Variant report

Variant	nsv548740
Chromosome Location	chr1:195997563-196033535
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	chr1:196005358-196005385	K562	blood:	n/a	n/a
2	BCL3	chr1:196014848-196015078	GM12878	blood:	n/a	n/a
3	BHLHE40	chr1:195997651-195997653	K562	blood:	n/a	n/a
4	CEBPB	chr1:196003479-196003827	HepG2	liver:	n/a	chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003644-196003657 chr1:196003646-196003655 chr1:196003644-196003655 chr1:196003644-196003657
5	CEBPB	chr1:196003525-196003768	A549	lung:	n/a	chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003644-196003657 chr1:196003646-196003655 chr1:196003644-196003655 chr1:196003644-196003657
6	CEBPB	chr1:196019089-196019289	K562	blood:	n/a	chr1:196019220-196019231 chr1:196019220-196019231
7	CEBPB	chr1:196003459-196003824	K562	blood:	n/a	chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003644-196003657 chr1:196003646-196003655 chr1:196003644-196003655 chr1:196003644-196003657
8	CEBPB	chr1:196003506-196003815	IMR90	lung:	n/a	chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003644-196003657 chr1:196003646-196003655 chr1:196003644-196003655 chr1:196003644-196003657
9	CEBPB	chr1:196032486-196032826	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr1:196003279-196003800	H1-hESC	embryonic stem cell:	n/a	chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003646-196003655 chr1:196003644-196003657 chr1:196003646-196003655 chr1:196003644-196003655 chr1:196003644-196003657
11	CTCF	chr1:196028440-196028590	WERI-Rb-1	eye:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
12	CTCF	chr1:196028438-196028658	GM12878	blood:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
13	CTCF	chr1:196028511-196028564	GM12878	blood:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
14	CTCF	chr1:195998640-195998790	HRPEpiC	eye:	n/a	n/a
15	CTCF	chr1:196028520-196028670	HepG2	liver:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
16	CTCF	chr1:196028489-196028599	NHEK	skin:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
17	CTCF	chr1:196028400-196028550	Hela-S3	cervix:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
18	CTCF	chr1:195998640-195998790	HMEC	breast:	n/a	n/a
19	CTCF	chr1:195998620-195998770	AG04449	skin:	n/a	n/a
20	CTCF	chr1:195998600-195998750	HCFaa	heart:	n/a	n/a
21	CTCF	chr1:195998700-195998850	BE2_C	brain:	n/a	n/a
22	CTCF	chr1:196028489-196028561	HepG2	liver:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
23	CTCF	chr1:196028480-196028630	HEK293	kidney:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
24	CTCF	chr1:196028480-196028630	GM12872	blood:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
25	CTCF	chr1:196028500-196028650	GM12874	blood:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
26	CTCF	chr1:196003560-196003710	Caco-2	colon:	n/a	n/a
27	CTCF	chr1:196028460-196028610	HPAF	blood vessel:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
28	CTCF	chr1:195998700-195998850	HCPEpiC	choroid plexus:	n/a	n/a
29	CTCF	chr1:195999180-195999330	WERI-Rb-1	eye:	n/a	n/a
30	CTCF	chr1:196028480-196028630	NB4	blood:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
31	CTCF	chr1:195998664-195998834	LNCaP	prostate:	n/a	n/a
32	CTCF	chr1:196013380-196013411	GM13977	blood:	n/a	n/a
33	CTCF	chr1:195998720-195998870	MCF-7	breast:	n/a	n/a
34	CTCF	chr1:196028413-196028679	K562	blood:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
35	CTCF	chr1:196028006-196028685	K562	blood:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
36	CTCF	chr1:196028500-196028650	HCPEpiC	choroid plexus:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
37	CTCF	chr1:195998660-195998810	HEEpiC	esophagus:	n/a	n/a
38	CTCF	chr1:196028420-196028570	MCF-7	breast:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
39	CTCF	chr1:195998680-195998830	SAEC	small airway:	n/a	n/a
40	CTCF	chr1:196028449-196028628	MCF-7	breast:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
41	CTCF	chr1:196028380-196028530	HFF-Myc	foreskin:	n/a	n/a
42	CTCF	chr1:195998620-195998770	HEEpiC	esophagus:	n/a	n/a
43	CTCF	chr1:196006893-196006963	GM13976	blood:	n/a	n/a
44	CTCF	chr1:196020900-196021050	HPAF	blood vessel:	n/a	n/a
45	CTCF	chr1:195998526-195999009	MCF-7	breast:	n/a	n/a
46	CTCF	chr1:196028580-196028730	GM06990	blood:	n/a	n/a
47	CTCF	chr1:196028520-196028670	BE2_C	brain:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
48	CTCF	chr1:195998702-195998802	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr1:196028436-196028619	MCF-7	breast:	n/a	chr1:196028521-196028539 chr1:196028526-196028536
50	CTCF	chr1:196028400-196028550	HEEpiC	esophagus:	n/a	chr1:196028521-196028539 chr1:196028526-196028536

