Variant report

Variant	rs3111520
Chromosome Location	chr5:179654017-179654018
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2386698	1.00[AFR][1000 genomes]
rs3099061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3099064	1.00[AMR][1000 genomes]
rs3111522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3111523	1.00[AFR][1000 genomes]
rs3111530	1.00[AFR][1000 genomes]
rs35997361	1.00[AMR][1000 genomes]
rs73811338	1.00[AMR][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:33 , 50 per page) page: 1

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	chr5:179647800-179656600	Weak transcription	Brain Anterior Caudate	brain
6	chr5:179649600-179657800	Weak transcription	Brain Germinal Matrix	brain
7	chr5:179649600-179660200	Weak transcription	Fetal Brain Female	brain
8	chr5:179650200-179655800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:179650200-179669000	Weak transcription	Fetal Brain Male	brain
10	chr5:179651600-179678000	Weak transcription	Fetal Heart	heart
11	chr5:179652000-179660000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:179652400-179660200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:179652800-179655800	Weak transcription	Primary B cells from cord blood	blood
14	chr5:179652800-179659000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:179653000-179654800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:179653000-179662800	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:179653200-179655000	Weak transcription	Primary T cells from cord blood	blood
18	chr5:179653200-179660000	Weak transcription	Fetal Lung	lung
19	chr5:179653400-179654200	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr5:179653400-179654400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
21	chr5:179653600-179654200	ZNF genes & repeats	Placenta	Placenta
22	chr5:179653600-179654400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
23	chr5:179653600-179654400	Strong transcription	Right Ventricle	heart
24	chr5:179653600-179662400	Weak transcription	Brain Substantia Nigra	brain
25	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:179653800-179659400	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:179653800-179662000	Weak transcription	Fetal Thymus	thymus
28	chr5:179654000-179655800	Weak transcription	Fetal Stomach	stomach
29	chr5:179654000-179655800	Weak transcription	Pancreas	Pancrea
30	chr5:179654000-179658400	Weak transcription	Left Ventricle	heart
31	chr5:179654000-179659000	Weak transcription	Ovary	ovary
32	chr5:179654000-179660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:179654000-179661800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links