Variant report

Variant	rs2470890
Chromosome Location	chr15:75047426-75047427
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	chr15:75047044..75048904-chr15:75049609..75051209,2	K562	blood:
2	chr15:74938979..74941178-chr15:75046252..75049001,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11072507	0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072508	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11630478	0.84[AMR][1000 genomes]
rs11632414	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635664	0.82[AMR][1000 genomes]
rs11854147	0.83[CEU][hapmap]
rs11857376	0.88[AFR][1000 genomes]
rs12591513	0.84[AMR][1000 genomes]
rs12594062	0.84[AMR][1000 genomes]
rs12898997	0.82[AMR][1000 genomes]
rs12903541	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12903896	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905199	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12909307	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1378940	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1378941	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1378942	0.89[ASW][hapmap];0.83[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2168518	0.89[ASW][hapmap];0.83[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2472299	0.80[CEU][hapmap]
rs2472304	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960192	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34862454	0.84[AMR][1000 genomes]
rs35206230	0.84[AMR][1000 genomes]
rs3784789	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886410	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs762551	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2470890	SCAMP5	cis	Artery Tibial	GTEx
rs2470890	ULK3	cis	multi-tissue	Pritchard
rs2470890	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75043800-75051200	Weak transcription	HepG2	liver
2	chr15:75044800-75062600	Weak transcription	Right Atrium	heart
3	chr15:75045400-75047600	Strong transcription	Liver	Liver
4	chr15:75045600-75053600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:75047200-75063000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:75047400-75054000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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