Variant report

Variant	esv3445182
Chromosome Location	chr3:50458687-50496660
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:48)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:48 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50480797..50482906-chr3:50483372..50486636,3	MCF-7	breast:
2	chr3:50475915..50477869-chr3:50482081..50483825,2	MCF-7	breast:
3	chr3:50491345..50493215-chr3:50495921..50497602,2	K562	blood:
4	chr3:50460270..50462499-chr3:50463846..50465815,2	MCF-7	breast:
5	chr3:50491345..50493215-chr3:50495921..50497602,2	K562	blood:
6	chr3:50473655..50474324-chr3:50587187..50588173,2	MCF-7	breast:
7	chr3:50388707..50391851-chr3:50462980..50465822,3	MCF-7	breast:
8	chr3:50464652..50467495-chr3:50469517..50472085,2	MCF-7	breast:
9	chr3:50459643..50461705-chr3:50463877..50466245,2	MCF-7	breast:
10	chr3:50486710..50489241-chr3:50648575..50650420,2	MCF-7	breast:
11	chr3:50373433..50376218-chr3:50478775..50480671,2	MCF-7	breast:
12	chr3:50394585..50396465-chr3:50463450..50466153,2	MCF-7	breast:
13	chr3:50480797..50482906-chr3:50483372..50486636,3	MCF-7	breast:
14	chr3:50456231..50458709-chr3:50462993..50464960,2	K562	blood:
15	chr3:50471606..50474364-chr3:50476758..50479663,3	K562	blood:
16	chr3:50473609..50474157-chr3:50556728..50557575,2	MCF-7	breast:
17	chr3:50456429..50459348-chr3:50470888..50473813,2	MCF-7	breast:
18	chr3:50484824..50486773-chr3:50549140..50551254,2	MCF-7	breast:
19	chr3:50456073..50458171-chr3:50458882..50461266,2	K562	blood:
20	chr3:50472878..50473722-chr3:50651256..50652161,4	K562	blood:
21	chr3:50386862..50388722-chr3:50472468..50474330,2	MCF-7	breast:
22	chr3:50473196..50473698-chr3:50588986..50589944,2	K562	blood:
23	chr3:50404490..50407147-chr3:50464074..50466361,2	K562	blood:
24	chr3:50374572..50376735-chr3:50471346..50473701,3	K562	blood:
25	chr3:50478777..50481371-chr3:50494134..50496538,2	K562	blood:
26	chr3:50473646..50476114-chr3:50476289..50479526,3	MCF-7	breast:
27	chr3:50473174..50474192-chr3:50587267..50588221,5	K562	blood:
28	chr3:50473271..50474185-chr3:50579555..50580461,5	K562	blood:
29	chr3:50476158..50479055-chr3:50482835..50485000,3	MCF-7	breast:
30	chr3:50483163..50485721-chr3:50593817..50596620,2	MCF-7	breast:
31	chr3:50433810..50435644-chr3:50457889..50460766,2	K562	blood:
32	chr3:50476158..50479055-chr3:50482835..50485000,3	MCF-7	breast:
33	chr3:50473157..50474126-chr3:50579445..50580285,9	MCF-7	breast:
34	chr3:50473195..50474158-chr3:50582352..50583122,3	MCF-7	breast:
35	chr3:50475915..50477869-chr3:50482081..50483825,2	MCF-7	breast:
36	chr3:50383805..50388003-chr3:50462564..50464902,4	MCF-7	breast:
37	chr3:50473646..50476114-chr3:50476289..50479526,3	MCF-7	breast:
38	chr3:50478777..50481371-chr3:50494134..50496538,2	K562	blood:
39	chr3:50471606..50474364-chr3:50476758..50479663,3	K562	blood:
40	chr3:50459643..50461705-chr3:50463877..50466245,2	MCF-7	breast:
41	chr3:50412196..50414182-chr3:50466596..50468838,2	MCF-7	breast:
42	chr3:50477103..50478834-chr3:50577541..50580324,2	MCF-7	breast:
43	chr3:50310267..50310922-chr3:50465221..50465893,2	MCF-7	breast:
44	chr3:50464652..50467495-chr3:50469517..50472085,2	MCF-7	breast:
45	chr3:50478507..50481167-chr3:50588405..50590760,2	K562	blood:
46	chr3:50478466..50481010-chr3:50538966..50541779,3	MCF-7	breast:
47	chr3:50460270..50462499-chr3:50463846..50465815,2	MCF-7	breast:
48	chr3:50473577..50474115-chr3:50579805..50580323,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYB561D2-6	chr3:50491615-50492080	NONHSAT089844
2	lnc-CYB561D2-6	chr3:50492804-50493445	NONHSAT089844

No data

Variant related genes	Relation type
ENSG00000271858	chromatin interactions
ENSG00000272104	chromatin interactions
ENSG00000004838	chromatin interactions
ENSG00000114738	chromatin interactions
ENSG00000007402	chromatin interactions
ENSG00000068028	chromatin interactions
ENSG00000114388	chromatin interactions
ENSG00000202322	chromatin interactions
ENSG00000114395	chromatin interactions
ENSG00000012171	chromatin interactions
ENSG00000114737	chromatin interactions

