Variant report

Variant	rs2153654
Chromosome Location	chr10:93502329-93502330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93345296..93347976-chr10:93501392..93503311,2	K562	blood:
2	chr10:93499838..93502353-chr10:93502549..93505542,2	MCF-7	breast:
3	chr10:93168502..93170905-chr10:93500372..93503062,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165338	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10509634	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10748566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786012	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10786014	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881951	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10881958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10881960	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10881966	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881967	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881969	0.80[EUR][1000 genomes]
rs10881971	0.80[EUR][1000 genomes]
rs10881975	0.81[AMR][1000 genomes]
rs11186660	0.90[ASN][1000 genomes]
rs11186664	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11186665	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11186667	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11186668	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186697	0.81[AMR][1000 genomes]
rs12221087	0.81[AMR][1000 genomes]
rs12782935	0.80[EUR][1000 genomes]
rs1341263	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1418160	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418162	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1539040	0.81[AMR][1000 genomes]
rs1592050	0.93[ASN][1000 genomes]
rs1856927	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1857060	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1935029	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2050913	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066275	0.80[EUR][1000 genomes]
rs2421692	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2901505	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4244929	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4933219	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61876144	0.91[ASN][1000 genomes]
rs7897499	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7918686	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	esv3420401	chr10:93497972-93502370	Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv975785	chr10:93501141-93525212	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2153654	TNKS2	cis	Nerve Tibial	GTEx
rs2153654	TNKS2-AS1	cis	Heart Left Ventricle	GTEx
rs2153654	TNKS2	cis	Esophagus Muscularis	GTEx
rs2153654	TNKS2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93500600-93504600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:93501200-93505200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:93501400-93502400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:93501600-93502600	Weak transcription	Fetal Lung	lung
5	chr10:93502000-93502600	Enhancers	Fetal Kidney	kidney
6	chr10:93502000-93502800	Flanking Active TSS	Liver	Liver
7	chr10:93502200-93502400	Enhancers	Stomach Mucosa	stomach

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