Variant report

Variant	rs7716613
Chromosome Location	chr5:52406642-52406643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:52406602-52406959	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:52406511-52406708	MCF10A-Er-Src	breast:	n/a	n/a
3	MAFF	chr5:52406295-52407295	K562	blood:	n/a	chr5:52407152-52407170
4	RCOR1	chr5:52406216-52406913	K562	blood:	n/a	n/a
5	POLR2A	chr5:52405161-52407007	Raji	blood:	n/a	n/a
6	POLR2A	chr5:52404935-52407094	GM12891	blood:	n/a	n/a
7	POLR2A	chr5:52404892-52406923	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52384729..52387843-chr5:52404184..52407459,4	MCF-7	breast:
2	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:

Variant related genes	Relation type
MOCS2	TF binding region
ENSG00000272123	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10057053	1.00[AMR][1000 genomes]
rs10065679	1.00[AMR][1000 genomes]
rs58822425	1.00[AMR][1000 genomes]
rs73105574	1.00[AMR][1000 genomes]
rs73111446	1.00[AMR][1000 genomes]
rs73756622	1.00[AMR][1000 genomes]
rs7727367	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv442948	chr5:52404519-52409439	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52404600-52407000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr5:52404800-52406800	Active TSS	Pancreas	Pancrea
3	chr5:52405000-52406800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:52405000-52407000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:52405000-52407000	Active TSS	Brain Substantia Nigra	brain
6	chr5:52405000-52407000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:52405200-52406800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:52405200-52406800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:52405600-52407000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:52405800-52406800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr5:52405800-52407000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:52405800-52407000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:52405800-52407000	Flanking Active TSS	Liver	Liver
14	chr5:52405800-52407000	Flanking Active TSS	Dnd41	blood
15	chr5:52406000-52407000	Enhancers	Small Intestine	intestine
16	chr5:52406000-52407000	Flanking Active TSS	NHEK	skin
17	chr5:52406000-52414200	Weak transcription	Gastric	stomach
18	chr5:52406200-52406800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:52406200-52406800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:52406200-52406800	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr5:52406200-52406800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr5:52406200-52406800	Flanking Active TSS	Osteobl	bone
23	chr5:52406200-52407000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:52406200-52407000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr5:52406200-52410200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:52406200-52411400	Weak transcription	Aorta	Aorta
27	chr5:52406400-52406800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr5:52406400-52406800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr5:52406400-52406800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:52406400-52406800	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:52406400-52406800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:52406400-52406800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr5:52406400-52406800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:52406400-52406800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:52406400-52406800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:52406400-52406800	Enhancers	Adipose Nuclei	Adipose
37	chr5:52406400-52406800	Enhancers	Brain Anterior Caudate	brain
38	chr5:52406400-52406800	Active TSS	Brain Germinal Matrix	brain
39	chr5:52406400-52406800	Enhancers	Fetal Intestine Large	intestine
40	chr5:52406400-52406800	Enhancers	Stomach Mucosa	stomach
41	chr5:52406400-52406800	Flanking Active TSS	GM12878-XiMat	blood
42	chr5:52406400-52406800	Flanking Active TSS	Hela-S3	cervix
43	chr5:52406400-52407000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:52406400-52407000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr5:52406400-52407000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr5:52406400-52407000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:52406400-52407000	Enhancers	Brain Cingulate Gyrus	brain
48	chr5:52406400-52407000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr5:52406400-52407000	Enhancers	Fetal Heart	heart
50	chr5:52406400-52407000	Enhancers	Fetal Lung	lung

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