Variant report

Variant	rs4585080
Chromosome Location	chr2:99557327-99557328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99552279..99554160-chr2:99555590..99558457,2	MCF-7	breast:
2	chr2:99551050..99554031-chr2:99555882..99558658,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10165534	0.81[EUR][1000 genomes]
rs10167390	0.82[AMR][1000 genomes]
rs10170063	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10181422	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10196680	0.81[EUR][1000 genomes]
rs10202452	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1115756	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1115757	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11903311	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12464710	0.81[EUR][1000 genomes]
rs12467679	0.80[EUR][1000 genomes]
rs12470471	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12473029	0.87[EUR][1000 genomes]
rs12477754	0.81[EUR][1000 genomes]
rs12477978	0.87[EUR][1000 genomes]
rs12619780	0.81[ASN][1000 genomes]
rs12987548	0.81[ASN][1000 genomes]
rs13396358	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13407840	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13412764	0.82[AMR][1000 genomes]
rs1349778	0.80[EUR][1000 genomes]
rs1349779	0.88[EUR][1000 genomes]
rs1453563	0.81[ASN][1000 genomes]
rs1453564	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1530996	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1563106	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1563107	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1563108	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1580068	0.81[EUR][1000 genomes]
rs17708262	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2084988	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28575117	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28648058	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35001733	0.84[EUR][1000 genomes]
rs4346438	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4622780	0.80[EUR][1000 genomes]
rs4851179	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851183	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62154638	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62156558	0.86[AMR][1000 genomes]
rs6542846	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542852	0.82[EUR][1000 genomes]
rs6704766	0.81[EUR][1000 genomes]
rs6707462	0.84[ASN][1000 genomes]
rs6721535	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6722164	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6724476	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6732579	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6735801	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6737257	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6740035	0.82[AMR][1000 genomes]
rs6740054	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740267	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6753650	0.81[ASN][1000 genomes]
rs6754843	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6759354	0.81[EUR][1000 genomes]
rs720229	0.83[ASN][1000 genomes]
rs72957109	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7558239	0.81[EUR][1000 genomes]
rs7570657	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7571390	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7586608	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7588059	0.86[ASN][1000 genomes]
rs7591794	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7599427	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7605734	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606635	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308816	0.81[EUR][1000 genomes]
rs9808541	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4585080	TSGA10	cis	Thyroid	GTEx
rs4585080	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs4585080	TSGA10	cis	multi-tissue	Pritchard
rs4585080	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs4585080	TSGA10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99555200-99562000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99556400-99557400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:99556600-99559000	Enhancers	HepG2	liver
4	chr2:99557000-99561000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:99557000-99565200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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