Variant report

Variant	rs58654424
Chromosome Location	chr9:98792909-98792910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98783900..98786083-chr9:98790874..98793453,2	K562	blood:
2	chr9:98790389..98794152-chr9:98794649..98798124,5	K562	blood:

Variant related genes	Relation type
ENSG00000225194	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs16910333	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16910342	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16910409	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16910427	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2297009	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2423	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3739755	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3739756	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4742801	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4743383	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4743460	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4743469	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743507	1.00[AFR][1000 genomes]
rs4743508	1.00[AFR][1000 genomes]
rs55797980	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55849673	1.00[AFR][1000 genomes]
rs55865494	0.87[AMR][1000 genomes]
rs55881510	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55888215	1.00[AFR][1000 genomes]
rs56063686	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56110216	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56319412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56372801	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56403401	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57096664	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57287260	1.00[AFR][1000 genomes]
rs59189545	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60351339	1.00[AFR][1000 genomes]
rs9792431	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9792684	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58654424	NCRNA00092	cis	cerebellar cortex	BrainEAC

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98789800-98793200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr9:98790000-98793600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:98790200-98793000	Weak transcription	Lung	lung
4	chr9:98790200-98793000	Weak transcription	Pancreas	Pancrea
5	chr9:98790200-98793200	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:98790200-98793200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:98790200-98793400	Weak transcription	Right Ventricle	heart
8	chr9:98790200-98795800	Weak transcription	Esophagus	oesophagus
9	chr9:98790400-98793000	Weak transcription	Right Atrium	heart
10	chr9:98790400-98793800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:98790400-98794200	Weak transcription	Spleen	Spleen
12	chr9:98790600-98793200	Weak transcription	Brain Anterior Caudate	brain
13	chr9:98790800-98793400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:98790800-98810800	Weak transcription	Brain Angular Gyrus	brain
15	chr9:98791000-98793000	Weak transcription	Fetal Lung	lung
16	chr9:98791200-98793200	Weak transcription	Brain Substantia Nigra	brain
17	chr9:98791200-98796800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:98792000-98795200	Enhancers	Ovary	ovary
19	chr9:98792200-98793400	Weak transcription	A549	lung
20	chr9:98792600-98793600	Weak transcription	Fetal Intestine Small	intestine
21	chr9:98792600-98794400	Enhancers	Fetal Stomach	stomach
22	chr9:98792600-98794600	Enhancers	Gastric	stomach
23	chr9:98792800-98793200	Weak transcription	Aorta	Aorta
24	chr9:98792800-98794600	Enhancers	Liver	Liver

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