Variant report

Variant	rs11071089
Chromosome Location	chr15:54880431-54880432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10152907	0.82[CEU][hapmap]
rs10518774	0.85[CEU][hapmap]
rs11071093	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs12438101	0.83[ASN][1000 genomes]
rs12592949	0.85[CEU][hapmap]
rs1589316	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs16974859	0.82[CHB][hapmap]
rs16974861	0.83[CHB][hapmap]
rs1851006	0.93[CEU][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs2037385	0.85[CEU][hapmap]
rs2414324	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2414325	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs2414326	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs2553222	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2553223	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs35584128	0.84[ASN][1000 genomes]
rs3848140	0.84[EUR][1000 genomes]
rs7163424	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs8040048	0.84[ASN][1000 genomes]
rs8040060	0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs8040619	0.83[ASN][1000 genomes]
rs8040774	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs8041576	0.83[ASN][1000 genomes]
rs9920919	0.82[CEU][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv904236	chr15:54820897-54912439	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1039548	chr15:54856965-54914519	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv569508	chr15:54876212-54904782	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv526413	chr15:54876423-54904782	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11071089	SCG3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54871200-54882400	Weak transcription	Fetal Lung	lung
2	chr15:54873800-54880800	Strong transcription	Fetal Heart	heart

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