Variant report

Variant	rs16956956
Chromosome Location	chr15:72743458-72743459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10438370	0.82[EUR][1000 genomes]
rs10518988	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11072372	0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11638897	0.82[EUR][1000 genomes]
rs12439127	0.82[EUR][1000 genomes]
rs12900846	0.85[CEU][hapmap]
rs12901966	0.82[EUR][1000 genomes]
rs16957064	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16957095	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16957189	1.00[CEU][hapmap]
rs1812842	0.82[EUR][1000 genomes]
rs1963894	0.82[EUR][1000 genomes]
rs2415135	0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2415137	0.82[EUR][1000 genomes]
rs28393893	0.92[EUR][1000 genomes]
rs35855297	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3842946	0.82[EUR][1000 genomes]
rs4146286	0.82[EUR][1000 genomes]
rs4777517	0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]
rs60702445	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7162856	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174825	0.86[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]
rs7175376	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72735120	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs72735137	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72735139	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72735141	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72735149	0.85[EUR][1000 genomes]
rs72735156	1.00[EUR][1000 genomes]
rs72735160	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72735166	1.00[EUR][1000 genomes]
rs72735170	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72735173	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72735181	0.91[EUR][1000 genomes]
rs72735185	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72735188	0.83[EUR][1000 genomes]
rs8023504	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8024715	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs8025088	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs8026681	0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs8037282	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
3	nsv534037	chr15:72659210-72964029	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv469704	chr15:72669374-72853927	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
5	nsv482685	chr15:72669374-72853927	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv976949	chr15:72737860-72743854	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1050558	chr15:72739150-72860350	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv542427	chr15:72739150-72860350	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16956956	PRPH2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72743200-72743600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:72743200-72743800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:72743400-72743600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:72743400-72744000	Flanking Bivalent TSS/Enh	HepG2	liver

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