Variant report

Variant	rs976645
Chromosome Location	chr5:54182326-54182327
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: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10044930	0.88[ASN][1000 genomes]
rs10056452	0.86[EUR][1000 genomes]
rs10805469	0.81[EUR][1000 genomes]
rs10805470	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10940431	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs10940432	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10940434	0.88[EUR][1000 genomes]
rs11738151	0.88[EUR][1000 genomes]
rs11742711	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12515327	0.81[EUR][1000 genomes]
rs12657845	0.86[EUR][1000 genomes]
rs1560165	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs1560166	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17588816	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1965716	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1988528	0.95[ASN][1000 genomes]
rs1991498	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2017082	0.92[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2017318	0.92[ASN][1000 genomes]
rs2017540	0.92[ASN][1000 genomes]
rs2019005	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2195392	0.92[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs2195393	0.92[CEU][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2407758	0.95[ASN][1000 genomes]
rs28564901	0.86[EUR][1000 genomes]
rs2897758	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3916738	0.86[EUR][1000 genomes]
rs3935813	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4074332	0.87[JPT][hapmap]
rs4242047	0.82[EUR][1000 genomes]
rs4315891	0.82[ASN][1000 genomes]
rs4373237	0.82[ASN][1000 genomes]
rs4407587	0.82[ASN][1000 genomes]
rs4446420	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4502767	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4865586	0.80[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4865587	0.83[ASN][1000 genomes]
rs4865880	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4865882	0.88[EUR][1000 genomes]
rs4865883	0.92[ASN][1000 genomes]
rs6860824	0.87[JPT][hapmap]
rs6863705	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs734097	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737526	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7708368	0.84[ASN][1000 genomes]
rs7709516	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7734613	0.86[ASN][1000 genomes]
rs981978	0.92[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
rs976645	ITGA2	cis	parietal	SCAN
rs976645	ARL15	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54180400-54187800	Weak transcription	Gastric	stomach
2	chr5:54180800-54185200	Weak transcription	Fetal Heart	heart

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