Variant report

Variant	esv1821449
Chromosome Location	chr13:53417010-53422112
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:2)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:53239189..53240278-chr13:53420342..53420888,4	MCF-7	breast:
2	chr13:53383426..53384206-chr13:53419815..53420378,2	MCF-7	breast:
3	chr13:53239322..53239980-chr13:53420318..53420910,2	MCF-7	breast:
4	chr13:53419410..53422161-chr13:53423908..53427048,5	MCF-7	breast:
5	chr13:53419539..53420191-chr13:53542097..53542726,2	MCF-7	breast:
6	chr13:53225538..53227071-chr13:53417980..53420315,2	MCF-7	breast:
7	chr13:53237822..53239845-chr13:53418461..53420570,2	MCF-7	breast:
8	chr13:53416128..53422445-chr13:53423052..53427915,11	MCF-7	breast:
9	chr13:53317860..53318834-chr13:53420019..53420858,3	MCF-7	breast:
10	chr13:53226555..53228977-chr13:53419370..53422779,3	MCF-7	breast:

No data

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

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	PCDH8	hsa-miR-200a-3p	chr13:53418620-53418644
2	PCDH8	hsa-miR-200a-3p	chr13:53418431-53418452

Variant related genes	Relation type
ENSG00000165416	chromatin interactions
ENSG00000211579	chromatin interactions

Extended variants
information (count: 199 )
Associated
traits (count: 112 )

Variant overlapped rSNPs/rCNVs (count:199 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1359046	chr13:53417010-53417011	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs571577033	chr13:53417077-53417078	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs533737751	chr13:53417100-53417101	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs369961629	chr13:53417130-53417131	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
5	rs183923693	chr13:53417133-53417134	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs188205736	chr13:53417134-53417135	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
7	rs181428575	chr13:53417135-53417136	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs57622965	chr13:53417167-53417168	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs576227544	chr13:53417169-53417170	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs545238487	chr13:53417179-53417180	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs558778770	chr13:53417182-53417183	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs572670143	chr13:53417183-53417184	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs148176477	chr13:53417308-53417309	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs561110053	chr13:53417338-53417339	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs374511804	chr13:53417340-53417341	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs144059835	chr13:53417429-53417430	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs543928257	chr13:53417442-53417443	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs563811699	chr13:53417460-53417461	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs531490787	chr13:53417470-53417471	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs4635226	chr13:53417473-53417474	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs551607476	chr13:53417509-53417510	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs141498454	chr13:53417553-53417554	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs571540462	chr13:53417579-53417580	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs527608678	chr13:53417590-53417591	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs185670497	chr13:53417629-53417630	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs191617394	chr13:53417631-53417632	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs536291963	chr13:53417689-53417690	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs555832137	chr13:53417692-53417693	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs569422230	chr13:53417721-53417722	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs147305375	chr13:53417752-53417753	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs558742117	chr13:53417808-53417809	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs572634591	chr13:53417871-53417872	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs368768568	chr13:53417908-53417909	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs373026343	chr13:53417913-53417914	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs534983127	chr13:53417919-53417920	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs117052615	chr13:53417947-53417948	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs574730357	chr13:53417951-53417952	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs543845547	chr13:53418143-53418144	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs181612605	chr13:53418158-53418159	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs577438570	chr13:53418191-53418192	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs545192193	chr13:53418219-53418220	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs564918682	chr13:53418238-53418239	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs527509496	chr13:53418302-53418303	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs187299535	chr13:53418379-53418380	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs533754235	chr13:53418434-53418435	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region miRNA target site	2 gene(s)	Overlapped CNVs	n/a
46	rs529603947	chr13:53418457-53418458	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs549387106	chr13:53418458-53418459	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs569376094	chr13:53418497-53418498	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs538330769	chr13:53418617-53418618	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs576979595	chr13:53418633-53418634	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:112)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Burkitt''s lymphoma	18698080	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Squamous cell cancer	20885788	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Thyroid cancer	19087340	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Colorectal cancer	16774939	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Myoepithelioma	18604193	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Paraganglioma	21461997	CNVD
Pheochromocytoma	21461997	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Prostate cancer	19242612	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	17245344	CNVD
Colorectal cancer	21586687	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Retinoblastoma	19183342	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Developmental delay	21147756	CNVD
Melanoma	18172304	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Multiple myeloma	19135901	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Prostate cancer	16461572	CNVD
Merkel cell carcinoma	19020549	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
lymphocytic leukemia	21291569	CNVD
Multiple myeloma	17550852	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21858162	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute myeloid leukemia	17237825	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	21922591	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Congenital anomalies of the kidney and urinary tract	20467480	CNVD
Gastric cancer	17908304	CNVD
Breast cancer	18852474	CNVD
Myelofibrosis	22110671	CNVD
craniofacial dysmorphism	21918468	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21750150	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Breast cancer	17393978	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Liposarcoma	21253554	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Urothelial carcinoma	21177765	CNVD
Prostate cancer	22341455	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:289 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53409200-53418800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:53413200-53418800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:53413200-53419200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:53416000-53418800	Weak transcription	Pancreas	Pancrea
5	chr13:53416400-53417200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:53416400-53417200	Bivalent Enhancer	Brain Germinal Matrix	brain
7	chr13:53416400-53417800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr13:53416600-53417200	Enhancers	HepG2	liver
9	chr13:53416800-53418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:53417000-53417200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:53417000-53417200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:53417000-53417600	Enhancers	Fetal Brain Female	brain
13	chr13:53417200-53417600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:53417200-53418600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:53417600-53418400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:53417800-53418600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr13:53418400-53422400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:53418600-53419200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:53418600-53419200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
20	chr13:53418600-53419400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr13:53418600-53419400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
22	chr13:53418600-53419400	Bivalent Enhancer	Fetal Brain Male	brain
23	chr13:53418600-53419800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr13:53418600-53419800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr13:53418600-53419800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
26	chr13:53418600-53420800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
27	chr13:53418600-53420800	Bivalent Enhancer	Spleen	Spleen
28	chr13:53418600-53421800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:53418800-53419000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:53418800-53419600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr13:53418800-53420600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
32	chr13:53418800-53422800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr13:53418800-53422800	Enhancers	Pancreas	Pancrea
34	chr13:53419000-53419200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr13:53419000-53419200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr13:53419000-53419400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr13:53419000-53419400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:53419000-53419400	Bivalent Enhancer	Right Ventricle	heart
39	chr13:53419000-53420400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
40	chr13:53419000-53420400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
41	chr13:53419000-53420600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
42	chr13:53419200-53419400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
43	chr13:53419200-53419400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
44	chr13:53419200-53419600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
45	chr13:53419200-53419800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr13:53419200-53420200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:53419200-53420800	Bivalent Enhancer	Fetal Thymus	thymus
48	chr13:53419400-53419600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
49	chr13:53419400-53419600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr13:53419400-53419600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links