Variant report

Variant	rs4472223
Chromosome Location	chr5:54087671-54087672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10064404	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs10066485	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10072474	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs10074079	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10075754	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs13436904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13436919	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17346285	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2121130	0.82[EUR][1000 genomes]
rs2166355	0.83[EUR][1000 genomes]
rs35463987	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4274943	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4355479	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4380600	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4425466	0.95[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4526067	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4572962	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55728436	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55944106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56145198	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56202300	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56207018	0.88[EUR][1000 genomes]
rs56298453	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56386053	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57059470	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs57348772	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60775366	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6450249	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66533726	0.83[EUR][1000 genomes]
rs66599423	0.84[EUR][1000 genomes]
rs66812968	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66955270	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67510332	0.83[EUR][1000 genomes]
rs6867643	0.88[EUR][1000 genomes]
rs6876730	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6897534	0.82[EUR][1000 genomes]
rs72757444	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72757446	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72760107	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7703792	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7710436	0.88[EUR][1000 genomes]
rs7733091	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7734384	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2754136	chr5:54083387-54107727	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4472223	ITGA2	cis	parietal	SCAN
rs4472223	ARL15	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54073000-54097600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:54082000-54088600	Weak transcription	Fetal Stomach	stomach
3	chr5:54083200-54088000	Weak transcription	Fetal Heart	heart
4	chr5:54083200-54088800	Weak transcription	Aorta	Aorta
5	chr5:54087400-54090400	Enhancers	Fetal Muscle Leg	muscle
6	chr5:54087600-54088400	Enhancers	Fetal Muscle Trunk	muscle
7	chr5:54087600-54103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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