Variant report

Variant	esv3412943
Chromosome Location	chr3:156377208-156379406
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156377877..156380030-chr3:156386212..156388367,2	MCF-7	breast:
2	chr3:156376696..156378719-chr3:156391982..156394592,2	MCF-7	breast:
3	chr3:156377079..156379353-chr3:156380561..156383322,2	K562	blood:
4	chr3:156371088..156373654-chr3:156376805..156378893,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-7	chr3:156359231-156383752	predAs_chen_BG181400_1

Variant related genes	Relation type
ENSG00000243926	chromatin interactions
ENSG00000163659	chromatin interactions

Extended variants
information (count: 76 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:76 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs34112658	chr3:156377214-156377215	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs190238907	chr3:156377275-156377276	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs372101135	chr3:156377295-156377296	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs550024498	chr3:156377349-156377350	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs571424297	chr3:156377350-156377351	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs538728690	chr3:156377403-156377404	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs547219833	chr3:156377455-156377456	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs113659615	chr3:156377633-156377634	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs151123695	chr3:156377640-156377641	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs58045284	chr3:156377667-156377668	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs181849983	chr3:156377684-156377685	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs184831948	chr3:156377693-156377694	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs537314914	chr3:156377694-156377695	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
14	rs188548027	chr3:156377724-156377725	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
15	rs371067741	chr3:156377739-156377740	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs79426788	chr3:156377756-156377757	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs141028029	chr3:156377827-156377828	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs559635184	chr3:156377870-156377871	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs6441092	chr3:156377871-156377872	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs544949648	chr3:156377914-156377915	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
21	rs150685415	chr3:156377950-156377951	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs563253547	chr3:156377964-156377965	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs56078043	chr3:156377965-156377966	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs58734463	chr3:156377972-156377973	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
25	rs59607866	chr3:156377988-156377989	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
26	rs147892071	chr3:156378010-156378011	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
27	rs550051132	chr3:156378035-156378036	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs9828326	chr3:156378050-156378051	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	mRNA abundance
29	rs55636408	chr3:156378117-156378118	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs113296366	chr3:156378137-156378138	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs59295926	chr3:156378140-156378141	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
32	rs377259918	chr3:156378142-156378143	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
33	rs10936036	chr3:156378193-156378194	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
34	rs547554737	chr3:156378216-156378217	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
35	rs565666050	chr3:156378239-156378240	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
36	rs529766123	chr3:156378254-156378255	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
37	rs367823973	chr3:156378259-156378260	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
38	rs560194578	chr3:156378390-156378391	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
39	rs572003119	chr3:156378402-156378403	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
40	rs547796660	chr3:156378428-156378429	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
41	rs147073670	chr3:156378466-156378467	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
42	rs73013957	chr3:156378570-156378571	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs558870294	chr3:156378577-156378578	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs74782290	chr3:156378580-156378581	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
45	rs534942918	chr3:156378586-156378587	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
46	rs553513082	chr3:156378596-156378597	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
47	rs531389901	chr3:156378612-156378613	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
48	rs542311390	chr3:156378613-156378614	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
49	rs147664146	chr3:156378700-156378701	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
50	rs185141593	chr3:156378709-156378710	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:54)

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
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	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
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Basal cell lymphoma	17170743	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Cancer	17440070	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21611746	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Neurodevelopmental disorder	22521361	CNVD

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156375000-156378600	Weak transcription	GM12878-XiMat	blood
2	chr3:156375400-156377400	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr3:156375400-156377600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:156375600-156381800	Weak transcription	K562	blood
5	chr3:156376200-156377400	Enhancers	HSMMtube	muscle
6	chr3:156376200-156377600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:156376600-156377400	Enhancers	Psoas Muscle	Psoas
8	chr3:156376600-156377600	Enhancers	Brain Germinal Matrix	brain
9	chr3:156376600-156382400	Weak transcription	Fetal Kidney	kidney
10	chr3:156376600-156383800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:156376600-156385600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:156376800-156377400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:156376800-156377600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:156376800-156377600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:156377000-156377400	Enhancers	Colon Smooth Muscle	Colon
16	chr3:156377200-156377400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:156377400-156381600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:156377400-156382200	Weak transcription	HSMMtube	muscle
19	chr3:156377400-156386000	Weak transcription	Psoas Muscle	Psoas
20	chr3:156377600-156382200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:156377600-156382200	Weak transcription	Brain Germinal Matrix	brain
22	chr3:156377600-156383000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:156378400-156379000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr3:156378400-156380000	Enhancers	Primary B cells from peripheral blood	blood
25	chr3:156378400-156380200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:156378600-156381800	Enhancers	GM12878-XiMat	blood
27	chr3:156378800-156379200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:156379000-156379200	Active TSS	Primary B cells from cord blood	blood
29	chr3:156379000-156379800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:156379000-156379800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr3:156379200-156379400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr3:156379200-156379800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:156379200-156381400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:156379400-156382000	Weak transcription	Primary B cells from cord blood	blood

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