Variant report

Variant	rs6876730
Chromosome Location	chr5:54091831-54091832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10064404	0.84[AMR][1000 genomes]
rs10066485	0.81[AMR][1000 genomes]
rs10072474	0.84[AMR][1000 genomes]
rs10074079	0.83[AMR][1000 genomes]
rs10075754	0.84[AMR][1000 genomes]
rs13436904	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13436919	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17346285	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2166355	0.80[EUR][1000 genomes]
rs35463987	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4274943	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4355479	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4380600	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4425466	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4472223	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4526067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4572962	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs55728436	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55944106	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56145198	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56202300	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56207018	0.85[EUR][1000 genomes]
rs56298453	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56386053	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57059470	0.96[EUR][1000 genomes]
rs57348772	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60775366	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450249	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66533726	0.81[EUR][1000 genomes]
rs66599423	0.81[EUR][1000 genomes]
rs66812968	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66955270	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67510332	0.80[EUR][1000 genomes]
rs6867643	0.85[EUR][1000 genomes]
rs72757444	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72757446	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72760107	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7710436	0.85[EUR][1000 genomes]
rs7733091	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7734384	0.89[AMR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6876730	ITGA2	cis	parietal	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	chr5:54087600-54103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:54087800-54092800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:54089000-54092000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:54091000-54103600	Weak transcription	Aorta	Aorta
6	chr5:54091400-54092000	Enhancers	Colon Smooth Muscle	Colon
7	chr5:54091600-54094600	Weak transcription	NHDF-Ad	bronchial

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