Variant report

Variant	esv1839008
Chromosome Location	chr3:162718988-162755783
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	CEBPB	chr3:162729049-162729851	MCF-7	breast:	n/a	n/a
2	CEBPB	chr3:162729383-162729666	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr3:162729092-162729733	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr3:162729220-162729874	MCF-7	breast:	n/a	n/a
5	CEBPB	chr3:162729522-162729600	A549	lung:	n/a	n/a
6	CTCF	chr3:162755338-162755408	LNCaP	prostate:	n/a	n/a
7	CTCF	chr3:162753290-162753354	GM13976	blood:	n/a	n/a
8	CTCF	chr3:162742000-162742150	HRPEpiC	eye:	n/a	n/a
9	CUX1	chr3:162730188-162730192	K562	blood:	n/a	n/a
10	E2F4	chr3:162742908-162743235	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F4	chr3:162739552-162739907	MCF10A-Er-Src	breast:	n/a	n/a
12	E2F4	chr3:162753864-162753982	MCF10A-Er-Src	breast:	n/a	n/a
13	EGR1	chr3:162729339-162729821	MCF-7	breast:	n/a	n/a
14	EP300	chr3:162729337-162729872	MCF-7	breast:	n/a	chr3:162729395-162729409 chr3:162729394-162729408
15	EP300	chr3:162729410-162729811	T-47D	breast:	n/a	n/a
16	EP300	chr3:162729442-162729816	MCF-7	breast:	n/a	n/a
17	EP300	chr3:162729436-162729796	T-47D	breast:	n/a	n/a
18	ESR1	chr3:162729405-162729760	T-47D	breast:	n/a	n/a
19	FOS	chr3:162733027-162733171	MCF10A-Er-Src	breast:	n/a	n/a
20	FOSL2	chr3:162729335-162729780	MCF-7	breast:	n/a	n/a
21	FOXA1	chr3:162753379-162753718	T-47D	breast:	n/a	chr3:162753575-162753587
22	FOXA1	chr3:162748258-162748556	T-47D	breast:	n/a	n/a
23	FOXA1	chr3:162729433-162729761	T-47D	breast:	n/a	n/a
24	FOXA1	chr3:162729356-162729790	T-47D	breast:	n/a	n/a
25	GATA3	chr3:162729330-162729894	T-47D	breast:	n/a	n/a
26	GATA3	chr3:162729079-162729877	MCF-7	breast:	n/a	n/a
27	GATA3	chr3:162748173-162748460	T-47D	breast:	n/a	chr3:162748302-162748313
28	GATA3	chr3:162729319-162729824	T-47D	breast:	n/a	n/a
29	GATA3	chr3:162729407-162729849	MCF-7	breast:	n/a	n/a
30	GATA3	chr3:162729072-162729975	MCF-7	breast:	n/a	n/a
31	HDAC2	chr3:162729301-162729859	MCF-7	breast:	n/a	chr3:162729396-162729410 chr3:162729394-162729408 chr3:162729397-162729411 chr3:162729398-162729412 chr3:162729393-162729407 chr3:162729395-162729409
32	HDAC2	chr3:162729402-162729796	MCF-7	breast:	n/a	n/a
33	IKZF1	chr3:162724908-162725043	GM12878	blood:	n/a	n/a
34	JUN	chr3:162742539-162742812	HepG2	liver:	n/a	chr3:162742661-162742670 chr3:162742657-162742670
35	JUND	chr3:162742492-162742846	HepG2	liver:	n/a	chr3:162742661-162742670
36	MAFF	chr3:162754689-162754883	HepG2	liver:	n/a	n/a
37	MAFK	chr3:162735759-162736025	HepG2	liver:	n/a	n/a
38	MAFK	chr3:162754694-162754800	HepG2	liver:	n/a	chr3:162754767-162754778 chr3:162754766-162754780
39	MAFK	chr3:162735918-162736003	Hela-S3	cervix:	n/a	n/a
40	MAFK	chr3:162745459-162745686	HepG2	liver:	n/a	n/a
41	MAFK	chr3:162754672-162754872	HepG2	liver:	n/a	chr3:162754767-162754778 chr3:162754766-162754780
42	MAX	chr3:162729489-162729944	MCF-7	breast:	n/a	n/a
43	MYC	chr3:162736844-162736863	MCF-7	breast:	n/a	n/a
44	NR2F2	chr3:162729366-162729899	MCF-7	breast:	n/a	n/a
45	NR2F2	chr3:162729271-162729999	MCF-7	breast:	n/a	n/a
46	POLR2A	chr3:162740432-162740435	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr3:162742497-162742697	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr3:162724358-162724627	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr3:162733778-162733960	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr3:162732767-162732822	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:162730866..162732605-chr3:162732763..162734314,2	MCF-7	breast:
2	chr3:162730866..162732605-chr3:162732763..162734314,2	MCF-7	breast:
3	chr3:162754967..162757825-chr3:162758379..162760616,2	MCF-7	breast:
4	chr14:60627662..60628534-chr3:162740219..162740719,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOL1-2	chr3:162744184-162744286	NONHSAT093026
2	lnc-OTOL1-2	chr3:162744184-162744286	ENSG00000241168.1

