Variant report

Variant	rs615470
Chromosome Location	chr15:78885988-78885989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs11637635	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12901300	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12910289	0.83[CEU][hapmap]
rs12911602	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17408276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878399	0.84[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2067808	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2456019	0.89[AMR][1000 genomes]
rs2869546	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]
rs3743073	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3743074	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]
rs3743075	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3743077	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3743078	0.84[JPT][hapmap]
rs471889	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs472054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481134	0.84[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs495090	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs495956	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs514743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518425	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs555018	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs564585	0.87[AFR][1000 genomes]
rs578776	0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57945453	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs584135	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588765	0.87[CEU][hapmap]
rs601079	0.84[CEU][hapmap]
rs61012457	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62010327	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62010328	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs621849	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs647041	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495306	0.84[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs6495307	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs660652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680244	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs692780	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7182583	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7495518	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8053	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv518840	chr15:78871288-78887171	Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs615470	CHRNA5	cis	cerebellum	SCAN
rs615470	CHRNA5	cis	parietal	SCAN
rs615470	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs615470	RP11-650L12.2	cis	lung	GTEx
rs615470	CHRNA3	cis	Muscle Skeletal	GTEx
rs615470	CHRNA5	cis	Esophagus Mucosa	GTEx
rs615470	IREB2	cis	cerebellum	SCAN
rs615470	CHRNA5	cis	Muscle Skeletal	GTEx
rs615470	CHRNA5	cis	lung	GTEx
rs615470	CHRNA5	cis	Nerve Tibial	GTEx
rs615470	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs615470	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs615470	RP11-650L12.2	cis	Nerve Tibial	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
2	chr15:78877800-78890400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:78880200-78893400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:78880200-78893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:78880200-78897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:78881600-78893200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:78882000-78887000	Weak transcription	K562	blood
8	chr15:78883000-78891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:78883000-78896000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:78883000-78896600	Weak transcription	A549	lung
11	chr15:78883200-78887400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:78883200-78888800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:78883200-78889200	Weak transcription	Hela-S3	cervix
14	chr15:78883200-78893600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:78883400-78891400	Weak transcription	Fetal Stomach	stomach
16	chr15:78883400-78897800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:78883600-78893800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:78883800-78895000	Weak transcription	Fetal Intestine Small	intestine
19	chr15:78884200-78893200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:78884400-78901000	Strong transcription	Thymus	Thymus
21	chr15:78884600-78888400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:78884600-78895600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:78884600-78898600	Strong transcription	Fetal Thymus	thymus
24	chr15:78885200-78886200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:78885200-78887400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:78885400-78886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:78885400-78888200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:78885400-78889000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:78885600-78886400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:78885600-78888200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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