Variant report

Variant	nsv528087
Chromosome Location	chr3:56608033-56628031
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:56625349-56625694	IMR90	lung:	n/a	n/a
2	CTCF	chr3:56617430-56617498	Kidney_OC	kidney:	n/a	n/a
3	CTCF	chr3:56617432-56617474	GM10248	blood:	n/a	n/a
4	CTCF	chr3:56617436-56617520	GM20000	blood:	n/a	n/a
5	FOXA1	chr3:56627522-56627727	T-47D	breast:	n/a	chr3:56627594-56627609
6	FOXA2	chr3:56615878-56616331	A549	lung:	n/a	n/a
7	GATA3	chr3:56627441-56627733	T-47D	breast:	n/a	n/a
8	IRF1	chr3:56624954-56624962	K562	blood:	n/a	n/a
9	JUN	chr3:56624951-56625154	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr3:56608586-56608747	HepG2	liver:	n/a	n/a
11	MYC	chr3:56609231-56609280	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr3:56616952-56617051	GM12878	blood:	n/a	n/a
13	NR2F2	chr3:56617334-56617667	K562	blood:	n/a	n/a
14	PAX5	chr3:56618791-56619145	GM12878	blood:	n/a	n/a
15	PAX5	chr3:56618786-56619147	GM12878	blood:	n/a	n/a
16	PAX5	chr3:56618759-56619192	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:56621946-56622361	K562	blood:	n/a	n/a
18	POLR2A	chr3:56622643-56625622	K562	blood:	n/a	n/a
19	POLR2A	chr3:56624185-56624201	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:56617114-56617284	K562	blood:	n/a	n/a
21	POLR2A	chr3:56623999-56624656	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:56622532-56622767	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:56607771-56608055	K562	blood:	n/a	n/a
24	POLR2A	chr3:56621591-56621623	K562	blood:	n/a	n/a
25	POLR2A	chr3:56620085-56620164	K562	blood:	n/a	n/a
26	POLR2A	chr3:56620653-56621729	K562	blood:	n/a	n/a
27	POLR2A	chr3:56615768-56615859	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:56620698-56621085	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:56624811-56624980	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:56624602-56624749	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:56621472-56621523	K562	blood:	n/a	n/a
32	POLR2A	chr3:56619471-56620173	K562	blood:	n/a	n/a
33	POLR2A	chr3:56625016-56625020	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:56608423-56609831	K562	blood:	n/a	n/a
35	POLR2A	chr3:56627132-56627492	K562	blood:	n/a	n/a
36	RXRA	chr3:56617293-56617524	HepG2	liver:	n/a	n/a
37	SP1	chr3:56617322-56617538	HepG2	liver:	n/a	n/a
38	TEAD4	chr3:56624760-56625260	ECC-1	luminal epithelium:	n/a	n/a
39	TEAD4	chr3:56624791-56625219	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56619803..56621869-chr3:56626645..56628418,2	K562	blood:
2	chr3:56590586..56593245-chr3:56606060..56608727,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPATA12-5	chr3:56626998-56627089	NONHSAT090054

No data

Variant related genes	Relation type
CCDC66	TF binding region
ENSG00000180376	chromatin interactions

Extended variants
information (count: 819 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:819 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13089169	chr3:56608033-56608034	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs551319047	chr3:56608055-56608056	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs186412517	chr3:56608074-56608075	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs539587418	chr3:56608093-56608094	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs372187221	chr3:56608105-56608106	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs557588315	chr3:56608152-56608153	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs572857229	chr3:56608158-56608159	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs535503884	chr3:56608167-56608168	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs190033584	chr3:56608188-56608189	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs9873754	chr3:56608240-56608241	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs182314491	chr3:56608248-56608249	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs564357343	chr3:56608261-56608262	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs372658562	chr3:56608294-56608295	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs201024139	chr3:56608327-56608328	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs9836539	chr3:56608345-56608346	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs13090343	chr3:56608369-56608370	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs376526543	chr3:56608389-56608390	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs386396713	chr3:56608390-56608391	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs78283952	chr3:56608403-56608404	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs386396714	chr3:56608404-56608405	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs59285810	chr3:56608405-56608406	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs79288055	chr3:56608406-56608407	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs374436807	chr3:56608508-56608509	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs577802524	chr3:56608518-56608519	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs540815933	chr3:56608549-56608550	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs369178004	chr3:56608609-56608610	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs145423463	chr3:56608692-56608693	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs559532682	chr3:56608706-56608707	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs138000397	chr3:56608755-56608756	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs548715873	chr3:56608800-56608801	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs562783326	chr3:56608845-56608846	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs552613835	chr3:56608878-56608879	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs141045826	chr3:56608930-56608931	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs551546184	chr3:56608971-56608972	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs373216997	chr3:56608994-56608995	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs187465968	chr3:56609005-56609006	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs546664084	chr3:56609066-56609067	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs546895406	chr3:56609086-56609087	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs143074074	chr3:56609121-56609122	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs535826801	chr3:56609183-56609184	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs148232314	chr3:56609218-56609219	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs569531582	chr3:56609230-56609231	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs12490920	chr3:56609242-56609243	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs538195043	chr3:56609260-56609261	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs149407195	chr3:56609285-56609286	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs192947884	chr3:56609362-56609363	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs141125607	chr3:56609379-56609380	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs375109292	chr3:56609430-56609431	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs79713701	chr3:56609459-56609460	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs9842283	chr3:56609469-56609470	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:80)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	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	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Cancer	20164919	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD

Chromatin state (count:540 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
5	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
6	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
8	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:56598000-56609200	Strong transcription	Fetal Thymus	thymus
22	chr3:56598000-56609800	Strong transcription	Primary T cells from cord blood	blood
23	chr3:56598600-56608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:56598600-56609600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:56600000-56608200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:56600000-56608600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:56600000-56608800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:56600000-56609000	Strong transcription	Adipose Nuclei	Adipose
29	chr3:56600200-56608200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:56600200-56608200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:56600200-56609600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:56600600-56640000	Weak transcription	NHLF	lung
33	chr3:56601800-56615800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:56602000-56609400	Strong transcription	Brain Hippocampus Middle	brain
35	chr3:56602400-56616200	Weak transcription	Dnd41	blood
36	chr3:56603000-56631600	Weak transcription	Fetal Brain Male	brain
37	chr3:56603200-56616600	Weak transcription	GM12878-XiMat	blood
38	chr3:56603200-56650400	Weak transcription	K562	blood
39	chr3:56603400-56610000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:56603600-56612200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:56603600-56615800	Weak transcription	Gastric	stomach
42	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:56603800-56615600	Weak transcription	Brain Germinal Matrix	brain
44	chr3:56604200-56615600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:56604200-56627600	Weak transcription	Brain Angular Gyrus	brain
46	chr3:56604600-56615800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:56604600-56624600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:56604600-56625000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:56604600-56625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:56604600-56627600	Weak transcription	HUVEC	blood vessel

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