Variant report

Variant	nsv515615
Chromosome Location	chr3:161405094-161563784
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	ATF2	chr3:161488337-161488752	GM12878	blood:	n/a	n/a
2	ATF2	chr3:161488305-161488790	GM12878	blood:	n/a	n/a
3	BACH1	chr3:161504615-161504661	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr3:161541802-161541998	H1-hESC	embryonic stem cell:	n/a	n/a
5	BATF	chr3:161418795-161419108	GM12878	blood:	n/a	chr3:161418926-161418937
6	BATF	chr3:161488271-161488720	GM12878	blood:	n/a	n/a
7	BCL11A	chr3:161488389-161488674	GM12878	blood:	n/a	n/a
8	BCL11A	chr3:161488253-161488765	GM12878	blood:	n/a	n/a
9	BCL3	chr3:161551481-161551803	GM12878	blood:	n/a	n/a
10	BCL3	chr3:161488407-161488728	GM12878	blood:	n/a	n/a
11	BCLAF1	chr3:161488182-161488765	GM12878	blood:	n/a	n/a
12	BHLHE40	chr3:161488384-161489161	GM12878	blood:	n/a	n/a
13	BHLHE40	chr3:161407993-161408142	GM12878	blood:	n/a	n/a
14	CEBPB	chr3:161477709-161477941	A549	lung:	n/a	n/a
15	CEBPB	chr3:161434452-161434636	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr3:161539002-161539550	MCF-7	breast:	n/a	chr3:161539354-161539363 chr3:161539354-161539363 chr3:161539354-161539363
17	CEBPB	chr3:161539040-161539599	MCF-7	breast:	n/a	chr3:161539354-161539363 chr3:161539354-161539363 chr3:161539354-161539363
18	CEBPB	chr3:161539202-161539496	IMR90	lung:	n/a	chr3:161539354-161539363 chr3:161539354-161539363 chr3:161539354-161539363
19	CEBPB	chr3:161455952-161456211	IMR90	lung:	n/a	n/a
20	CEBPB	chr3:161455871-161456197	A549	lung:	n/a	n/a
21	CEBPB	chr3:161529517-161529827	IMR90	lung:	n/a	n/a
22	CEBPB	chr3:161409707-161409956	A549	lung:	n/a	chr3:161409866-161409877
23	CEBPB	chr3:161434515-161434579	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPB	chr3:161477731-161477931	HepG2	liver:	n/a	n/a
25	CEBPB	chr3:161434031-161434132	H1-hESC	embryonic stem cell:	n/a	chr3:161434032-161434045
26	CEBPB	chr3:161539126-161539564	A549	lung:	n/a	chr3:161539354-161539363 chr3:161539354-161539363 chr3:161539354-161539363
27	CEBPB	chr3:161529583-161529774	K562	blood:	n/a	n/a
28	CEBPB	chr3:161539178-161539513	HepG2	liver:	n/a	chr3:161539354-161539363 chr3:161539354-161539363 chr3:161539354-161539363
29	CEBPB	chr3:161511062-161511366	A549	lung:	n/a	n/a
30	CEBPB	chr3:161455943-161456209	HepG2	liver:	n/a	n/a
31	CEBPB	chr3:161456021-161456143	Hela-S3	cervix:	n/a	n/a
32	CEBPB	chr3:161529582-161529777	MCF-7	breast:	n/a	n/a
33	CEBPB	chr3:161539263-161539518	H1-hESC	embryonic stem cell:	n/a	chr3:161539354-161539363 chr3:161539354-161539363 chr3:161539354-161539363
34	CEBPB	chr3:161409755-161410007	HepG2	liver:	n/a	chr3:161409866-161409877
35	CEBPB	chr3:161529555-161529754	H1-hESC	embryonic stem cell:	n/a	n/a
36	CEBPB	chr3:161511048-161511487	A549	lung:	n/a	n/a
37	CEBPB	chr3:161456026-161456063	H1-hESC	embryonic stem cell:	n/a	n/a
38	CEBPB	chr3:161539192-161539511	A549	lung:	n/a	chr3:161539354-161539363 chr3:161539354-161539363 chr3:161539354-161539363
39	CEBPB	chr3:161410363-161410427	HepG2	liver:	n/a	n/a
40	CEBPB	chr3:161488287-161488818	GM12878	blood:	n/a	n/a
41	CEBPB	chr3:161477631-161477939	Hela-S3	cervix:	n/a	n/a
42	CEBPB	chr3:161508558-161508610	A549	lung:	n/a	n/a
43	CHD1	chr3:161418793-161418872	GM12878	blood:	n/a	n/a
44	CHD2	chr3:161488043-161488771	GM12878	blood:	n/a	n/a
45	CREB1	chr3:161488226-161488772	GM12878	blood:	n/a	n/a
46	CTCF	chr3:161488260-161488410	HPAF	blood vessel:	n/a	n/a
47	CTCF	chr3:161419020-161419170	GM12878	blood:	n/a	n/a
48	CTCF	chr3:161419080-161419195	LNCaP	prostate:	n/a	n/a
49	CTCF	chr3:161419045-161419197	GM12878	blood:	n/a	n/a
50	CTCF	chr3:161470198-161470438	GM12878	blood:	n/a	chr3:161470333-161470351

