Variant report

Variant	rs12715708
Chromosome Location	chr4:62994770-62994771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10006606	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10013024	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10017162	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10023749	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10030005	0.84[EUR][1000 genomes]
rs10030906	0.87[ASN][1000 genomes]
rs10032372	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10033565	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11131359	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12642767	0.94[ASN][1000 genomes]
rs12645804	0.83[ASN][1000 genomes]
rs13108623	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13122283	0.81[ASN][1000 genomes]
rs13138506	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1563796	0.83[EUR][1000 genomes]
rs17082585	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2160498	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2193118	0.88[ASN][1000 genomes]
rs2193121	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2193122	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2216198	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2344677	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922274	0.84[ASN][1000 genomes]
rs4397024	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4446347	0.84[ASN][1000 genomes]
rs4464598	0.81[ASN][1000 genomes]
rs4510488	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4549412	0.83[ASN][1000 genomes]
rs4860107	0.90[ASN][1000 genomes]
rs4860454	0.87[ASN][1000 genomes]
rs58634974	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6551678	0.88[ASN][1000 genomes]
rs6551682	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6551685	0.83[EUR][1000 genomes]
rs66917394	0.97[ASN][1000 genomes]
rs67603454	0.97[ASN][1000 genomes]
rs6814490	0.90[ASN][1000 genomes]
rs6822974	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664211	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7667700	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7674516	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7696902	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9991183	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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	nsv879078	chr4:62923797-63054757	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv594332	chr4:62976756-63034074	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1005620	chr4:62978115-63035387	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1013327	chr4:62989426-63149048	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12715708	LPHN3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62992400-62995800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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