Variant report

Variant	nsv967190
Chromosome Location	chr3:162932772-162983278
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:15)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:162978995-162979027	K562	blood:	n/a	n/a
2	CHD2	chr3:162976142-162976148	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr3:162953064-162953107	Spleen_OC	spleen:	n/a	n/a
4	CTCF	chr3:162973547-162973685	Medullo	brain:	n/a	chr3:162973613-162973621 chr3:162973609-162973625 chr3:162973610-162973631
5	CTCF	chr3:162946522-162946561	GM20000	blood:	n/a	n/a
6	CTCF	chr3:162968471-162968556	GM20000	blood:	n/a	n/a
7	EBF1	chr3:162975133-162975166	GM12878	blood:	n/a	n/a
8	EBF1	chr3:162978952-162979124	GM12878	blood:	n/a	chr3:162979034-162979045
9	ELK1	chr3:162935493-162935499	Hela-S3	cervix:	n/a	n/a
10	FOXA2	chr3:162954989-162955392	A549	lung:	n/a	n/a
11	FOXA2	chr3:162954899-162955485	A549	lung:	n/a	n/a
12	GATA3	chr3:162965902-162966184	SH-SY5Y	brain:	n/a	n/a
13	GATA3	chr3:162946554-162946752	SH-SY5Y	brain:	n/a	n/a
14	IRF1	chr3:162978801-162978908	K562	blood:	n/a	n/a
15	JUN	chr3:162939168-162939270	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAFK	chr3:162950725-162950744	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAFK	chr3:162945809-162945821	K562	blood:	n/a	chr3:162945810-162945821
18	MYC	chr3:162974907-162974908	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr3:162963651-162963897	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr3:162980793-162980992	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:162942403-162942588	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr3:162973714-162973755	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:162960831-162960922	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:162975099-162975279	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:162964060-162964153	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:162951394-162951539	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:162974567-162974728	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr3:162960907-162961287	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:162941014-162941115	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr3:162963425-162963830	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr3:162942982-162943122	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr3:162981441-162981525	MCF10A-Er-Src	breast:	n/a	n/a
33	RAD21	chr3:162973481-162973768	Hela-S3	cervix:	n/a	chr3:162973609-162973628
34	RCOR1	chr3:162974716-162974730	GM12878	blood:	n/a	n/a
35	REST	chr3:162966169-162966363	Hela-S3	cervix:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
36	REST	chr3:162966086-162966488	HL-60	blood:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
37	REST	chr3:162966121-162966521	PANC-1	pancreas:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
38	REST	chr3:162966127-162966428	MCF-7	breast:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
39	REST	chr3:162966087-162966490	ECC-1	luminal epithelium:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
40	RFX5	chr3:162973564-162973693	Hela-S3	cervix:	n/a	n/a
41	STAT3	chr3:162978775-162978822	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

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

(count:15 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
2	lnc-OTOL1-2	chr3:162948497-162949937	ENSG00000241168.1
3	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
4	lnc-OTOL1-2	chr3:162937866-162937980	NONHSAT093026
5	lnc-SI-4	chr3:162967053-162967162	ENSG00000241369
6	lnc-OTOL1-2	chr3:162948497-162949934	NONHSAT093026
7	lnc-SI-4	chr3:162937704-162937975	ENSG00000241369
8	lnc-OTOL1-2	chr3:162946486-162946540	NONHSAT093026
9	lnc-OTOL1-2	chr3:162946486-162946540	ENSG00000241168.1
10	lnc-SI-4	chr3:162937889-162937929	ENSG00000241369
11	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
12	lnc-OTOL1-2	chr3:162937866-162937980	ENSG00000241168.1
13	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
14	lnc-SI-4	chr3:162937889-162937975	ENSG00000241369
15	lnc-SI-4	chr3:162936848-162936965	ENSG00000241369

No data

Variant related genes	Relation type
CT64	TF binding region

Extended variants
information (count: 729 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:729 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534014284	chr3:162936401-162936402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs149438677	chr3:162936453-162936454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs146400163	chr3:162936546-162936547	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs542251513	chr3:162936592-162936593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs556136506	chr3:162936654-162936655	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs539462579	chr3:162936666-162936667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs551020434	chr3:162936774-162936775	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs576615515	chr3:162936810-162936811	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs551332414	chr3:162936834-162936835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs139058463	chr3:162936837-162936838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs4538378	chr3:162936850-162936851	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs541273521	chr3:162936949-162936950	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs142362307	chr3:162936963-162936964	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs375696173	chr3:162936997-162936998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs117586221	chr3:162937066-162937067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs548667406	chr3:162937077-162937078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs189467046	chr3:162937094-162937095	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs367744093	chr3:162937113-162937114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs563724239	chr3:162937120-162937121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs531472622	chr3:162937123-162937124	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs376905191	chr3:162937186-162937187	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs397769679	chr3:162937192-162937193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs200967832	chr3:162937193-162937194	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs202132338	chr3:162937194-162937195	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs200340183	chr3:162937195-162937196	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs551687165	chr3:162937226-162937227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs571595275	chr3:162937309-162937310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs139658848	chr3:162937397-162937398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs376095787	chr3:162937467-162937468	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs5854028	chr3:162937497-162937498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs371842621	chr3:162937498-162937499	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs533975386	chr3:162937531-162937532	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs371577372	chr3:162937583-162937584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs548113803	chr3:162937598-162937599	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs536351839	chr3:162937610-162937611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs555849272	chr3:162937629-162937630	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs11374574	chr3:162937679-162937680	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs575973346	chr3:162937688-162937689	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs373174528	chr3:162937689-162937690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs182048325	chr3:162937698-162937699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs558820623	chr3:162937715-162937716	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs572445511	chr3:162937734-162937735	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs185014956	chr3:162937826-162937827	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs561149340	chr3:162937835-162937836	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs4021822	chr3:162937939-162937940	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs543913302	chr3:162938044-162938045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs142157298	chr3:162938050-162938051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs532517116	chr3:162938051-162938052	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs190652475	chr3:162938110-162938111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs534797287	chr3:162938159-162938160	Weak transcription	n/a	n/a	Overlapped CNVs	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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162936400-162950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:162947400-162954200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:162953800-162954800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:162954200-162954800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:162954200-162954800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:162975800-162976200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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