	Thymus	Thymus
25	chr2:230989200-230990200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:230989200-230990400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr2:230989200-230990400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:230989200-230990600	Enhancers	Primary B cells from peripheral blood	blood
29	chr2:230989400-230989600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:230989400-230989800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:230989400-230990000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:230989400-230993800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:230989600-230989800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
34	chr2:230989600-230989800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:230989600-230990000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr2:230989600-230990200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr2:230989600-230990200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr2:230989600-230990400	Enhancers	Primary T cells from cord blood	blood
39	chr2:230989600-230990400	Enhancers	GM12878-XiMat	blood
40	chr2:230989800-230990200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:230989800-230990200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:230989800-230992800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr2:230989800-230992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:230990000-230990200	Active TSS	Duodenum Mucosa	Duodenum
45	chr2:230990000-230990600	Active TSS	Brain Hippocampus Middle	brain
46	chr2:230990000-230993600	Weak transcription	Placenta	Placenta
47	chr2:230990200-230990400	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr2:230990200-230990600	Enhancers	Primary B cells from cord blood	blood
49	chr2:230990200-230990600	Active TSS	Brain Substantia Nigra	brain
50	chr2:230990200-230991200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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