Variant report

Variant	rs17408276
Chromosome Location	chr15:78881618-78881619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78843350..78846204-chr15:78880835..78882358,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11637635	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12901300	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911602	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1878399	0.81[CEU][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2067808	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2456019	0.90[AMR][1000 genomes]
rs2869546	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3743073	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3743074	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3743075	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3743077	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3743078	0.85[JPT][hapmap]
rs471889	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs472054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481134	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs495090	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs495956	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs514743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518425	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs555018	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs578776	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs57945453	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs584135	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs588765	0.83[CEU][hapmap]
rs601079	0.81[CEU][hapmap]
rs61012457	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs615470	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]
rs62010327	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62010328	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs621849	0.84[CEU][hapmap]
rs647041	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495306	0.84[CEU][hapmap]
rs6495307	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs660652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680244	0.84[CEU][hapmap]
rs692780	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7182583	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7495518	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17408276	CHRNA3	cis	Muscle Skeletal	GTEx
rs17408276	CHRNA5	cis	lung	GTEx
rs17408276	CHRNA5	cis	Nerve Tibial	GTEx
rs17408276	CHRNA5	cis	Muscle Skeletal	GTEx
rs17408276	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs17408276	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs17408276	CHRNA5	cis	Esophagus Mucosa	GTEx
rs17408276	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs17408276	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs17408276	RP11-650L12.2	cis	lung	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78859200-78882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:78860200-78882200	Weak transcription	Hela-S3	cervix
3	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
4	chr15:78869600-78882000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:78869800-78882200	Weak transcription	A549	lung
6	chr15:78877400-78884400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:78877800-78882200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:78877800-78882200	Weak transcription	Thymus	Thymus
9	chr15:78877800-78890400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:78878600-78882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:78878800-78884000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:78880000-78882200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:78880200-78882000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:78880200-78883000	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:78880200-78893400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:78880200-78893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:78880200-78897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:78880400-78882600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:78880600-78882200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:78881000-78884600	Weak transcription	Fetal Thymus	thymus
21	chr15:78881200-78883400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:78881400-78883000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:78881400-78883800	Weak transcription	HepG2	liver
24	chr15:78881400-78885400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:78881600-78883000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:78881600-78883200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:78881600-78883400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:78881600-78883600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:78881600-78893200	Weak transcription	Stomach Smooth Muscle	stomach

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