Variant report

Variant	rs8039600
Chromosome Location	chr15:78990300-78990301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11072793	0.84[ASN][1000 genomes]
rs1114829	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11629824	0.83[ASN][1000 genomes]
rs11633170	0.83[ASN][1000 genomes]
rs11633519	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11634628	0.83[ASN][1000 genomes]
rs12899940	0.83[ASN][1000 genomes]
rs12907511	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1809415	0.83[EUR][1000 genomes]
rs28661610	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2869552	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58717592	0.84[EUR][1000 genomes]
rs62010552	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62010554	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6495317	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495318	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7163236	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170552	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7170563	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72625802	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8039600	CHRNA5	cis	Muscle Skeletal	GTEx
rs8039600	RP11-650L12.2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78988000-78990400	Enhancers	Liver	Liver
2	chr15:78988600-78994800	Weak transcription	Esophagus	oesophagus
3	chr15:78988600-79001600	Weak transcription	Pancreas	Pancrea
4	chr15:78990200-78990400	Enhancers	Fetal Heart	heart

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