Variant report

Variant	nsv877796
Chromosome Location	chr3:162839973-162975100
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:231)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:48)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:231 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:162929409-162929718	IMR90	lung:	n/a	chr3:162929588-162929605 chr3:162929590-162929601 chr3:162929560-162929571 chr3:162929562-162929573
2	CEBPB	chr3:162929432-162929720	Hela-S3	cervix:	n/a	chr3:162929588-162929605 chr3:162929590-162929601 chr3:162929560-162929571 chr3:162929562-162929573
3	CEBPB	chr3:162932427-162932441	A549	lung:	n/a	n/a
4	CEBPB	chr3:162856075-162856324	MCF-7	breast:	n/a	n/a
5	CEBPB	chr3:162929413-162929748	A549	lung:	n/a	chr3:162929588-162929605 chr3:162929590-162929601 chr3:162929560-162929571 chr3:162929562-162929573
6	CEBPB	chr3:162929418-162929759	HepG2	liver:	n/a	chr3:162929588-162929605 chr3:162929590-162929601 chr3:162929560-162929571 chr3:162929562-162929573
7	CEBPB	chr3:162929417-162929749	K562	blood:	n/a	chr3:162929588-162929605 chr3:162929590-162929601 chr3:162929560-162929571 chr3:162929562-162929573
8	CEBPB	chr3:162893798-162893837	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPB	chr3:162932325-162932463	IMR90	lung:	n/a	n/a
10	CEBPB	chr3:162897199-162897419	A549	lung:	n/a	n/a
11	CEBPB	chr3:162932353-162932482	K562	blood:	n/a	n/a
12	CHD2	chr3:162900110-162900118	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:162870820-162870854	GM20000	blood:	n/a	n/a
14	CTCF	chr3:162887978-162888033	GM13976	blood:	n/a	n/a
15	CTCF	chr3:162843640-162843790	HEK293	kidney:	n/a	n/a
16	CTCF	chr3:162843760-162843910	BE2_C	brain:	n/a	n/a
17	CTCF	chr3:162968471-162968556	GM20000	blood:	n/a	n/a
18	CTCF	chr3:162946522-162946561	GM20000	blood:	n/a	n/a
19	CTCF	chr3:162843680-162843830	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr3:162850580-162850730	HCT-116	colon:	n/a	n/a
21	CTCF	chr3:162849313-162849338	Fibrobl	skin:	n/a	n/a
22	CTCF	chr3:162843696-162843728	K562	blood:	n/a	n/a
23	CTCF	chr3:162884697-162884750	GM20000	blood:	n/a	n/a
24	CTCF	chr3:162843700-162843850	HBMEC	blood vessel:	n/a	n/a
25	CTCF	chr3:162887986-162888003	Pancreas_OC	pancreas:	n/a	n/a
26	CTCF	chr3:162888037-162888039	GM13976	blood:	n/a	n/a
27	CTCF	chr3:162843540-162843690	BE2_C	brain:	n/a	n/a
28	CTCF	chr3:162857527-162857550	MCF-7	breast:	n/a	n/a
29	CTCF	chr3:162884766-162884837	Lung_OC	lung:	n/a	n/a
30	CTCF	chr3:162917440-162917590	AG09319	gingival:	n/a	n/a
31	CTCF	chr3:162973547-162973685	Medullo	brain:	n/a	chr3:162973613-162973621 chr3:162973609-162973625 chr3:162973610-162973631
32	CTCF	chr3:162843720-162843870	A549	lung:	n/a	n/a
33	CTCF	chr3:162953064-162953107	Spleen_OC	spleen:	n/a	n/a
34	CUX1	chr3:162904026-162904103	K562	blood:	n/a	n/a
35	CUX1	chr3:162926637-162926663	GM12878	blood:	n/a	n/a
36	E2F4	chr3:162923860-162924015	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr3:162853012-162853212	MCF10A-Er-Src	breast:	n/a	n/a
38	E2F4	chr3:162924253-162924397	MCF10A-Er-Src	breast:	n/a	n/a
39	E2F4	chr3:162920670-162920867	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F4	chr3:162912011-162912176	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F4	chr3:162902166-162902451	MCF10A-Er-Src	breast:	n/a	n/a
42	E2F4	chr3:162895680-162895880	MCF10A-Er-Src	breast:	n/a	n/a
43	E2F4	chr3:162926919-162927032	MCF10A-Er-Src	breast:	n/a	n/a
44	E2F4	chr3:162862212-162862415	MCF10A-Er-Src	breast:	n/a	n/a
45	E2F4	chr3:162863651-162863841	MCF10A-Er-Src	breast:	n/a	n/a
46	E2F4	chr3:162839868-162840221	MCF10A-Er-Src	breast:	n/a	n/a
47	ELK1	chr3:162935493-162935499	Hela-S3	cervix:	n/a	n/a
48	EP300	chr3:162855997-162856485	MCF-7	breast:	n/a	n/a
49	EP300	chr3:162912401-162912480	GM12878	blood:	n/a	n/a
50	FOS	chr3:162862255-162862566	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:162468849..162471720-chr3:162897232..162899564,2	K562	blood:
2	chr3:162973215..162973789-chr3:163207913..163208691,2	MCF-7	breast:
3	chr3:162965564..162967593-chr3:162971986..162973917,2	K562	blood:
4	chr3:162965564..162967593-chr3:162971986..162973917,2	K562	blood:
5	chr3:162924888..162927929-chr3:162929573..162933579,3	K562	blood:
6	chr3:162924888..162927929-chr3:162929573..162933579,3	K562	blood:
7	chr10:69265595..69266499-chr3:162973315..162973821,2	MCF-7	breast:

