Variant report

Variant	rs200879585
Chromosome Location	chr13:53419774-53419775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:53225538..53227071-chr13:53417980..53420315,2	MCF-7	breast:
2	chr13:53419539..53420191-chr13:53542097..53542726,2	MCF-7	breast:
3	chr13:53237822..53239845-chr13:53418461..53420570,2	MCF-7	breast:
4	chr13:53416128..53422445-chr13:53423052..53427915,11	MCF-7	breast:
5	chr13:53419410..53422161-chr13:53423908..53427048,5	MCF-7	breast:
6	chr13:53226555..53228977-chr13:53419370..53422779,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900089	chr13:53385334-53429453	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1810064	chr13:53412849-53441018	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1822518	chr13:53412849-53441018	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv1829072	chr13:53412849-53441018	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
7	esv1821449	chr13:53417010-53422112	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv523092	chr13:53419139-53429453	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	esv3405352	chr13:53419176-53421724	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53418400-53422400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:53418600-53419800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:53418600-53419800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr13:53418600-53419800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
5	chr13:53418600-53420800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
6	chr13:53418600-53420800	Bivalent Enhancer	Spleen	Spleen
7	chr13:53418600-53421800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:53418800-53420600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
9	chr13:53418800-53422800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:53418800-53422800	Enhancers	Pancreas	Pancrea
11	chr13:53419000-53420400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
12	chr13:53419000-53420400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
13	chr13:53419000-53420600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
14	chr13:53419200-53419800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
15	chr13:53419200-53420200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:53419200-53420800	Bivalent Enhancer	Fetal Thymus	thymus
17	chr13:53419400-53419800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
18	chr13:53419400-53420200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr13:53419400-53420200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr13:53419400-53420200	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr13:53419400-53420400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr13:53419400-53420400	Bivalent/Poised TSS	Right Ventricle	heart
23	chr13:53419400-53421000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr13:53419400-53422000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr13:53419400-53422200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr13:53419400-53422600	Bivalent Enhancer	Lung	lung
27	chr13:53419400-53422800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr13:53419400-53423000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr13:53419400-53423200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr13:53419400-53423200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr13:53419400-53423200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
32	chr13:53419600-53419800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr13:53419600-53419800	Active TSS	Primary hematopoietic stem cells	blood
34	chr13:53419600-53419800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:53419600-53419800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:53419600-53419800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
37	chr13:53419600-53419800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
38	chr13:53419600-53420000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr13:53419600-53420000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
40	chr13:53419600-53420000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
41	chr13:53419600-53420200	Bivalent Enhancer	Fetal Stomach	stomach
42	chr13:53419600-53420600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr13:53419600-53421000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr13:53419600-53421000	Enhancers	Gastric	stomach
45	chr13:53419600-53421200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
46	chr13:53419600-53421200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
47	chr13:53419600-53421400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:53419600-53422400	Bivalent Enhancer	Fetal Brain Male	brain
49	chr13:53419600-53422600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr13:53419600-53422600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links