Variant report

Variant	rs3743074
Chromosome Location	chr15:78909480-78909481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11637635	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12901300	0.81[EUR][1000 genomes]
rs12910289	0.83[CEU][hapmap]
rs12911602	0.81[EUR][1000 genomes]
rs17408276	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1878399	0.84[CEU][hapmap]
rs1948	0.91[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs2067808	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2869546	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3743073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743077	0.88[CEU][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs471889	0.93[EUR][1000 genomes]
rs472054	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs481134	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs495090	0.93[EUR][1000 genomes]
rs495956	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs514743	1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs555018	0.83[CEU][hapmap]
rs57945453	0.92[EUR][1000 genomes]
rs584135	0.97[EUR][1000 genomes]
rs588765	0.87[CEU][hapmap]
rs601079	0.84[CEU][hapmap]
rs61012457	0.92[EUR][1000 genomes]
rs615470	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62010327	0.89[EUR][1000 genomes]
rs62010328	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs621849	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs647041	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6495306	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs6495307	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs660652	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs680244	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs692780	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7182583	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7495518	0.81[AMR][1000 genomes];0.90[EUR][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	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3743074	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs3743074	CHRNA3	cis	Muscle Skeletal	GTEx
rs3743074	CHRNA5	cis	cerebellum	SCAN
rs3743074	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs3743074	CHRNA5	cis	Nerve Tibial	GTEx
rs3743074	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs3743074	CHRNA5	cis	Muscle Skeletal	GTEx
rs3743074	CHRNA5	cis	Esophagus Mucosa	GTEx
rs3743074	RP11-650L12.2	cis	lung	GTEx
rs3743074	IREB2	cis	cerebellum	SCAN
rs3743074	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs3743074	CHRNA5	cis	parietal	SCAN
rs3743074	CHRNA5	cis	lung	GTEx

Chromatin state (count:7 , 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	chr15:78906200-78910600	Strong transcription	Fetal Thymus	thymus
3	chr15:78907200-78910000	Strong transcription	Thymus	Thymus
4	chr15:78909000-78910600	Genic enhancers	Stomach Smooth Muscle	stomach
5	chr15:78909000-78910800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:78909200-78910000	Strong transcription	Fetal Stomach	stomach
7	chr15:78909400-78909600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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