(count:48 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOL1-2	chr3:162946486-162946540	ENSG00000241168.1
2	lnc-SI-4	chr3:162917363-162917542	ENSG00000241369
3	lnc-SI-4	chr3:162921206-162921303	ENSG00000241369
4	lnc-SI-4	chr3:162925431-162925545	ENSG00000241369
5	lnc-SI-4	chr3:162919326-162919405	ENSG00000241369
6	lnc-SI-4	chr3:162936848-162936965	ENSG00000241369
7	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
8	lnc-SI-4	chr3:162917662-162917739	ENSG00000241369
9	lnc-SI-4	chr3:162937889-162937929	ENSG00000241369
10	lnc-SI-4	chr3:162904856-162905052	ENSG00000241369
11	lnc-SI-4	chr3:162921206-162921303	ENSG00000241369
12	lnc-SI-4	chr3:162917416-162917542	NONHSAT093031
13	lnc-SI-4	chr3:162967053-162967162	ENSG00000241369
14	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
15	lnc-SI-4	chr3:162919326-162919405	ENSG00000241369
16	lnc-SI-4	chr3:162917662-162917739	ENSG00000241369
17	lnc-OTOL1-2	chr3:162948497-162949937	ENSG00000241168.1
18	lnc-SI-4	chr3:162937704-162937975	ENSG00000241369
19	lnc-OTOL1-2	chr3:162925763-162925882	ENSG00000241168.1
20	lnc-SI-4	chr3:162900619-162900716	ENSG00000241369
21	lnc-OTOL1-2	chr3:162937866-162937980	NONHSAT093026
22	lnc-SI-4	chr3:162919871-162920037	NONHSAT093037
23	lnc-SI-4	chr3:162919326-162919405	ENSG00000241369
24	lnc-OTOL1-2	chr3:162925763-162925882	NONHSAT093026
25	lnc-SI-4	chr3:162917363-162917542	ENSG00000241369
26	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
27	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
28	lnc-SI-4	chr3:162900619-162900698	ENSG00000241369
29	lnc-SI-4	chr3:162917365-162917542	ENSG00000241369
30	lnc-SI-4	chr3:162905018-162905052	NONHSAT093031
31	lnc-OTOL1-2	chr3:162948497-162949934	NONHSAT093026
32	lnc-SI-4	chr3:162919326-162919405	ENSG00000241369
33	lnc-SI-4	chr3:162895689-162895889	ENSG00000241369
34	lnc-SI-4	chr3:162917662-162917719	NONHSAT093031
35	lnc-SI-4	chr3:162919326-162919405	ENSG00000241369
36	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
37	lnc-SI-4	chr3:162895031-162895889	ENSG00000241369
38	lnc-SI-4	chr3:162921206-162921298	NONHSAT093037
39	lnc-SI-4	chr3:162919326-162919405	ENSG00000241369
40	lnc-SI-4	chr3:162917366-162917542	ENSG00000241369
41	lnc-OTOL1-2	chr3:162937866-162937980	ENSG00000241168.1
42	lnc-SI-4	chr3:162845711-162845859	ENSG00000241369
43	lnc-SI-4	chr3:162917662-162917739	ENSG00000241369
44	lnc-SI-4	chr3:162917662-162917739	ENSG00000241369
45	lnc-SI-4	chr3:162917416-162917542	ENSG00000241369
46	lnc-SI-4	chr3:162917411-162917542	ENSG00000241369
47	lnc-OTOL1-2	chr3:162946486-162946540	NONHSAT093026
48	lnc-SI-4	chr3:162919870-162920037	ENSG00000241369

