Variant report

Variant	rs58528869
Chromosome Location	chr5:179657184-179657185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179657151-179657569	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:179657104-179657359	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:179656582-179657701	MCF-7	breast:	n/a	n/a
4	POLR2A	chr5:179657157-179657435	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179656618..179658945-chr5:179717672..179719756,2	MCF-7	breast:
2	chr5:179646868..179648525-chr5:179656321..179659011,2	K562	blood:
3	chr5:179655112..179657294-chr5:179678114..179680572,2	MCF-7	breast:
4	chr5:179653930..179656240-chr5:179656674..179659051,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229721	TF binding region
ENSG00000050748	Chromatin interaction
ENSG00000229721	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1127575	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955223	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4362908	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481314	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56131100	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61478999	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6601104	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6703	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6860142	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710896	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7726664	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9605	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179645600-179660200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:179646800-179659200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:179647600-179659800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:179647600-179660200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:179649600-179657800	Weak transcription	Brain Germinal Matrix	brain
6	chr5:179649600-179660200	Weak transcription	Fetal Brain Female	brain
7	chr5:179650200-179669000	Weak transcription	Fetal Brain Male	brain
8	chr5:179651600-179678000	Weak transcription	Fetal Heart	heart
9	chr5:179652000-179660000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:179652400-179660200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:179652800-179659000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:179653000-179662800	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:179653200-179660000	Weak transcription	Fetal Lung	lung
14	chr5:179653600-179662400	Weak transcription	Brain Substantia Nigra	brain
15	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:179653800-179659400	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:179653800-179662000	Weak transcription	Fetal Thymus	thymus
18	chr5:179654000-179658400	Weak transcription	Left Ventricle	heart
19	chr5:179654000-179659000	Weak transcription	Ovary	ovary
20	chr5:179654000-179660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:179654000-179661800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:179654200-179659000	Weak transcription	Placenta	Placenta
23	chr5:179654200-179660400	Weak transcription	Fetal Intestine Small	intestine
24	chr5:179654400-179660800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:179654800-179660800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:179655000-179657400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:179655000-179679600	Weak transcription	Stomach Mucosa	stomach
28	chr5:179655200-179657400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:179655200-179658400	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:179655200-179663200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr5:179655400-179658000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:179655400-179660600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
34	chr5:179655800-179657400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
35	chr5:179655800-179657600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:179655800-179659400	ZNF genes & repeats	Pancreas	Pancrea
37	chr5:179655800-179661600	ZNF genes & repeats	Lung	lung
38	chr5:179655800-179666400	ZNF genes & repeats	Aorta	Aorta
39	chr5:179655800-179675400	Strong transcription	Primary B cells from cord blood	blood
40	chr5:179656000-179657200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:179656000-179659400	ZNF genes & repeats	Gastric	stomach
42	chr5:179656200-179659200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:179656200-179660200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:179656200-179675000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:179656400-179657400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
46	chr5:179656400-179657400	Weak transcription	Fetal Stomach	stomach
47	chr5:179656400-179658000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:179656400-179658400	Weak transcription	Primary T cells from cord blood	blood
49	chr5:179656400-179658800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:179656400-179659200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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