Variant report

Variant	nsv963286
Chromosome Location	chr3:162941559-162967897
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	CTCF	chr3:162946522-162946561	GM20000	blood:	n/a	n/a
2	CTCF	chr3:162953064-162953107	Spleen_OC	spleen:	n/a	n/a
3	FOXA2	chr3:162954899-162955485	A549	lung:	n/a	n/a
4	FOXA2	chr3:162954989-162955392	A549	lung:	n/a	n/a
5	GATA3	chr3:162946554-162946752	SH-SY5Y	brain:	n/a	n/a
6	GATA3	chr3:162965902-162966184	SH-SY5Y	brain:	n/a	n/a
7	MAFK	chr3:162950725-162950744	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAFK	chr3:162945809-162945821	K562	blood:	n/a	chr3:162945810-162945821
9	MYC	chr3:162963651-162963897	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:162942982-162943122	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:162951394-162951539	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:162960831-162960922	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:162942403-162942588	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:162960907-162961287	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:162963425-162963830	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr3:162964060-162964153	MCF10A-Er-Src	breast:	n/a	n/a
17	REST	chr3:162966087-162966490	ECC-1	luminal epithelium:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
18	REST	chr3:162966121-162966521	PANC-1	pancreas:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
19	REST	chr3:162966169-162966363	Hela-S3	cervix:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
20	REST	chr3:162966086-162966488	HL-60	blood:	n/a	chr3:162966282-162966302 chr3:162966282-162966302
21	REST	chr3:162966127-162966428	MCF-7	breast:	n/a	chr3:162966282-162966302 chr3:162966282-162966302

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:162965564..162967593-chr3:162971986..162973917,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOL1-2	chr3:162946486-162946540	ENSG00000241168.1
2	lnc-OTOL1-2	chr3:162948497-162949937	ENSG00000241168.1
3	lnc-OTOL1-2	chr3:162948497-162949934	NONHSAT093026
4	lnc-OTOL1-2	chr3:162946486-162946540	NONHSAT093026
5	lnc-SI-4	chr3:162967053-162967162	ENSG00000241369

Variant related genes	Relation type
CT64	TF binding region

Extended variants
information (count: 526 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:526 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs149789399	chr3:162941635-162941636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs556997872	chr3:162941665-162941666	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs145767068	chr3:162941678-162941679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs184873966	chr3:162941681-162941682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs540908156	chr3:162941762-162941763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs563357577	chr3:162941844-162941845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs1994750	chr3:162941903-162941904	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs148969229	chr3:162941918-162941919	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs549599468	chr3:162941935-162941936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs374954853	chr3:162941936-162941937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs189233026	chr3:162941960-162941961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs530360294	chr3:162942013-162942014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs35645329	chr3:162942028-162942029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs181529648	chr3:162942034-162942035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs536565893	chr3:162942062-162942063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs571327067	chr3:162942102-162942103	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs145838306	chr3:162942144-162942145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs552830266	chr3:162942165-162942166	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs371716727	chr3:162942175-162942176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs138469270	chr3:162942203-162942204	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs141455417	chr3:162942223-162942224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs533347112	chr3:162942228-162942229	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs555548602	chr3:162942241-162942242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs575217683	chr3:162942299-162942300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs544347684	chr3:162942320-162942321	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs73013506	chr3:162942322-162942323	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs577697222	chr3:162942342-162942343	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs2035871	chr3:162942351-162942352	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs148183961	chr3:162942433-162942434	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs372792681	chr3:162942475-162942476	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs184996108	chr3:162942477-162942478	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs375230709	chr3:162942489-162942490	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs369512424	chr3:162942573-162942574	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs111386455	chr3:162942591-162942592	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs373973828	chr3:162942723-162942724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs563112157	chr3:162942725-162942726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs531663931	chr3:162942771-162942772	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs530953832	chr3:162942805-162942806	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs367998739	chr3:162942828-162942829	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs552142052	chr3:162942831-162942832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs35108258	chr3:162942841-162942842	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs1873644	chr3:162942905-162942906	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs6786504	chr3:162942993-162942994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs180906538	chr3:162942995-162942996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs544235848	chr3:162943059-162943060	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs150732294	chr3:162943184-162943185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs138005445	chr3:162943229-162943230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs185760215	chr3:162943246-162943247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs143622084	chr3:162943255-162943256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs538073800	chr3:162943288-162943289	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:5 , 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

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