No data

Variant related genes	Relation type
CT64	TF binding region
ENSG00000238398	TF binding region

Extended variants
information (count: 1330 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:1330 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73025010	chr3:162841000-162841001	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs556251902	chr3:162841003-162841004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs564410411	chr3:162841004-162841005	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs576406126	chr3:162841012-162841013	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs145250328	chr3:162841114-162841115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs187376468	chr3:162841137-162841138	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs558042882	chr3:162841157-162841158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs35688023	chr3:162841195-162841196	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs578029361	chr3:162841256-162841257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs7628970	chr3:162841271-162841272	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs537438609	chr3:162841295-162841296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs560417061	chr3:162841303-162841304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs539968898	chr3:162841313-162841314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs117848472	chr3:162841352-162841353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs147629390	chr3:162841354-162841355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs142314409	chr3:162841357-162841358	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs6548389	chr3:162841398-162841399	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs551744454	chr3:162841408-162841409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs565571915	chr3:162841447-162841448	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs572297843	chr3:162841458-162841459	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs528008325	chr3:162841491-162841492	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs147033933	chr3:162841571-162841572	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs545429857	chr3:162841580-162841581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs572092123	chr3:162841584-162841585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs201352738	chr3:162841616-162841617	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs11385345	chr3:162841617-162841618	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs386398415	chr3:162841618-162841619	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs375617466	chr3:162841622-162841623	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs371487216	chr3:162841623-162841624	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs536320100	chr3:162841631-162841632	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs550252504	chr3:162841636-162841637	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs73025013	chr3:162841638-162841639	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs9851405	chr3:162841668-162841669	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs138330301	chr3:162841755-162841756	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs7429204	chr3:162841759-162841760	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs577982614	chr3:162841766-162841767	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs534114219	chr3:162841802-162841803	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs553973075	chr3:162841810-162841811	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs573900900	chr3:162841812-162841813	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs201733047	chr3:162841852-162841853	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs7632261	chr3:162841868-162841869	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs562608612	chr3:162841910-162841911	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs149159889	chr3:162841913-162841914	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs143276379	chr3:162841915-162841916	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs73156265	chr3:162841925-162841926	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs527946746	chr3:162841953-162841954	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs541349134	chr3:162841976-162841977	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs561100366	chr3:162841995-162841996	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs115482783	chr3:162842048-162842049	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs9818446	chr3:162842049-162842050	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21364760	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Sudden cardiac death	19188705	CNVD
Mantle cell lymphoma	19029149	CNVD
Malformation	19546859	CNVD
Schizophrenia	19546859	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Bladder cancer	21909424	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162841000-162841600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:162841600-162844400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:162841800-162842200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:162842200-162843000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:162843000-162843800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
6	chr3:162843000-162845000	ZNF genes & repeats	Dnd41	blood
7	chr3:162843400-162844400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:162844000-162844600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
9	chr3:162844000-162845000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
10	chr3:162847000-162847400	ZNF genes & repeats	Dnd41	blood
11	chr3:162847200-162847400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:162858000-162858800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:162889800-162894200	Weak transcription	Fetal Heart	heart
14	chr3:162892200-162892400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:162892200-162892800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:162892200-162892800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:162892800-162893800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:162893800-162894000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:162894200-162895200	Enhancers	Fetal Heart	heart
20	chr3:162904600-162905000	ZNF genes & repeats	Dnd41	blood
21	chr3:162914400-162915000	Enhancers	Dnd41	blood
22	chr3:162936400-162950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:162947400-162954200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:162953800-162954800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:162954200-162954800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr3:162954200-162954800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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