Variant report

Variant	rs4865879
Chromosome Location	chr5:54160345-54160346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:54158673..54160817-chr5:54181128..54182793,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10040872	0.94[ASN][1000 genomes]
rs10042734	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1005622	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10056452	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10805470	0.93[EUR][1000 genomes]
rs10940430	0.99[ASN][1000 genomes]
rs10940431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940434	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11738151	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11742711	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11953607	0.99[ASN][1000 genomes]
rs12657845	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13181749	0.99[ASN][1000 genomes]
rs1560165	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560166	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560167	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17588816	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1965716	0.93[EUR][1000 genomes]
rs2017082	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2019005	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2195392	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2195393	0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28564901	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2897758	0.89[EUR][1000 genomes]
rs3916738	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3935813	0.83[EUR][1000 genomes]
rs4242050	0.94[ASN][1000 genomes]
rs4320216	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4446420	0.86[EUR][1000 genomes]
rs4502767	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4865880	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865881	0.99[ASN][1000 genomes]
rs4865882	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs734097	0.92[EUR][1000 genomes]
rs737526	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7709516	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4865879	ITGA2	cis	parietal	SCAN
rs4865879	ARL15	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54155800-54163000	Weak transcription	Aorta	Aorta
2	chr5:54158200-54163000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:54158200-54163000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:54158200-54163000	Weak transcription	Ovary	ovary
5	chr5:54158200-54166600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:54158400-54163000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:54158400-54163000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:54158400-54163000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:54158800-54163000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:54159200-54162200	Weak transcription	NHLF	lung

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