Variant report

Variant	rs12908409
Chromosome Location	chr15:54548816-54548817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10518760	0.84[EUR][1000 genomes]
rs11071064	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11638986	0.83[CHB][hapmap];0.82[YRI][hapmap]
rs11856476	0.84[EUR][1000 genomes]
rs12899415	0.83[EUR][1000 genomes]
rs12899426	0.83[EUR][1000 genomes]
rs12901994	0.85[CEU][hapmap]
rs12902112	0.81[EUR][1000 genomes]
rs12902524	0.85[CHB][hapmap]
rs12903779	0.84[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes]
rs12906606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907062	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908083	0.85[CHB][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12911007	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911506	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917198	0.83[CHB][hapmap]
rs1807348	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414287	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414289	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34057643	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4517736	0.81[ASW][hapmap];0.85[CHB][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6493667	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68018837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172577	0.85[CHB][hapmap]
rs8024165	0.85[CEU][hapmap]
rs8025731	0.84[EUR][1000 genomes]
rs8026128	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs8028549	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036716	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs8037101	0.91[CHB][hapmap]
rs8039848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12908409	USP8	cis	parietal	SCAN
rs12908409	GALK2	cis	parietal	SCAN
rs12908409	ATP8B4	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54519000-54554400	Weak transcription	Aorta	Aorta
2	chr15:54519400-54549600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:54542600-54549800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:54547000-54652600	Weak transcription	Fetal Lung	lung

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