Variant report

Variant	rs6867643
Chromosome Location	chr5:54055062-54055063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:54053223..54055714-chr5:54058772..54060813,2	K562	blood:
2	chr5:54053223..54055714-chr5:54058237..54060813,3	K562	blood:
3	chr5:54049192..54051114-chr5:54052944..54055675,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13436904	0.85[EUR][1000 genomes]
rs13436919	0.85[EUR][1000 genomes]
rs17346285	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2121130	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2166355	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35463987	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4274943	0.85[EUR][1000 genomes]
rs4355479	0.85[EUR][1000 genomes]
rs4380600	0.85[EUR][1000 genomes]
rs4425466	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4472223	0.88[EUR][1000 genomes]
rs4526067	0.88[EUR][1000 genomes]
rs4572962	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55728436	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55944106	0.87[EUR][1000 genomes]
rs56145198	0.88[EUR][1000 genomes]
rs56202300	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56207018	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56298453	0.87[EUR][1000 genomes]
rs56386053	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57059470	0.86[EUR][1000 genomes]
rs57348772	0.84[EUR][1000 genomes]
rs60775366	0.85[EUR][1000 genomes]
rs6450249	0.88[EUR][1000 genomes]
rs66533726	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66599423	0.96[EUR][1000 genomes]
rs66812968	0.89[EUR][1000 genomes]
rs67510332	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6876730	0.85[EUR][1000 genomes]
rs6897534	0.91[EUR][1000 genomes]
rs72757444	0.89[EUR][1000 genomes]
rs72757446	0.88[EUR][1000 genomes]
rs72760107	0.85[EUR][1000 genomes]
rs7710436	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7734384	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6867643	ITGA2	cis	parietal	SCAN
rs6867643	ARL15	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54044800-54056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:54049000-54056200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:54049200-54056200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:54049200-54057000	Weak transcription	Fetal Heart	heart
5	chr5:54049400-54055200	Weak transcription	Aorta	Aorta
6	chr5:54049400-54056400	Weak transcription	Left Ventricle	heart
7	chr5:54052200-54059800	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:54052600-54058600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:54052600-54058800	Enhancers	NHDF-Ad	bronchial
10	chr5:54053000-54055200	Weak transcription	Primary B cells from cord blood	blood
11	chr5:54053200-54056000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:54053200-54057000	Weak transcription	Ovary	ovary
13	chr5:54053800-54056000	Weak transcription	HMEC	breast
14	chr5:54053800-54056600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:54054000-54055200	Weak transcription	Brain Anterior Caudate	brain
16	chr5:54054200-54055200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:54054200-54055200	Weak transcription	NHLF	lung
18	chr5:54054200-54056000	Weak transcription	HSMM	muscle
19	chr5:54054200-54056000	Weak transcription	HSMMtube	muscle
20	chr5:54054400-54055200	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:54054400-54055400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:54054400-54056000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:54054400-54056600	Weak transcription	NH-A	brain
24	chr5:54054800-54055200	Weak transcription	Osteobl	bone
25	chr5:54055000-54056200	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr5:54055000-54057200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:54055000-54058400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:54055000-54058600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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