No.	Distal block	Cell Line	Cell type
1	chr3:161469489..161471513-chr3:161473255..161475165,2	K562	blood:
2	chr3:161547471..161549402-chr3:161554856..161557293,2	MCF-7	breast:
3	chr3:161472760..161474501-chr3:161478505..161480497,2	K562	blood:
4	chr3:161518824..161521549-chr3:161537494..161539506,2	MCF-7	breast:
5	chr3:161472760..161474501-chr3:161478505..161480497,2	K562	blood:
6	chr3:161547471..161549402-chr3:161554856..161557293,2	MCF-7	breast:
7	chr3:161518824..161521549-chr3:161537494..161539506,2	MCF-7	breast:
8	chr3:161277802..161278537-chr3:161469868..161470746,2	MCF-7	breast:
9	chr16:89006271..89008204-chr3:161471043..161472567,2	MCF-7	breast:
10	chr3:161469489..161471513-chr3:161473255..161475165,2	K562	blood:
11	chr3:161398334..161399929-chr3:161403036..161405549,2	MCF-7	breast:
12	chr3:161536736..161539708-chr3:161543704..161546343,4	MCF-7	breast:
13	chr3:161545972..161548808-chr3:161568962..161570462,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTOL1-6	chr3:161441001-161441074	NONHSAT093019
2	lnc-OTOL1-6	chr3:161441260-161441395	NONHSAT093019
3	lnc-SPTSSB-1	chr3:161534697-161534967	XLOC_003310
4	lnc-SPTSSB-1	chr3:161539485-161539696	XLOC_003310

Variant related genes	Relation type
ENSG00000240354	TF binding region
ENSG00000240354	chromatin interactions
ENSG00000129993	chromatin interactions

Extended variants
information (count: 3068 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:3068 , 50 per page) page: 1 2 3 4 5 6 7 ... 62

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546977078	chr3:161407024-161407025	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs113106303	chr3:161407097-161407098	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs564523378	chr3:161407125-161407126	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs372986106	chr3:161407126-161407127	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs529586524	chr3:161407134-161407135	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs549437099	chr3:161407148-161407149	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs377111675	chr3:161407150-161407151	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs536203859	chr3:161407163-161407164	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs185309991	chr3:161407200-161407201	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs190169525	chr3:161407201-161407202	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs182787981	chr3:161407225-161407226	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs570165559	chr3:161407264-161407265	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs187299238	chr3:161407276-161407277	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs13315704	chr3:161407304-161407305	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs552922641	chr3:161407312-161407313	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs369605981	chr3:161407345-161407346	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs149133472	chr3:161407369-161407370	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs192029715	chr3:161407382-161407383	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs373563479	chr3:161407387-161407388	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs557996153	chr3:161407389-161407390	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs76743566	chr3:161407391-161407392	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs540415661	chr3:161407415-161407416	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs60384830	chr3:161407418-161407419	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs560515619	chr3:161407442-161407443	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs201575432	chr3:161407459-161407460	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs565267438	chr3:161407461-161407462	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs140857951	chr3:161407485-161407486	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs6789001	chr3:161407513-161407514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs371117847	chr3:161407591-161407592	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs373313692	chr3:161407642-161407643	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs576943475	chr3:161407643-161407644	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs544436027	chr3:161407650-161407651	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs562812951	chr3:161407675-161407676	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs531886406	chr3:161407717-161407718	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs373361605	chr3:161407753-161407754	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs567070763	chr3:161407772-161407773	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs183839441	chr3:161407818-161407819	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs538905388	chr3:161407857-161407858	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs532842727	chr3:161407888-161407889	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs73877458	chr3:161407907-161407908	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs566578202	chr3:161407947-161407948	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs535078379	chr3:161407976-161407977	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs73017205	chr3:161407991-161407992	Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs569135469	chr3:161408030-161408031	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs538185158	chr3:161408049-161408050	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs562732410	chr3:161408058-161408059	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs557983644	chr3:161408068-161408069	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs577937602	chr3:161408069-161408070	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs189256640	chr3:161408097-161408098	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs112224320	chr3:161408102-161408103	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

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
Prostate cancer	18632612	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
Bladder cancer	21909424	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
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:187 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161407000-161409000	Enhancers	Fetal Brain Male	brain
2	chr3:161407400-161407800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:161407400-161408800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:161407600-161408000	Enhancers	Fetal Brain Female	brain
5	chr3:161407600-161408400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:161407600-161408600	Enhancers	Brain Germinal Matrix	brain
7	chr3:161407800-161408400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:161407800-161408400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:161407800-161408400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:161407800-161408400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:161407800-161408400	Enhancers	Brain Angular Gyrus	brain
12	chr3:161408000-161408400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:161408000-161408400	Flanking Active TSS	Fetal Brain Female	brain
14	chr3:161408200-161408600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:161408400-161408600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:161408400-161409400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:161408600-161409000	Weak transcription	Brain Germinal Matrix	brain
18	chr3:161408600-161409400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:161408800-161409000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:161409000-161409400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:161409000-161409600	Enhancers	Brain Germinal Matrix	brain
22	chr3:161409200-161409800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:161409400-161409600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:161409400-161409600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:161409400-161410200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:161410200-161410400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:161410400-161410600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:161410400-161417200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:161417200-161418000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:161418800-161419000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:161418800-161419000	Enhancers	Pancreas	Pancrea
32	chr3:161424800-161425200	Enhancers	Gastric	stomach
33	chr3:161425000-161425200	Enhancers	HepG2	liver
34	chr3:161425000-161425400	Enhancers	Placenta	Placenta
35	chr3:161428800-161431200	Weak transcription	Fetal Heart	heart
36	chr3:161434600-161436200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:161435000-161435800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:161438400-161439800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr3:161438600-161439400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:161438800-161439000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr3:161439400-161441800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:161439600-161439800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:161439600-161439800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr3:161439800-161443000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:161439800-161444600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:161441800-161447200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:161443000-161443600	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:161444200-161445200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
49	chr3:161444600-161445200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr3:161444600-161445200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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