Variant report

Variant	rs10202452
Chromosome Location	chr2:99569409-99569410
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	chr2:99567888..99569888-chr2:99587161..99588849,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10165534	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10170063	0.82[EUR][1000 genomes]
rs10179043	0.91[EUR][1000 genomes]
rs10181422	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10193019	0.94[EUR][1000 genomes]
rs10193113	0.91[EUR][1000 genomes]
rs10196680	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1115757	0.80[EUR][1000 genomes]
rs11695751	0.81[AFR][1000 genomes]
rs12464710	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12467679	0.97[EUR][1000 genomes]
rs12473029	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12477754	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12477978	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13396358	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407840	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13412764	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1349778	0.97[EUR][1000 genomes]
rs1349779	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1453564	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1530996	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1580068	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17708218	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1993230	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2045057	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2084988	0.82[EUR][1000 genomes]
rs2309524	0.93[EUR][1000 genomes]
rs28575117	0.81[AMR][1000 genomes]
rs35001733	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4585080	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4622780	0.97[EUR][1000 genomes]
rs4851179	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851183	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60012524	0.82[EUR][1000 genomes]
rs62154638	0.83[EUR][1000 genomes]
rs62156364	0.82[EUR][1000 genomes]
rs62156558	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542846	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6542852	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6542858	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6704766	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6721535	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6722164	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6724476	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6732579	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735801	0.82[EUR][1000 genomes]
rs6736064	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6740035	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6740054	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6740267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6759354	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs720228	0.81[AFR][1000 genomes]
rs7558239	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7571390	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7586608	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7591794	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7605734	0.83[EUR][1000 genomes]
rs7606635	0.83[EUR][1000 genomes]
rs896886	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9308816	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs972768	0.91[EUR][1000 genomes]
rs9808541	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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
rs10202452	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs10202452	TSGA10	cis	Thyroid	GTEx
rs10202452	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs10202452	TSGA10	cis	multi-tissue	Pritchard
rs10202452	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99569000-99570000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:99569000-99570000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr2:99569200-99569600	Enhancers	Osteobl	bone
4	chr2:99569200-99570000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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