Variant report

Variant	esv15877
Chromosome Location	chr3:134043427-134044513
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134043979..134045775-chr3:134201828..134204069,2	MCF-7	breast:
2	chr3:134025978..134037323-chr3:134040972..134053086,34	MCF-7	breast:
3	chr3:134044455..134047309-chr3:134153979..134155678,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMOTL2-2	chr3:134042592-134045369	XLOC_003261

Variant related genes	Relation type
ENSG00000240006	chromatin interactions
ENSG00000129055	chromatin interactions

Extended variants
information (count: 31 )
Associated
traits (count: 51 )

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs577829724	chr3:134043429-134043430	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs138473988	chr3:134043439-134043440	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs7614069	chr3:134043457-134043458	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs529094314	chr3:134043497-134043498	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs568494782	chr3:134043498-134043499	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs191100707	chr3:134043516-134043517	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs183763030	chr3:134043522-134043523	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs577024134	chr3:134043548-134043549	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs200531523	chr3:134043563-134043564	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs571644578	chr3:134043603-134043604	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs190623165	chr3:134043686-134043687	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs141670991	chr3:134043756-134043757	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs182226586	chr3:134043768-134043769	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs7638751	chr3:134043833-134043834	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs536793269	chr3:134043859-134043860	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs11928672	chr3:134043922-134043923	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs72988445	chr3:134043942-134043943	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs11917363	chr3:134043988-134043989	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs77198497	chr3:134043997-134043998	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs185215422	chr3:134044044-134044045	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
21	rs386666103	chr3:134044068-134044069	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs189845349	chr3:134044069-134044070	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs550911933	chr3:134044084-134044085	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs554082298	chr3:134044176-134044177	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
25	rs115280265	chr3:134044263-134044264	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
26	rs181662977	chr3:134044288-134044289	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
27	rs185508089	chr3:134044295-134044296	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs569461299	chr3:134044324-134044325	Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs6809909	chr3:134044473-134044474	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs146209747	chr3:134044489-134044490	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs6772791	chr3:134044501-134044502	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:51)

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
Cancer	21129771	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
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	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
Intracranial aneurysm	16715129	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Myelofibrosis	22110671	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134034600-134046200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134034800-134044200	Weak transcription	Right Ventricle	heart
3	chr3:134035000-134044000	Weak transcription	Fetal Heart	heart
4	chr3:134035000-134044200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:134035000-134045000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:134035000-134058800	Weak transcription	Liver	Liver
7	chr3:134036600-134044200	Weak transcription	Esophagus	oesophagus
8	chr3:134036600-134045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:134036600-134050600	Weak transcription	Fetal Brain Female	brain
10	chr3:134039800-134044000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:134039800-134044200	Weak transcription	Hela-S3	cervix
12	chr3:134039800-134045000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:134039800-134045600	Enhancers	NHEK	skin
14	chr3:134040000-134044000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:134040000-134044600	Weak transcription	NH-A	brain
16	chr3:134040000-134044800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:134041200-134046000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:134041200-134056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:134041600-134044400	Enhancers	A549	lung
20	chr3:134041600-134047400	Enhancers	Pancreas	Pancrea
21	chr3:134041800-134044800	Weak transcription	Psoas Muscle	Psoas
22	chr3:134042000-134060800	Enhancers	Placenta	Placenta
23	chr3:134042200-134043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:134042200-134050600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:134042200-134052400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:134042600-134045000	Enhancers	Adipose Nuclei	Adipose
27	chr3:134042600-134046000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:134042600-134046600	Enhancers	Spleen	Spleen
29	chr3:134042600-134054000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:134042600-134054400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:134042800-134045600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:134042800-134046000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:134042800-134046000	Enhancers	Osteobl	bone
34	chr3:134042800-134057000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:134043000-134046200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:134043200-134044200	Weak transcription	HepG2	liver
37	chr3:134043200-134045400	Enhancers	Gastric	stomach
38	chr3:134043200-134046000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:134043200-134046000	Enhancers	NHDF-Ad	bronchial
40	chr3:134043200-134046200	Enhancers	NHLF	lung
41	chr3:134043200-134046800	Enhancers	Lung	lung
42	chr3:134043200-134047600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:134043400-134044600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:134043400-134046000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:134043400-134046000	Enhancers	HMEC	breast
46	chr3:134043400-134046000	Enhancers	HSMM	muscle
47	chr3:134043400-134046200	Enhancers	HSMMtube	muscle
48	chr3:134043600-134046200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:134044000-134046200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:134044000-134047200	Enhancers	Fetal Heart	heart

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