Variant report

Variant	rs4425466
Chromosome Location	chr5:54064575-54064576
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:54061560..54063270-chr5:54063643..54065154,2	K562	blood:
2	chr5:53813350..53815474-chr5:54061824..54064648,2	MCF-7	breast:
3	chr5:54036001..54038527-chr5:54062839..54065440,2	MCF-7	breast:
4	chr5:53812258..53815199-chr5:54063024..54066576,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178996	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13436904	0.86[EUR][1000 genomes]
rs13436919	0.86[EUR][1000 genomes]
rs17346285	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2121130	0.93[EUR][1000 genomes]
rs2166355	0.94[EUR][1000 genomes]
rs35463987	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4274943	0.86[EUR][1000 genomes]
rs4355479	0.86[EUR][1000 genomes]
rs4380600	0.86[EUR][1000 genomes]
rs4472223	0.89[EUR][1000 genomes]
rs4526067	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4572962	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55728436	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55944106	0.88[EUR][1000 genomes]
rs56145198	0.89[EUR][1000 genomes]
rs56202300	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56207018	0.99[EUR][1000 genomes]
rs56298453	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56386053	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57059470	0.86[EUR][1000 genomes]
rs57348772	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60775366	0.86[EUR][1000 genomes]
rs6450249	0.89[EUR][1000 genomes]
rs66533726	0.95[EUR][1000 genomes]
rs66599423	0.95[EUR][1000 genomes]
rs66812968	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67510332	0.94[EUR][1000 genomes]
rs6867643	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6876730	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6897534	0.90[EUR][1000 genomes]
rs72757444	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72757446	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72760107	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7710436	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7734384	0.86[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	nsv880717	chr5:54025701-54106378	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4425466	ITGA2	cis	parietal	SCAN
rs4425466	ARL15	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54060600-54070000	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:54061000-54070400	Weak transcription	NHLF	lung
3	chr5:54061200-54067000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:54064000-54064800	Enhancers	HSMMtube	muscle
5	chr5:54064200-54067000	Weak transcription	Primary B cells from peripheral blood	blood

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