Variant report

Variant	rs6495306
Chromosome Location	chr15:78865893-78865894
allele	A/G
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	chr15:78860117..78862211-chr15:78865447..78867547,2	K562	blood:
3	chr15:78864327..78866155-chr15:78867684..78869455,2	K562	blood:

Variant related genes	Relation type
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11632604	0.84[CEU][hapmap]
rs11636131	0.84[CEU][hapmap]
rs11637635	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11858230	0.81[CEU][hapmap]
rs12901300	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12902493	0.84[CEU][hapmap]
rs12906951	0.84[CEU][hapmap]
rs12907966	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs12910289	0.88[CEU][hapmap]
rs12911602	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12914694	0.84[CEU][hapmap]
rs12916483	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs12916999	0.84[CEU][hapmap]
rs1504545	0.84[CEU][hapmap]
rs1504546	0.84[CEU][hapmap]
rs17408276	0.84[CEU][hapmap]
rs1878399	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1979905	0.84[CEU][hapmap]
rs1979906	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1979907	0.86[CEU][hapmap]
rs2292117	0.84[CEU][hapmap]
rs2456019	0.81[AMR][1000 genomes]
rs2869546	0.88[CEU][hapmap]
rs3743073	0.83[CEU][hapmap]
rs3743074	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs3743075	0.84[CEU][hapmap];0.87[GIH][hapmap]
rs3743077	0.96[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3813571	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs3813572	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs3829787	0.84[ASN][1000 genomes]
rs4243083	0.83[CEU][hapmap]
rs4275821	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs472054	0.84[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs481134	0.86[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];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886571	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs4887063	0.83[CEU][hapmap]
rs4887064	0.84[CEU][hapmap]
rs495956	0.88[CEU][hapmap]
rs514743	0.84[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs555018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57945453	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs588765	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601079	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61012457	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs615470	0.84[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs621849	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs647041	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6495307	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs660652	0.84[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs680244	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs692780	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7164030	0.84[CEU][hapmap]
rs7173512	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs8025188	0.87[EUR][1000 genomes]
rs8025429	0.86[CEU][hapmap]
rs8053	0.84[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs880395	0.84[CEU][hapmap]
rs905740	0.84[CEU][hapmap]
rs952215	0.84[CEU][hapmap]
rs952216	0.83[CEU][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	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6495306	PSMA4	cis	cerebellum	SCAN
rs6495306	CHRNA5	cis	lung	GTEx
rs6495306	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs6495306	CHRNA3	cis	Muscle Skeletal	GTEx
rs6495306	RP11-650L12.2	cis	lung	GTEx
rs6495306	IREB2	cis	cerebellum	SCAN
rs6495306	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs6495306	CHRNA5	cis	Esophagus Mucosa	GTEx
rs6495306	CHRNA5	cis	Muscle Skeletal	GTEx
rs6495306	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs6495306	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs6495306	CHRNA5	cis	cerebellum	SCAN
rs6495306	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs6495306	CHRNA5	cis	Nerve Tibial	GTEx
rs6495306	IREB2	cis	parietal	SCAN
rs6495306	CHRNA5	cis	multi-tissue	Pritchard
rs6495306	CHRNA5	cis	Heart Left Ventricle	GTEx
rs6495306	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs6495306	CHRNA5	cis	parietal	SCAN

Chromatin state (count:9 , 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	chr15:78860200-78881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:78860200-78881600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:78860200-78882200	Weak transcription	Hela-S3	cervix
6	chr15:78863600-78867200	Weak transcription	GM12878-XiMat	blood
7	chr15:78864600-78869200	Weak transcription	A549	lung
8	chr15:78865800-78866200	Enhancers	Fetal Brain Female	brain
9	chr15:78865800-78873200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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