Variant report

Variant	nsv1007906
Chromosome Location	chr3:34466966-34607465
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	chr3:34524768-34525196	GM12878	blood:	n/a	n/a
2	BATF	chr3:34524832-34525244	GM12878	blood:	n/a	chr3:34525161-34525169
3	BCL11A	chr3:34524747-34525185	GM12878	blood:	n/a	chr3:34525022-34525031 chr3:34525164-34525173
4	CEBPB	chr3:34493497-34493562	A549	lung:	n/a	n/a
5	CEBPB	chr3:34585653-34586003	A549	lung:	n/a	chr3:34585814-34585825 chr3:34585813-34585824 chr3:34585813-34585826
6	CEBPB	chr3:34545869-34546195	HepG2	liver:	n/a	chr3:34546009-34546020
7	CEBPB	chr3:34585648-34585949	K562	blood:	n/a	chr3:34585814-34585825 chr3:34585813-34585824 chr3:34585813-34585826
8	CEBPB	chr3:34522281-34522567	HepG2	liver:	n/a	chr3:34522416-34522427
9	CEBPB	chr3:34585656-34585959	IMR90	lung:	n/a	chr3:34585814-34585825 chr3:34585813-34585824 chr3:34585813-34585826
10	CEBPB	chr3:34585654-34585997	HepG2	liver:	n/a	chr3:34585814-34585825 chr3:34585813-34585824 chr3:34585813-34585826
11	CEBPB	chr3:34523754-34523867	A549	lung:	n/a	n/a
12	CEBPB	chr3:34554096-34554263	HepG2	liver:	n/a	chr3:34554138-34554149 chr3:34554138-34554147 chr3:34554136-34554149 chr3:34554136-34554147
13	CEBPB	chr3:34522278-34522597	IMR90	lung:	n/a	chr3:34522416-34522427
14	CEBPB	chr3:34522309-34522509	H1-hESC	embryonic stem cell:	n/a	chr3:34522416-34522427
15	CEBPB	chr3:34570437-34570605	A549	lung:	n/a	n/a
16	CTCF	chr3:34576380-34576530	GM12875	blood:	n/a	n/a
17	CTCF	chr3:34498300-34498450	WERI-Rb-1	eye:	n/a	n/a
18	CTCF	chr3:34596120-34596270	SK-N-SH_RA	brain:	n/a	n/a
19	CTCF	chr3:34498271-34498375	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:34469130-34469179	GM13976	blood:	n/a	n/a
21	CTCF	chr3:34581880-34582030	HPF	lung:	n/a	n/a
22	CTCF	chr3:34576504-34576526	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr3:34498307-34498341	MCF-7	breast:	n/a	n/a
24	CTCF	chr3:34551408-34551462	GM13976	blood:	n/a	n/a
25	CTCF	chr3:34576400-34576550	A549	lung:	n/a	n/a
26	CTCF	chr3:34494640-34494790	HVMF	connective:	n/a	n/a
27	CTCF	chr3:34498271-34498376	MCF-7	breast:	n/a	n/a
28	CTCF	chr3:34534814-34534848	Fibrobl	skin:	n/a	n/a
29	CTCF	chr3:34498293-34498351	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr3:34560900-34560934	Lung_OC	lung:	n/a	n/a
31	CTCF	chr3:34498260-34498410	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:34567585-34567588	A549	lung:	n/a	n/a
33	CTCF	chr3:34518040-34518190	GM12874	blood:	n/a	chr3:34518112-34518125
34	CTCF	chr3:34468801-34468838	Pancreas_OC	pancreas:	n/a	n/a
35	CTCF	chr3:34498285-34498379	MCF-7	breast:	n/a	n/a
36	E2F4	chr3:34594734-34594928	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr3:34523244-34523466	MCF10A-Er-Src	breast:	n/a	n/a
38	E2F4	chr3:34529873-34529943	MCF10A-Er-Src	breast:	n/a	n/a
39	E2F4	chr3:34599900-34600152	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F4	chr3:34606651-34606982	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F4	chr3:34591480-34591873	MCF10A-Er-Src	breast:	n/a	n/a
42	EP300	chr3:34484005-34484147	GM12878	blood:	n/a	n/a
43	EP300	chr3:34546291-34546543	SK-N-SH_RA	brain:	n/a	n/a
44	EP300	chr3:34546046-34546912	SK-N-SH	brain:	n/a	chr3:34546796-34546810 chr3:34546794-34546808 chr3:34546797-34546811 chr3:34546795-34546809
45	FAM48A	chr3:34478121-34478214	GM12878	blood:	n/a	n/a
46	FAM48A	chr3:34555039-34555119	GM12878	blood:	n/a	n/a
47	FOS	chr3:34588981-34589050	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr3:34521490-34521684	HUVEC	blood vessel:	n/a	n/a
49	FOS	chr3:34575792-34576109	MCF10A-Er-Src	breast:	n/a	n/a
50	FOS	chr3:34575818-34576031	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:34576054..34578921-chr3:34584615..34587187,2	K562	blood:
2	chr3:34599336..34601588-chr3:34604895..34606899,3	K562	blood:
3	chr3:34599336..34601588-chr3:34604895..34606899,3	K562	blood:
4	chr3:34462063..34464661-chr3:34482246..34484310,2	K562	blood:
5	chr3:34325094..34326771-chr3:34500714..34502668,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDCD6IP-2	chr3:34476785-34477124	XLOC_002612
2	lnc-CLASP2-2	chr3:34577438-34577567	XLOC_003080
3	lnc-PDCD6IP-2	chr3:34476785-34476954	XLOC_002612
4	lnc-PDCD6IP-2	chr3:34476785-34476954	XLOC_002612
5	lnc-PDCD6IP-2	chr3:34598080-34598194	XLOC_002612
6	lnc-CLASP2-2	chr3:34585173-34585372	XLOC_003080
