Variant report

Variant	rs5025252
Chromosome Location	chr15:54557102-54557103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10851563	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851564	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11071065	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11071066	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11630366	0.92[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11630766	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs11635242	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11635437	0.96[CEU][hapmap]
rs12439702	0.92[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs12441013	0.88[CEU][hapmap]
rs12900325	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12902524	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs12903297	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12903779	0.82[CEU][hapmap]
rs12908083	0.84[CEU][hapmap]
rs12914912	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916984	0.84[CEU][hapmap]
rs12917198	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs2414285	0.92[CEU][hapmap];0.86[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2414288	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2414292	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4144949	0.92[CEU][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs4517736	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs4569201	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774690	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4774691	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776216	0.88[CEU][hapmap]
rs4776219	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.87[LWK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4776220	0.84[CEU][hapmap]
rs4776222	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5027653	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58301914	0.82[EUR][1000 genomes]
rs6493669	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493670	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7162346	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs7169339	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7170994	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7172577	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs7176603	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7183952	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs8026128	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs8030563	0.96[EUR][1000 genomes]
rs8031083	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs8032432	0.88[CEU][hapmap]
rs8034428	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038466	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1845471	chr15:54556063-54685463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5025252	USP50	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54547000-54652600	Weak transcription	Fetal Lung	lung

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