No.	Distal block	Cell Line	Cell type
1	chr1:196025146..196027992-chr1:196038512..196040205,2	K562	blood:
2	chr1:196026031..196027668-chr1:196032772..196035089,2	K562	blood:
3	chr1:196024750..196028209-chr1:196030222..196033690,4	K562	blood:
4	chr1:196023127..196024805-chr1:196041898..196043914,2	K562	blood:
5	chr1:196024750..196028209-chr1:196030222..196033690,4	K562	blood:
6	chr1:196001222..196002860-chr1:196004252..196007155,2	K562	blood:
7	chr1:195908810..195909713-chr1:195998289..195999101,3	MCF-7	breast:
8	chr1:196001222..196002860-chr1:196004252..196007155,2	K562	blood:
9	chr1:196025180..196026882-chr1:196027419..196029109,2	K562	blood:
10	chr1:196026031..196027668-chr1:196032772..196035089,2	K562	blood:
11	chr1:195993999..195996870-chr1:195997208..196000349,3	K562	blood:
12	chr1:196025180..196026882-chr1:196027419..196029109,2	K562	blood:
13	chr1:196030521..196032166-chr1:196617172..196619617,2	K562	blood:
14	chr1:195908822..195909639-chr1:195998328..195999154,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNT2-1	chr1:196030127-196030203	XLOC_001138
2	lnc-KCNT2-1	chr1:196014057-196014669	XLOC_001138
3	lnc-KCNT2-1	chr1:196014126-196014669	XLOC_001138

Variant related genes	Relation type
ENSG00000227421	TF binding region
CFTR	miRNA target sites
SDF2	miRNA target sites

Extended variants
information (count: 414 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:414 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs575282107	chr1:195999204-195999205	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs546371441	chr1:195999205-195999206	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs564388698	chr1:195999245-195999246	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs528666608	chr1:195999247-195999248	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs546853714	chr1:195999263-195999264	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs562063715	chr1:195999266-195999267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs188918298	chr1:195999268-195999269	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs550730186	chr1:195999270-195999271	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs562564077	chr1:195999285-195999286	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs569325008	chr1:195999375-195999376	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs139362926	chr1:195999420-195999421	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs551854941	chr1:195999421-195999422	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs570619604	chr1:195999426-195999427	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs191684704	chr1:195999429-195999430	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs141824118	chr1:195999457-195999458	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs74136416	chr1:195999467-195999468	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs535415144	chr1:195999474-195999475	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs566165301	chr1:195999480-195999481	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs1160224	chr1:195999508-195999509	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs184753350	chr1:195999513-195999514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs189267159	chr1:195999529-195999530	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs181019773	chr1:195999535-195999536	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs549304990	chr1:195999616-195999617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs185901164	chr1:195999625-195999626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs540450628	chr1:195999629-195999630	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs368838947	chr1:195999695-195999696	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs562026666	chr1:195999706-195999707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs529600197	chr1:195999712-195999713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs1160223	chr1:195999730-195999731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs116158982	chr1:195999747-195999748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs143775821	chr1:195999770-195999771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs1160222	chr1:195999804-195999805	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs566993404	chr1:195999808-195999809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs6677077	chr1:195999865-195999866	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs527820015	chr1:195999874-195999875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs546850404	chr1:195999885-195999886	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs189621434	chr1:195999902-195999903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs200775721	chr1:195999947-195999948	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs535431086	chr1:195999969-195999970	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs557227425	chr1:195999997-195999998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs376304110	chr1:196000073-196000074	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs148134439	chr1:196000112-196000113	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs12124497	chr1:196000119-196000120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs560285190	chr1:196000228-196000229	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs150638794	chr1:196000242-196000243	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs3008590	chr1:196000244-196000245	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs181916719	chr1:196000247-196000248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs540415122	chr1:196000249-196000250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs186110356	chr1:196000259-196000260	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs569342001	chr1:196000260-196000261	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Lung cancer	18438408	CNVD
Metanephric adenoma	20802469	CNVD
Melanoma	20688739	CNVD
Breast cancer	21611746	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-small cell lung cancer	19010865	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Glioblastoma multiforme	22286061	CNVD
Urothelial carcinoma	21177765	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16272173	CNVD
Mental retardation	21062444	CNVD
Liver carcinoma	19366792	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:195999200-195999400	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr1:195999200-195999600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:195999200-195999600	Enhancers	H9 Cell Line	embryonic stem cell
4	chr1:195999200-195999600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:195999200-195999600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:195999200-195999600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:195999200-195999600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:195999400-195999600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:195999600-196002600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:195999600-196002800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:195999600-196003000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:195999600-196003000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:195999600-196003000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:196000000-196002400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:196001400-196001600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:196002400-196003000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:196002600-196003600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:196002600-196004800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:196002800-196003000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:196002800-196004400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:196003000-196003200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:196003000-196003200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:196003000-196003600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:196003000-196003600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:196003000-196003600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:196003000-196003800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:196003000-196003800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:196003200-196003400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr1:196003200-196003600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr1:196003200-196003600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:196003200-196003600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:196003200-196003600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:196003400-196003600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:196003600-196003800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:196003600-196003800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:196003600-196005000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr1:196025000-196025400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr1:196025400-196025800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:196025800-196026600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:196026000-196026400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:196026000-196026600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:196026000-196027000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:196026000-196027000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr1:196026200-196026600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:196026200-196026600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:196026200-196027000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr1:196032200-196032600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:196032400-196033200	Enhancers	A549	lung
49	chr1:196032600-196033400	Enhancers	Hela-S3	cervix
50	chr1:196032600-196033400	Enhancers	NH-A	brain

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