Variant report

Variant	esv3496002
Chromosome Location	chr3:143218912-143222210
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	chr3:143212932..143214521-chr3:143217945..143220851,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAQR9-6	chr3:143222117-143223115	NONHSAT092527

Extended variants
information (count: 102 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:102 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540763374	chr3:143218919-143218920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs565300509	chr3:143219039-143219040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs532762167	chr3:143219057-143219058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs374838402	chr3:143219146-143219147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs73008900	chr3:143219187-143219188	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs541552097	chr3:143219206-143219207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs141649765	chr3:143219244-143219245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs530367202	chr3:143219259-143219260	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs561116253	chr3:143219289-143219290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs528445059	chr3:143219318-143219319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs115546701	chr3:143219395-143219396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs150112856	chr3:143219401-143219402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs183330587	chr3:143219466-143219467	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs118014727	chr3:143219504-143219505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs538050824	chr3:143219530-143219531	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs556123187	chr3:143219599-143219600	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs11274042	chr3:143219676-143219677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs189182339	chr3:143219710-143219711	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs535775615	chr3:143219887-143219888	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs138419279	chr3:143219930-143219931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs573289619	chr3:143219947-143219948	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs542280557	chr3:143219954-143219955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs565382934	chr3:143220016-143220017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs577325288	chr3:143220038-143220039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs528672221	chr3:143220049-143220050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs556189961	chr3:143220110-143220111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs193077885	chr3:143220115-143220116	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs142757964	chr3:143220149-143220150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs546745291	chr3:143220223-143220224	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs77551545	chr3:143220283-143220284	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs117544757	chr3:143220320-143220321	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs183030666	chr3:143220366-143220367	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs187603914	chr3:143220386-143220387	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs565008282	chr3:143220459-143220460	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs570515602	chr3:143220488-143220489	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs532483867	chr3:143220489-143220490	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191258634	chr3:143220494-143220495	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs537587298	chr3:143220496-143220497	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs184229084	chr3:143220528-143220529	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs568294156	chr3:143220560-143220561	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs376015391	chr3:143220583-143220584	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs535712006	chr3:143220584-143220585	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs147396033	chr3:143220594-143220595	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs114226887	chr3:143220619-143220620	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs576065346	chr3:143220658-143220659	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs838602	chr3:143220697-143220698	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs530322176	chr3:143220722-143220723	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs188596994	chr3:143220729-143220730	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs544408245	chr3:143220754-143220755	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs556324118	chr3:143220762-143220763	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Adrenocortical carcinoma	18281524	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143174400-143220400	Weak transcription	Fetal Lung	lung
2	chr3:143176800-143220400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:143179400-143220400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:143186000-143223000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
6	chr3:143201800-143226400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:143209000-143226800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:143212600-143224800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:143212600-143247400	Weak transcription	Primary T cells from cord blood	blood
10	chr3:143215600-143226800	Weak transcription	Fetal Stomach	stomach
11	chr3:143219800-143222200	Weak transcription	Esophagus	oesophagus
12	chr3:143220200-143220800	Enhancers	Brain Angular Gyrus	brain
13	chr3:143220200-143220800	Enhancers	Brain Germinal Matrix	brain
14	chr3:143220200-143221200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:143220200-143221200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:143220200-143221200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:143220200-143221200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:143220400-143220800	Enhancers	Brain Cingulate Gyrus	brain
19	chr3:143220400-143220800	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:143220400-143221000	Enhancers	Brain Substantia Nigra	brain
21	chr3:143220400-143221200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:143220400-143221200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:143220400-143221200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:143220400-143221200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr3:143220400-143221200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:143220400-143221200	Enhancers	Brain Hippocampus Middle	brain
27	chr3:143220400-143221400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:143220400-143221800	Enhancers	Fetal Lung	lung
29	chr3:143220400-143226400	Weak transcription	HSMMtube	muscle
30	chr3:143220600-143220800	Enhancers	Brain Anterior Caudate	brain
31	chr3:143220600-143221200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr3:143220600-143221200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:143220800-143221200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:143220800-143221200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
35	chr3:143220800-143226600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:143221000-143222400	Weak transcription	Spleen	Spleen
37	chr3:143221000-143227200	Weak transcription	Brain Substantia Nigra	brain
38	chr3:143221200-143224000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:143221200-143226800	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:143221200-143228200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:143221400-143223800	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:143221400-143224600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:143221800-143222200	Weak transcription	Fetal Lung	lung
44	chr3:143222200-143222400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:143222200-143222600	Enhancers	Gastric	stomach
46	chr3:143222200-143222800	Strong transcription	Fetal Lung	lung
47	chr3:143222200-143223000	ZNF genes & repeats	Esophagus	oesophagus

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