Extended variants
information (count: 1258 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:1258 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539838851	chr3:50458705-50458706	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs185551372	chr3:50458736-50458737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs189868691	chr3:50458747-50458748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs73082927	chr3:50458765-50458766	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs57278600	chr3:50458799-50458800	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs372571500	chr3:50458896-50458897	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs180771493	chr3:50458939-50458940	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs537680898	chr3:50458950-50458951	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs556028168	chr3:50459045-50459046	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs547160865	chr3:50459065-50459066	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs577521490	chr3:50459078-50459079	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs535772960	chr3:50459124-50459125	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs544567451	chr3:50459152-50459153	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs553747604	chr3:50459212-50459213	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs572020052	chr3:50459244-50459245	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs542686911	chr3:50459275-50459276	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs560854360	chr3:50459279-50459280	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs529481139	chr3:50459305-50459306	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs2236966	chr3:50459323-50459324	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs568757388	chr3:50459335-50459336	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs533676960	chr3:50459352-50459353	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs551763638	chr3:50459372-50459373	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs187277602	chr3:50459376-50459377	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs192211169	chr3:50459470-50459471	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs549439823	chr3:50459472-50459473	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs145860787	chr3:50459502-50459503	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs537644159	chr3:50459562-50459563	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs555952528	chr3:50459569-50459570	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs112893841	chr3:50459580-50459581	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs538569948	chr3:50459588-50459589	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs553810159	chr3:50459612-50459613	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs571993004	chr3:50459617-50459618	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs376041562	chr3:50459658-50459659	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs542298771	chr3:50459689-50459690	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs554646568	chr3:50459711-50459712	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs576207367	chr3:50459722-50459723	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs183538208	chr3:50459759-50459760	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs138482599	chr3:50459769-50459770	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs565979716	chr3:50459789-50459790	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs373841140	chr3:50459791-50459792	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs183926786	chr3:50459793-50459794	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs533637960	chr3:50459855-50459856	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs149652214	chr3:50459863-50459864	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs560653910	chr3:50459867-50459868	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs188639268	chr3:50459920-50459921	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs567924310	chr3:50459930-50459931	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs531710192	chr3:50459974-50459975	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs191339868	chr3:50459988-50459989	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs571090289	chr3:50460000-50460001	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs60273100	chr3:50460018-50460019	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:97)

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
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:622 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50443600-50460400	Weak transcription	Gastric	stomach
2	chr3:50445600-50471400	Weak transcription	Spleen	Spleen
3	chr3:50448800-50461000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:50449600-50461400	Weak transcription	Lung	lung
5	chr3:50450600-50471000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:50454400-50460200	Weak transcription	Brain Anterior Caudate	brain
7	chr3:50456600-50459400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:50457200-50459400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:50457600-50461200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:50459200-50460200	Enhancers	HepG2	liver
11	chr3:50459400-50459800	Enhancers	Right Ventricle	heart
12	chr3:50459400-50460000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:50459400-50460200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:50459400-50470200	Enhancers	Brain Germinal Matrix	brain
15	chr3:50460000-50460400	Enhancers	Right Ventricle	heart
16	chr3:50460000-50462600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:50460200-50461600	Enhancers	Brain Anterior Caudate	brain
18	chr3:50460200-50461600	Enhancers	Brain Hippocampus Middle	brain
19	chr3:50460200-50461800	Bivalent Enhancer	HepG2	liver
20	chr3:50460200-50462000	Enhancers	Fetal Muscle Leg	muscle
21	chr3:50460200-50462200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr3:50460200-50462200	Enhancers	Stomach Mucosa	stomach
23	chr3:50460200-50465800	Weak transcription	Right Atrium	heart
24	chr3:50460200-50467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:50460400-50461000	Enhancers	Brain Angular Gyrus	brain
26	chr3:50460400-50461600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:50460400-50461600	Enhancers	Fetal Intestine Large	intestine
28	chr3:50460400-50462000	Enhancers	Fetal Lung	lung
29	chr3:50460400-50462200	Enhancers	Gastric	stomach
30	chr3:50460400-50462200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr3:50460600-50461200	Enhancers	Brain Cingulate Gyrus	brain
32	chr3:50460600-50461600	Enhancers	Brain Substantia Nigra	brain
33	chr3:50460600-50461800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:50460800-50461200	Bivalent Enhancer	Fetal Intestine Small	intestine
35	chr3:50461000-50461400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:50461000-50461600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:50461200-50461600	Enhancers	Fetal Intestine Small	intestine
38	chr3:50461200-50462600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:50461400-50461800	Bivalent Enhancer	Fetal Brain Male	brain
40	chr3:50461400-50462400	Enhancers	Lung	lung
41	chr3:50461400-50465200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:50461600-50467400	Weak transcription	Brain Anterior Caudate	brain
43	chr3:50462200-50463200	Weak transcription	Stomach Mucosa	stomach
44	chr3:50462200-50471400	Weak transcription	Gastric	stomach
45	chr3:50462400-50462800	Weak transcription	Lung	lung
46	chr3:50462600-50462800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:50462600-50467600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:50462800-50463000	Enhancers	Lung	lung
49	chr3:50462800-50463200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:50463000-50467600	Weak transcription	Lung	lung

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