Variant report

Variant	rs13412764
Chromosome Location	chr2:99583733-99583734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10165534	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10170063	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10179043	0.90[EUR][1000 genomes]
rs10181422	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10193019	0.93[EUR][1000 genomes]
rs10193113	0.89[EUR][1000 genomes]
rs10196680	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10202452	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1115756	0.80[AMR][1000 genomes]
rs1115757	0.80[AMR][1000 genomes]
rs11695751	0.85[AFR][1000 genomes]
rs11900670	0.82[AFR][1000 genomes]
rs12464710	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12467679	0.95[EUR][1000 genomes]
rs12473029	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12477754	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12477978	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13396358	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13407840	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1349778	0.95[EUR][1000 genomes]
rs1349779	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1453564	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1530996	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1580068	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17708218	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1993230	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2045057	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2084988	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2309524	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35001733	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4585080	0.82[AMR][1000 genomes]
rs4622780	0.95[EUR][1000 genomes]
rs4851179	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851183	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60012524	0.81[EUR][1000 genomes]
rs62154638	0.81[EUR][1000 genomes]
rs62156364	0.81[EUR][1000 genomes]
rs62156558	0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6542846	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6542852	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6542858	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6704766	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6721535	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6722164	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6724476	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6732579	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6735801	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6736064	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6737257	0.81[AMR][1000 genomes]
rs6740035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740054	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6740267	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6753650	0.81[AFR][1000 genomes]
rs6754843	0.81[AMR][1000 genomes]
rs6759354	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs720228	0.85[AFR][1000 genomes]
rs7558239	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7570657	0.81[AMR][1000 genomes]
rs7571390	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7586608	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7591794	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7605734	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7606635	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs896886	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9308816	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs972768	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9808541	0.85[AFR][1000 genomes];0.97[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
rs13412764	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs13412764	TSGA10	cis	multi-tissue	Pritchard
rs13412764	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs13412764	TSGA10	cis	Thyroid	GTEx
rs13412764	TSGA10	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99583400-99583800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99583400-99584200	ZNF genes & repeats	Gastric	stomach
3	chr2:99583400-99584200	ZNF genes & repeats	Pancreas	Pancrea
4	chr2:99583600-99584000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:99583600-99584000	ZNF genes & repeats	Esophagus	oesophagus

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