Variant related genes	Relation type
ENSG00000241168	TF binding region

Extended variants
information (count: 921 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:921 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557819778	chr3:162724805-162724806	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs373577404	chr3:162724826-162724827	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs1488176	chr3:162724843-162724844	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs148697553	chr3:162724868-162724869	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs1488175	chr3:162724877-162724878	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs180707174	chr3:162724881-162724882	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs541767162	chr3:162724927-162724928	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs555628023	chr3:162725011-162725012	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs1488174	chr3:162725033-162725034	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs1488173	chr3:162725052-162725053	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs9283624	chr3:162725098-162725099	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs142778635	chr3:162725122-162725123	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs151046587	chr3:162725141-162725142	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs9283625	chr3:162725151-162725152	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs529499733	chr3:162725180-162725181	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs140987408	chr3:162725200-162725201	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs186013465	chr3:162725205-162725206	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs76756948	chr3:162725222-162725223	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs144723523	chr3:162725227-162725228	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs189738088	chr3:162725228-162725229	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs12637768	chr3:162725275-162725276	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs113601642	chr3:162725300-162725301	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs141766362	chr3:162725330-162725331	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs6799495	chr3:162725338-162725339	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs10559077	chr3:162725418-162725419	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs57644318	chr3:162725421-162725422	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs398062985	chr3:162725426-162725427	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs181372336	chr3:162725448-162725449	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs147106774	chr3:162725461-162725462	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs376873500	chr3:162725491-162725492	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs575519892	chr3:162725522-162725523	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs570648526	chr3:162725537-162725538	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs186034744	chr3:162725583-162725584	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs113319132	chr3:162735411-162735412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs112618151	chr3:162735423-162735424	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs535994291	chr3:162735451-162735452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs549058671	chr3:162735510-162735511	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs7642479	chr3:162735564-162735565	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs143773062	chr3:162735582-162735583	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs147456845	chr3:162735583-162735584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs574674395	chr3:162735589-162735590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs111367738	chr3:162735608-162735609	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs542142908	chr3:162735623-162735624	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs534698983	chr3:162735626-162735627	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs190024368	chr3:162735632-162735633	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs1586501	chr3:162735677-162735678	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs35786055	chr3:162735734-162735735	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs397719674	chr3:162735741-162735742	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs150805385	chr3:162735742-162735743	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs552977652	chr3:162735817-162735818	Weak transcription Enhancers	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	21293372	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162724800-162725600	Enhancers	Dnd41	blood
2	chr3:162735400-162745200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:162735600-162736400	Enhancers	Fetal Heart	heart
4	chr3:162736600-162737400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:162741000-162765600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:162745200-162745600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr3:162745600-162746000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:162752200-162752800	Enhancers	Dnd41	blood
9	chr3:162752800-162753200	Weak transcription	Dnd41	blood
10	chr3:162753200-162753400	Enhancers	Dnd41	blood
11	chr3:162753400-162756000	Weak transcription	Dnd41	blood

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