Variant report

Variant	rs2869546
Chromosome Location	chr15:78907345-78907346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11637635	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11858230	0.82[CEU][hapmap]
rs12901300	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910289	0.84[CEU][hapmap]
rs12911602	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916999	0.80[CEU][hapmap]
rs17408276	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1878399	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2067808	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2904130	0.80[EUR][1000 genomes]
rs3743073	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3743074	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3743075	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3743077	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743078	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs471889	0.89[EUR][1000 genomes]
rs472054	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs481134	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs495090	0.89[EUR][1000 genomes]
rs495956	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs514743	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs518425	0.83[JPT][hapmap]
rs555018	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs578776	0.83[JPT][hapmap]
rs57945453	0.88[EUR][1000 genomes]
rs584135	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs588765	0.87[CEU][hapmap]
rs601079	0.85[CEU][hapmap]
rs61012457	0.88[EUR][1000 genomes]
rs615470	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62010327	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62010328	0.89[EUR][1000 genomes]
rs621849	0.88[CEU][hapmap]
rs647041	0.88[CEU][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6495306	0.88[CEU][hapmap]
rs6495307	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs660652	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs680244	0.88[CEU][hapmap]
rs692780	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7182583	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7495518	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2869546	CHRNA5	cis	lung	GTEx
rs2869546	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs2869546	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs2869546	RP11-650L12.2	cis	lung	GTEx
rs2869546	CHRNA3	cis	Muscle Skeletal	GTEx
rs2869546	CHRNA5	cis	Muscle Skeletal	GTEx
rs2869546	CHRNA5	cis	Nerve Tibial	GTEx
rs2869546	CHRNA5	cis	Esophagus Mucosa	GTEx
rs2869546	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs2869546	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78894200-78910600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78896600-78908800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:78900800-78909200	Weak transcription	Fetal Stomach	stomach
4	chr15:78906200-78910600	Strong transcription	Fetal Thymus	thymus
5	chr15:78907200-78910000	Strong transcription	Thymus	Thymus

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