Variant report

Variant	esv3347713
Chromosome Location	chr3:56604012-56605960
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56595109..56597404-chr3:56602239..56604027,2	K562	blood:

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

Extended variants
information (count: 81 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:81 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11712821	chr3:56604107-56604108	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs531820057	chr3:56604123-56604124	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs551541886	chr3:56604124-56604125	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs71621824	chr3:56604155-56604156	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs571715780	chr3:56604181-56604182	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs552162119	chr3:56604203-56604204	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs186875615	chr3:56604279-56604280	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs547848064	chr3:56604356-56604357	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs62255973	chr3:56604421-56604422	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs9881005	chr3:56604425-56604426	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs556709207	chr3:56604459-56604460	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs368512702	chr3:56604460-56604461	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs9881152	chr3:56604502-56604503	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs558342910	chr3:56604504-56604505	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs12715490	chr3:56604506-56604507	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs369490462	chr3:56604509-56604510	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs145464126	chr3:56604525-56604526	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs12636773	chr3:56604536-56604537	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs543390573	chr3:56604564-56604565	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs137918814	chr3:56604594-56604595	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs548239184	chr3:56604634-56604635	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs576915790	chr3:56604647-56604648	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs148430349	chr3:56604701-56604702	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs566965250	chr3:56604730-56604731	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs55823301	chr3:56604733-56604734	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs574317214	chr3:56604774-56604775	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs77964160	chr3:56604786-56604787	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs138747024	chr3:56604954-56604955	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs73832782	chr3:56604955-56604956	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs527817662	chr3:56604972-56604973	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs116265276	chr3:56605046-56605047	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs79362032	chr3:56605082-56605083	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs530126776	chr3:56605143-56605144	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs550161673	chr3:56605173-56605174	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs570350529	chr3:56605182-56605183	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs538821841	chr3:56605188-56605189	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191367320	chr3:56605191-56605192	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs565415594	chr3:56605209-56605210	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs534457489	chr3:56605213-56605214	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs556042658	chr3:56605241-56605242	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs201396147	chr3:56605266-56605267	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs200344512	chr3:56605273-56605274	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs556945544	chr3:56605295-56605296	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs79655969	chr3:56605311-56605312	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs140174274	chr3:56605324-56605325	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs199716046	chr3:56605325-56605326	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs368619960	chr3:56605326-56605327	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs182818409	chr3:56605334-56605335	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs375730712	chr3:56605339-56605340	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs34099535	chr3:56605404-56605405	Weak transcription Strong transcription	lncRNA	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:176 , 50 per page) page: 1 2 3 4

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	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
4	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
6	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
7	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
9	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:56597600-56605400	Strong transcription	Hela-S3	cervix
28	chr3:56597600-56608000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:56597800-56607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:56598000-56607000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:56598000-56607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:56598000-56609200	Strong transcription	Fetal Thymus	thymus
33	chr3:56598000-56609800	Strong transcription	Primary T cells from cord blood	blood
34	chr3:56598600-56608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:56598600-56609600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:56598800-56607600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:56599600-56606000	Strong transcription	Thymus	Thymus
38	chr3:56599600-56606200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:56599800-56606000	Strong transcription	Fetal Stomach	stomach
40	chr3:56599800-56606200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:56599800-56607800	Strong transcription	Fetal Lung	lung
42	chr3:56599800-56608000	Strong transcription	Liver	Liver
43	chr3:56600000-56604200	Strong transcription	Colonic Mucosa	Colon
44	chr3:56600000-56604400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:56600000-56606000	Strong transcription	Fetal Intestine Small	intestine
46	chr3:56600000-56606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:56600000-56606800	Strong transcription	Osteobl	bone
48	chr3:56600000-56607800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:56600000-56607800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:56600000-56607800	Strong transcription	Fetal Muscle Leg	muscle

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