7	lnc-PDCD6IP-2	chr3:34600671-34600861	XLOC_002612
8	lnc-PDCD6IP-2	chr3:34598080-34598194	XLOC_002612
9	lnc-PDCD6IP-2	chr3:34593396-34593480	XLOC_002612
10	lnc-PDCD6IP-2	chr3:34604268-34604551	XLOC_002612
11	lnc-PDCD6IP-2	chr3:34598080-34598194	XLOC_002612
12	lnc-PDCD6IP-2	chr3:34604268-34604551	XLOC_002612
13	lnc-CLASP2-2	chr3:34566310-34566553	XLOC_003080
14	lnc-PDCD6IP-2	chr3:34600671-34600861	XLOC_002612
15	lnc-PDCD6IP-2	chr3:34476785-34477097	XLOC_002612
16	lnc-PDCD6IP-2	chr3:34604268-34604369	XLOC_002612

Variant related genes	Relation type
ENSG00000227498	TF binding region
ENSG00000227498	chromatin interactions
PTK2	miRNA target sites
CLASP1	miRNA target sites

Extended variants
information (count: 2052 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:2052 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs563550898	chr3:34476636-34476637	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs530846821	chr3:34476719-34476720	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs187897740	chr3:34476729-34476730	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs143664867	chr3:34476739-34476740	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs112474250	chr3:34476750-34476751	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs6768570	chr3:34476773-34476774	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs192356833	chr3:34476792-34476793	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs539633109	chr3:34476815-34476816	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs368958882	chr3:34476825-34476826	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs148260328	chr3:34476869-34476870	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs537364594	chr3:34476895-34476896	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs141344620	chr3:34476928-34476929	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs567257807	chr3:34476929-34476930	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs534361365	chr3:34476958-34476959	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs67251788	chr3:34477022-34477023	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs200937703	chr3:34477035-34477036	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs184998236	chr3:34477050-34477051	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs545194199	chr3:34477066-34477067	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs150386788	chr3:34477089-34477090	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs188681093	chr3:34498438-34498439	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs192489521	chr3:34498446-34498447	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs76388883	chr3:34498504-34498505	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs183378931	chr3:34498537-34498538	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs78887632	chr3:34498553-34498554	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs373580532	chr3:34498569-34498570	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs564400692	chr3:34498590-34498591	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs114939789	chr3:34498656-34498657	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs550110748	chr3:34498657-34498658	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs567943415	chr3:34498661-34498662	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs528920009	chr3:34498667-34498668	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs547143652	chr3:34498678-34498679	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs543841563	chr3:34498695-34498696	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs565790568	chr3:34498698-34498699	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs539595970	chr3:34498722-34498723	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs557993935	chr3:34498790-34498791	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs569907318	chr3:34498791-34498792	Active TSS Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs563634057	chr3:34498801-34498802	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs537338641	chr3:34498807-34498808	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs555660938	chr3:34498810-34498811	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs11918350	chr3:34498844-34498845	