Variant report

Variant	rs1563796
Chromosome Location	chr4:63067995-63067996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10006606	0.84[EUR][1000 genomes]
rs10013024	0.96[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10017162	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11131359	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12500756	0.84[ASN][1000 genomes]
rs12645804	0.84[ASN][1000 genomes]
rs12715708	0.83[EUR][1000 genomes]
rs13138506	0.84[EUR][1000 genomes]
rs17082585	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2160498	0.91[CEU][hapmap]
rs2193121	0.83[EUR][1000 genomes]
rs2193122	0.83[EUR][1000 genomes]
rs2216198	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2344677	0.84[EUR][1000 genomes]
rs4397024	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4446347	0.82[ASN][1000 genomes]
rs4464598	0.82[ASN][1000 genomes]
rs4510488	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4549412	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58263916	0.82[ASN][1000 genomes]
rs58634974	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6551682	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6551685	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6551686	0.96[ASN][1000 genomes]
rs6822974	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7664211	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7667700	0.83[EUR][1000 genomes]
rs7696902	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9991183	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1012093	chr4:63014592-63568580	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537113	chr4:63014592-63568580	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv534618	chr4:63025655-63568620	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv997505	chr4:63025663-63575696	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv594333	chr4:63025823-63467034	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv461378	chr4:63037324-63158560	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv594334	chr4:63037324-63158560	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv1013850	chr4:63049885-63568580	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv537114	chr4:63049885-63568580	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv594335	chr4:63054757-63183246	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	nsv879079	chr4:63059672-63184850	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1563796	LPHN3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:63059800-63075600	Weak transcription	Fetal Heart	heart
2	chr4:63065400-63074400	Weak transcription	Fetal Muscle Leg	muscle

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