Variant report

Variant	rs601079
Chromosome Location	chr15:78869579-78869580
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:78869507-78869620	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CHRNA5	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11632604	0.85[CEU][hapmap]
rs11636131	0.85[CEU][hapmap]
rs11637635	0.85[CEU][hapmap]
rs12901300	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902493	0.84[CEU][hapmap]
rs12906951	0.84[CEU][hapmap]
rs12907966	0.84[CEU][hapmap]
rs12910289	0.88[CEU][hapmap]
rs12911602	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12914694	0.84[CEU][hapmap]
rs12916483	0.84[CEU][hapmap]
rs12916999	0.84[CEU][hapmap]
rs1504545	0.84[CEU][hapmap]
rs1504546	0.85[CEU][hapmap]
rs17408276	0.81[CEU][hapmap]
rs1878399	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs1979905	0.85[CEU][hapmap]
rs1979906	0.84[CEU][hapmap]
rs1979907	0.87[CEU][hapmap]
rs2292117	0.84[CEU][hapmap]
rs2869546	0.85[CEU][hapmap]
rs3743073	0.81[CEU][hapmap]
rs3743074	0.84[CEU][hapmap]
rs3743075	0.84[CEU][hapmap]
rs3743077	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3813571	0.84[CEU][hapmap]
rs3813572	0.84[CEU][hapmap]
rs4243083	0.84[CEU][hapmap]
rs471889	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs472054	0.84[CEU][hapmap]
rs481134	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4886571	0.84[CEU][hapmap]
rs4887062	0.81[CEU][hapmap]
rs4887063	0.83[CEU][hapmap]
rs4887064	0.85[CEU][hapmap]
rs495090	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs495956	0.85[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs514743	0.84[CEU][hapmap]
rs555018	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs588765	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs615470	0.84[CEU][hapmap]
rs621849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs647041	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6495306	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6495307	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs660652	0.84[CEU][hapmap]
rs680244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692780	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7164030	0.85[CEU][hapmap]
rs8025188	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8025429	0.87[CEU][hapmap]
rs8053	0.84[CEU][hapmap]
rs880395	0.85[CEU][hapmap]
rs905740	0.85[CEU][hapmap]
rs952215	0.84[CEU][hapmap]
rs952216	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
3	esv1818155	chr15:78866785-78874073	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs601079	CHRNA5	cis	Esophagus Mucosa	GTEx
rs601079	CHRNA5	cis	Heart Left Ventricle	GTEx
rs601079	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs601079	CHRNA5	cis	Nerve Tibial	GTEx
rs601079	CHRNA5	cis	lung	GTEx
rs601079	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs601079	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs601079	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs601079	CHRNA3	cis	Muscle Skeletal	GTEx
rs601079	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs601079	CHRNA5	cis	Muscle Skeletal	GTEx
rs601079	RP11-650L12.2	cis	lung	GTEx
rs601079	RP11-650L12.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:8 , 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	chr15:78860200-78881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:78860200-78881600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:78860200-78882200	Weak transcription	Hela-S3	cervix
5	chr15:78865800-78873200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
7	chr15:78869200-78869800	Enhancers	A549	lung
8	chr15:78869400-78869600	Enhancers	HUES64 Cell Line	embryonic stem cell

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