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs377658308	chr3:34498846-34498847	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs542222418	chr3:34498850-34498851	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs146282720	chr3:34498927-34498928	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs76445156	chr3:34499019-34499020	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs201039083	chr3:34499021-34499022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs370978691	chr3:34499023-34499024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs367621215	chr3:34499026-34499027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs71070193	chr3:34499031-34499032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs572208080	chr3:34499096-34499097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs77164968	chr3:34499111-34499112	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:76)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Myelofibrosis	22110671	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:34476600-34477000	Enhancers	Thymus	Thymus
2	chr3:34498400-34498800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:34498400-34499000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:34498600-34499000	ZNF genes & repeats	Aorta	Aorta
5	chr3:34499000-34501600	Weak transcription	Aorta	Aorta
6	chr3:34501600-34502000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:34501600-34502400	ZNF genes & repeats	Aorta	Aorta
8	chr3:34505200-34506400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr3:34506000-34507200	Enhancers	Fetal Brain Male	brain
10	chr3:34513000-34513600	Enhancers	Thymus	Thymus
11	chr3:34513600-34517200	Weak transcription	Thymus	Thymus
12	chr3:34515000-34515200	Weak transcription	Dnd41	blood
13	chr3:34517200-34517400	Enhancers	Thymus	Thymus
14	chr3:34517200-34518200	Enhancers	Dnd41	blood
15	chr3:34517200-34518600	Enhancers	Fetal Thymus	thymus
16	chr3:34517400-34517600	ZNF genes & repeats	Aorta	Aorta
17	chr3:34517400-34518600	Flanking Active TSS	Thymus	Thymus
18	chr3:34517600-34519000	Weak transcription	Aorta	Aorta
19	chr3:34518600-34519600	Active TSS	Thymus	Thymus
20	chr3:34519600-34520400	Weak transcription	Thymus	Thymus
21	chr3:34520400-34520600	Enhancers	Thymus	Thymus
22	chr3:34524000-34524800	Weak transcription	Aorta	Aorta
23	chr3:34524400-34524800	Enhancers	Dnd41	blood
24	chr3:34524800-34525200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:34524800-34525200	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:34524800-34525200	Active TSS	A549	lung
27	chr3:34524800-34525400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:34524800-34525400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:34524800-34525400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:34524800-34525400	Active TSS	Aorta	Aorta
31	chr3:34524800-34525600	Active TSS	Primary T cells from cord blood	blood
32	chr3:34524800-34525600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr3:34524800-34525800	Flanking Active TSS	Dnd41	blood
34	chr3:34525000-34525200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:34525000-34525400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:34525000-34525400	Active TSS	Primary T cells fromperipheralblood	blood
37	chr3:34525000-34525400	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr3:34525000-34525400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:34525000-34525400	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:34525000-34525400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:34525000-34525400	Active TSS	Brain Angular Gyrus	brain
42	chr3:34525000-34525400	Active TSS	Brain Hippocampus Middle	brain
43	chr3:34525000-34525600	Active TSS	Brain Anterior Caudate	brain
44	chr3:34525000-34525600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:34525000-34525600	Active TSS	Thymus	Thymus
46	chr3:34525200-34525400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:34525200-34525600	Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr3:34525200-34525600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:34525400-34525800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:34525400-34526000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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