Variant report

Variant	rs719211
Chromosome Location	chr15:54523909-54523910
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	chr15:54520149..54522088-chr15:54523753..54525995,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10518760	0.85[ASN][1000 genomes]
rs11071065	0.87[CEU][hapmap]
rs11071066	0.88[CEU][hapmap]
rs11630366	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs11630766	0.91[CEU][hapmap]
rs11635437	0.88[CEU][hapmap]
rs11635678	0.89[EUR][1000 genomes]
rs11856476	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12439702	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs12441013	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs12899415	0.85[ASN][1000 genomes]
rs12899426	0.85[ASN][1000 genomes]
rs12902112	0.85[ASN][1000 genomes]
rs12902524	0.84[CEU][hapmap]
rs12903297	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs12903779	0.82[CEU][hapmap]
rs12906904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907862	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12908083	0.84[CEU][hapmap]
rs12914912	0.87[CEU][hapmap]
rs12916984	0.84[CEU][hapmap]
rs12917198	0.84[CEU][hapmap]
rs2414285	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs2414288	0.90[CEU][hapmap]
rs4144949	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs4517736	0.84[CEU][hapmap]
rs4774689	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774691	0.88[CEU][hapmap]
rs4776215	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776216	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776220	0.84[CEU][hapmap]
rs4776222	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs5025252	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs6493669	0.92[CEU][hapmap]
rs6493670	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs7162346	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172577	0.84[CEU][hapmap]
rs7183052	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183952	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023723	0.91[EUR][1000 genomes]
rs8025731	0.85[ASN][1000 genomes]
rs8027105	0.89[EUR][1000 genomes]
rs8030298	0.90[EUR][1000 genomes]
rs8032432	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033291	0.88[EUR][1000 genomes]
rs8034428	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1043666	chr15:54415970-54548495	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1043823	chr15:54468477-54532985	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs719211	VBP1	trans	cerebellum	SCAN
rs719211	COPS2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54516800-54529000	Weak transcription	Fetal Lung	lung
2	chr15:54519000-54554400	Weak transcription	Aorta	Aorta
3	chr15:54519400-54549600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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