Variant report

Variant	esv998611
Chromosome Location	chr3:50519293-50526732
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50526587..50528932-chr3:50530037..50531864,2	MCF-7	breast:
2	chr3:50525621..50528608-chr3:50539997..50541654,2	MCF-7	breast:
3	chr3:50520730..50523538-chr3:50529107..50531015,2	MCF-7	breast:
4	chr3:50524606..50527623-chr3:50538971..50541993,3	K562	blood:

Variant related genes	Relation type
ENSG00000007402	chromatin interactions

Extended variants
information (count: 300 )
Associated
traits (count: 95 )

Variant overlapped rSNPs/rCNVs (count:300 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs368343685	chr3:50519296-50519297	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs527281351	chr3:50519309-50519310	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs111499432	chr3:50519316-50519317	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs554195778	chr3:50519352-50519353	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs572719071	chr3:50519354-50519355	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs141913692	chr3:50519383-50519384	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs736471	chr3:50519392-50519393	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs377743224	chr3:50519460-50519461	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs114614876	chr3:50519490-50519491	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs375689738	chr3:50519516-50519517	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs531764508	chr3:50519521-50519522	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs541726483	chr3:50519536-50519537	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs543977518	chr3:50519546-50519547	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs565079316	chr3:50519597-50519598	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs184445955	chr3:50519615-50519616	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs541245017	chr3:50519731-50519732	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs531360503	chr3:50519743-50519744	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs549992670	chr3:50519763-50519764	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs529950457	chr3:50519827-50519828	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs201504248	chr3:50519847-50519848	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs150136610	chr3:50519915-50519916	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs374297797	chr3:50519969-50519970	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs138606887	chr3:50519993-50519994	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs367941339	chr3:50520006-50520007	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs371684180	chr3:50520008-50520009	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs149316967	chr3:50520013-50520014	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs571791081	chr3:50520027-50520028	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs538827967	chr3:50520042-50520043	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs6787890	chr3:50520128-50520129	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs566200951	chr3:50520154-50520155	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs536948486	chr3:50520178-50520179	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs372417938	chr3:50520195-50520196	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs369030607	chr3:50520197-50520198	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs547767320	chr3:50520209-50520210	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs188857172	chr3:50520215-50520216	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs146278800	chr3:50520235-50520236	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs558809261	chr3:50520371-50520372	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs577285037	chr3:50520401-50520402	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs116885806	chr3:50520534-50520535	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs559505956	chr3:50520572-50520573	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs80049775	chr3:50520639-50520640	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs541763132	chr3:50520645-50520646	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs562931134	chr3:50520685-50520686	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs6788459	chr3:50520695-50520696	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs139054326	chr3:50520707-50520708	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs373552446	chr3:50520713-50520714	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs377101326	chr3:50520764-50520765	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs142352113	chr3:50520790-50520791	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs563989326	chr3:50520810-50520811	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs145952405	chr3:50520811-50520812	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:95)

Disease	PMID	Source
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
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
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
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cancer	20164919	CNVD

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50492600-50528400	Weak transcription	Gastric	stomach
2	chr3:50502800-50520800	Weak transcription	Brain Anterior Caudate	brain
3	chr3:50512000-50523000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:50512600-50524200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:50513000-50527400	Weak transcription	Right Atrium	heart
6	chr3:50517000-50520200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:50517200-50520200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:50518000-50519800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:50518000-50520400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:50518000-50520400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:50518000-50520800	Enhancers	Fetal Muscle Leg	muscle
12	chr3:50518000-50521600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:50518000-50522000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:50518400-50519400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr3:50518400-50519400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:50518400-50520000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:50518400-50520200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:50518400-50520200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:50518400-50520200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr3:50518400-50520200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:50518400-50520200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:50518400-50521000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:50518600-50520000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:50518600-50520200	Enhancers	Primary T cells from cord blood	blood
25	chr3:50518600-50520200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:50518600-50520400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:50518600-50520400	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr3:50518600-50522000	Enhancers	Lung	lung
29	chr3:50518600-50523600	Enhancers	Fetal Muscle Trunk	muscle
30	chr3:50518800-50520000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:50518800-50520000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:50518800-50520000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:50518800-50520000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:50518800-50521800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:50519000-50519800	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:50519000-50520000	Weak transcription	Brain Germinal Matrix	brain
37	chr3:50519000-50520000	Weak transcription	Fetal Thymus	thymus
38	chr3:50519000-50520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:50519600-50519800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr3:50519600-50520800	Enhancers	Spleen	Spleen
41	chr3:50519800-50520800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:50519800-50524600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:50520000-50520200	Enhancers	Brain Germinal Matrix	brain
44	chr3:50520000-50520200	Enhancers	Fetal Thymus	thymus
45	chr3:50520000-50520200	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr3:50520000-50524600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:50520000-50524800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:50520200-50520600	Weak transcription	Brain Germinal Matrix	brain
49	chr3:50520200-50522200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:50520200-50522400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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