Variant report

Variant	rs57945453
Chromosome Location	chr15:78862845-78862846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78856758..78860631-chr15:78862609..78867440,7	MCF-7	breast:
2	chr15:78856760..78859758-chr15:78860194..78863212,4	K562	blood:
3	chr15:78856659..78859424-chr15:78860580..78863119,3	K562	blood:

Variant related genes	Relation type
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11637635	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17408276	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2067808	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2456019	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2869546	0.88[EUR][1000 genomes]
rs3743073	0.92[EUR][1000 genomes]
rs3743074	0.92[EUR][1000 genomes]
rs3743075	0.91[EUR][1000 genomes]
rs3829787	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4275821	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs471889	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs472054	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs481134	0.88[ASN][1000 genomes]
rs495090	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs495956	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs514743	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs555018	0.88[ASN][1000 genomes]
rs584135	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs588765	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61012457	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615470	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62010327	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62010328	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6495306	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs660652	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs692780	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7173512	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7182583	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7495518	0.90[AMR][1000 genomes];0.85[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	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs57945453	CHRNA5	cis	lung	GTEx
rs57945453	CHRNA5	cis	Muscle Skeletal	GTEx
rs57945453	RP11-650L12.2	cis	lung	GTEx
rs57945453	CHRNA5	cis	Esophagus Mucosa	GTEx
rs57945453	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs57945453	CHRNA5	cis	Nerve Tibial	GTEx
rs57945453	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs57945453	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs57945453	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs57945453	CHRNA3	cis	Muscle Skeletal	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78859000-78868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78859200-78882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:78860000-78865800	Weak transcription	Fetal Brain Female	brain
4	chr15:78860200-78863200	Weak transcription	A549	lung
5	chr15:78860200-78881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:78860200-78881600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:78860200-78882200	Weak transcription	Hela-S3	cervix
8	chr15:78860400-78864200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:78860600-78864200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:78861200-78865200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:78861800-78863200	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links