Variant report

Variant	esv3390225
Chromosome Location	chr10:26855181-26855642
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	chr10:26854569..26856089-chrX:118738967..118740548,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDSS1-7	chr10:26854425-26855838	NONHSAT011828
2	lnc-ABI1-4	chr10:26854421-26855838	ENSG00000246873

Variant related genes	Relation type
ENSG00000186416	chromatin interactions
RAB11FIP5	miRNA target sites

Extended variants
information (count: 17 )
Associated
traits (count: 43 )

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs551240187	chr10:26855193-26855194	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs10829025	chr10:26855194-26855195	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs78725031	chr10:26855196-26855197	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs142676663	chr10:26855208-26855209	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs567254483	chr10:26855214-26855215	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs74738866	chr10:26855289-26855290	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs1539407	chr10:26855327-26855328	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs572575599	chr10:26855329-26855330	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs114140183	chr10:26855375-26855376	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs558502726	chr10:26855410-26855411	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs189602687	chr10:26855460-26855461	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs543841220	chr10:26855481-26855482	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs557280811	chr10:26855482-26855483	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs146039817	chr10:26855509-26855510	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs543106002	chr10:26855526-26855527	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs72481170	chr10:26855571-26855572	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs148266526	chr10:26855575-26855576	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:43)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Glioblastoma multiforme	21080181	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Phyllodes tumor	17334353	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Lung cancer	18438408	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
Oral cancer	21386901	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
T-cell lymphomas	19863542	CNVD
Esophageal cancer	21851588	CNVD
small cell lung cancer	20016488	CNVD
Behavioral abnormalities	21522184	CNVD
Dysmorphic features	21522184	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Myelofibrosis	22110671	CNVD
Autism	21439084	CNVD
Maculopathy	20981449	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Adrenocortical carcinoma	18281524	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
abnormal development	18461090	CNVD

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26834800-26858400	Strong transcription	Dnd41	blood
2	chr10:26839600-26860800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr10:26839800-26861200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr10:26840000-26860000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr10:26840200-26855200	Weak transcription	Placenta	Placenta
6	chr10:26840200-26863200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:26845000-26855600	Weak transcription	Esophagus	oesophagus
8	chr10:26845400-26863000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr10:26846000-26859600	Strong transcription	Primary B cells from cord blood	blood
10	chr10:26846200-26859000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:26846400-26860800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr10:26846400-26861600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr10:26846600-26858200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:26846600-26858400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:26846600-26859600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr10:26846600-26860800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr10:26846800-26859400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:26846800-26861200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr10:26846800-26863000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr10:26847600-26857400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:26848200-26861000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:26848400-26863000	Strong transcription	Fetal Thymus	thymus
23	chr10:26848600-26855600	Weak transcription	Gastric	stomach
24	chr10:26848800-26855400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr10:26848800-26857800	Strong transcription	Liver	Liver
26	chr10:26849000-26855400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
27	chr10:26849000-26855600	Strong transcription	Adipose Nuclei	Adipose
28	chr10:26849000-26857600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr10:26849000-26859000	Strong transcription	GM12878-XiMat	blood
30	chr10:26849000-26860600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:26849200-26855400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr10:26849200-26855400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr10:26849400-26855600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr10:26849400-26855600	Weak transcription	Pancreas	Pancrea
35	chr10:26849600-26855400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr10:26853000-26855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:26853400-26855200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:26853400-26856600	Strong transcription	Spleen	Spleen
39	chr10:26853800-26855200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr10:26854000-26860800	Strong transcription	Thymus	Thymus
41	chr10:26854600-26855600	Weak transcription	Lung	lung
42	chr10:26854600-26860200	Strong transcription	Primary T cells from cord blood	blood
43	chr10:26854800-26856400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:26855000-26859800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:26855200-26855400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:26855200-26855600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr10:26855200-26856000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr10:26855200-26856400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr10:26855200-26856800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr10:26855400-26855600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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