Variant report

Variant	esv3338042
Chromosome Location	chr3:56602712-56606910
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:56590931..56593644-chr3:56601004..56602846,2	K562	blood:
2	chr3:56595109..56597404-chr3:56602239..56604027,2	K562	blood:
3	chr3:56590586..56593245-chr3:56606060..56608727,2	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPATA12-5	chr3:56606365-56606456	NONHSAT090054
2	lnc-SPATA12-5	chr3:56605209-56605330	NONHSAT090053
3	lnc-SPATA12-5	chr3:56605209-56605330	NONHSAT090054
4	lnc-SPATA12-5	chr3:56606365-56606938	NONHSAT090053
5	lnc-SPATA12-5	chr3:56605209-56605407	NONHSAT090055

No data

Variant related genes	Relation type
ENSG00000180376	chromatin interactions

Extended variants
information (count: 168 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:168 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs186543715	chr3:56602733-56602734	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs140296165	chr3:56602763-56602764	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs562576999	chr3:56602791-56602792	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs34110166	chr3:56602795-56602796	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs7626378	chr3:56602885-56602886	Strong transcription Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs551108116	chr3:56602905-56602906	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs141654360	chr3:56602906-56602907	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs36029237	chr3:56602907-56602908	Strong transcription Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs374438701	chr3:56602924-56602925	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs547187869	chr3:56602926-56602927	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs375150977	chr3:56602945-56602946	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs115900282	chr3:56602951-56602952	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs75130039	chr3:56602961-56602962	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs111708968	chr3:56603184-56603185	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs56126040	chr3:56603204-56603205	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs538202780	chr3:56603214-56603215	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs557899206	chr3:56603215-56603216	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs373652743	chr3:56603217-56603218	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs534544165	chr3:56603219-56603220	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs554395462	chr3:56603223-56603224	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs201238744	chr3:56603234-56603235	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs574242332	chr3:56603244-56603245	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs543267729	chr3:56603262-56603263	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs562572173	chr3:56603286-56603287	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs145205237	chr3:56603341-56603342	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs544969369	chr3:56603355-56603356	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs386661199	chr3:56603365-56603366	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs564776481	chr3:56603376-56603377	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs527574973	chr3:56603378-56603379	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs149148234	chr3:56603402-56603403	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs534836207	chr3:56603405-56603406	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs143181508	chr3:56603413-56603414	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs549579433	chr3:56603465-56603466	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs569318620	chr3:56603512-56603513	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs531738417	chr3:56603555-56603556	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs551747976	chr3:56603576-56603577	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs571589712	chr3:56603581-56603582	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs534190788	chr3:56603643-56603644	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs13097030	chr3:56603675-56603676	Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs555045710	chr3:56603695-56603696	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs73081823	chr3:56603719-56603720	Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs574570199	chr3:56603723-56603724	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs574783352	chr3:56603737-56603738	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs543762171	chr3:56603743-56603744	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs544818457	chr3:56603745-56603746	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs369621255	chr3:56603749-56603750	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs558629201	chr3:56603779-56603780	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs73081825	chr3:56603863-56603864	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs148285796	chr3:56603884-56603885	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs141697411	chr3:56603893-56603894	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:79)

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

Chromatin state (count:255 , 50 per page) page: 1 2 3 4 5 6

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	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
4	chr3:56592400-56602800	Weak transcription	Gastric	stomach
5	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
6	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
7	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
8	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
10	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
11	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
13	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
15	chr3:56593000-56603000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:56594000-56603000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:56596600-56602800	Weak transcription	NHDF-Ad	bronchial
34	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:56597600-56603800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:56597600-56605400	Strong transcription	Hela-S3	cervix
39	chr3:56597600-56608000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:56597800-56603800	Strong transcription	NH-A	brain
41	chr3:56597800-56607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:56598000-56607000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:56598000-56607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:56598000-56609200	Strong transcription	Fetal Thymus	thymus
45	chr3:56598000-56609800	Strong transcription	Primary T cells from cord blood	blood
46	chr3:56598600-56608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:56598600-56609600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:56598800-56607600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:56599600-56606000	Strong transcription	Thymus	Thymus
50	chr3:56599600-56606200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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