Variant report

Variant	rs12629380
Chromosome Location	chr3:156616080-156616081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10936043	0.87[ASN][1000 genomes]
rs11707914	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11709901	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712111	0.97[ASN][1000 genomes]
rs12492968	0.81[EUR][1000 genomes]
rs12634915	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638253	0.97[ASN][1000 genomes]
rs1320011	0.82[ASN][1000 genomes]
rs13322318	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1384538	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1574980	0.82[ASN][1000 genomes]
rs17382070	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060015	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2321290	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2321292	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2321293	0.81[ASN][1000 genomes]
rs2321455	0.87[ASN][1000 genomes]
rs2874495	0.87[ASN][1000 genomes]
rs34667021	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3910072	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4589888	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680311	0.83[ASN][1000 genomes]
rs4680312	0.97[ASN][1000 genomes]
rs4680314	0.82[ASN][1000 genomes]
rs62275765	0.90[ASN][1000 genomes]
rs6780427	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7615304	0.87[ASN][1000 genomes]
rs7622309	0.82[ASN][1000 genomes]
rs7637701	0.95[ASN][1000 genomes]
rs7638625	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812895	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818684	0.81[EUR][1000 genomes]
rs9837038	0.92[ASN][1000 genomes]
rs9844054	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847187	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858158	0.85[ASN][1000 genomes]
rs9863643	0.83[ASN][1000 genomes]
rs9865905	0.95[ASN][1000 genomes]
rs9866373	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9867621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9870137	0.84[ASN][1000 genomes]
rs9871817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9875585	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9875688	0.93[ASN][1000 genomes]
rs9876010	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876148	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12629380	LINC00886	cis	Adipose Subcutaneous	GTEx
rs12629380	LINC00886	cis	Nerve Tibial	GTEx
rs12629380	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs12629380	LINC00886	cis	Artery Aorta	GTEx
rs12629380	LINC00886	cis	Stomach	GTEx
rs12629380	LINC00886	cis	Esophagus Muscularis	GTEx
rs12629380	LINC00886	cis	lung	GTEx
rs12629380	LINC00886	cis	Artery Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156611600-156621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:156612000-156621200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:156613000-156617000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:156616000-156616200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:156616000-156616800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:156616000-156617000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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