Variant report

Variant	rs12578754
Chromosome Location	chr12:66494707-66494708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10459263	0.90[EUR][1000 genomes]
rs10506475	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10506479	0.90[EUR][1000 genomes]
rs10748036	0.83[ASN][1000 genomes]
rs10878379	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10878380	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10878384	0.90[EUR][1000 genomes]
rs10878387	0.90[EUR][1000 genomes]
rs10878388	0.90[EUR][1000 genomes]
rs11176031	0.84[ASN][1000 genomes]
rs11176040	0.88[EUR][1000 genomes]
rs11176041	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11176042	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11176044	0.90[EUR][1000 genomes]
rs11176046	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11176047	0.90[EUR][1000 genomes]
rs11176048	0.90[EUR][1000 genomes]
rs11176050	0.90[EUR][1000 genomes]
rs11176051	0.90[EUR][1000 genomes]
rs11176058	0.90[EUR][1000 genomes]
rs11176059	0.90[EUR][1000 genomes]
rs11176061	0.90[EUR][1000 genomes]
rs11176062	0.90[EUR][1000 genomes]
rs12230221	0.90[EUR][1000 genomes]
rs12230240	0.85[EUR][1000 genomes]
rs12230800	0.90[EUR][1000 genomes]
rs12301212	0.83[ASN][1000 genomes]
rs12422789	0.81[ASN][1000 genomes]
rs12426813	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12578364	0.83[EUR][1000 genomes]
rs12578752	0.83[EUR][1000 genomes]
rs12578994	0.83[EUR][1000 genomes]
rs12581033	0.90[EUR][1000 genomes]
rs12581836	0.90[EUR][1000 genomes]
rs12582384	0.90[EUR][1000 genomes]
rs12814331	0.83[EUR][1000 genomes]
rs12814606	0.83[EUR][1000 genomes]
rs12822410	0.88[EUR][1000 genomes]
rs12823732	0.90[EUR][1000 genomes]
rs12825992	0.90[EUR][1000 genomes]
rs12827665	0.83[ASN][1000 genomes]
rs1370129	0.90[EUR][1000 genomes]
rs17245364	0.83[EUR][1000 genomes]
rs17825943	0.85[EUR][1000 genomes]
rs1921080	0.90[EUR][1000 genomes]
rs2870786	0.90[EUR][1000 genomes]
rs2904498	0.90[EUR][1000 genomes]
rs34406211	0.85[EUR][1000 genomes]
rs34552143	0.83[EUR][1000 genomes]
rs35085853	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35131575	0.85[EUR][1000 genomes]
rs35187440	0.83[EUR][1000 genomes]
rs35447479	0.90[EUR][1000 genomes]
rs35971570	0.83[EUR][1000 genomes]
rs36073795	0.83[EUR][1000 genomes]
rs4281516	0.90[EUR][1000 genomes]
rs56788341	0.82[ASN][1000 genomes]
rs59112451	0.85[EUR][1000 genomes]
rs60102429	0.88[EUR][1000 genomes]
rs66767092	0.90[EUR][1000 genomes]
rs71450848	0.90[EUR][1000 genomes]
rs73315943	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737614	0.83[EUR][1000 genomes]
rs7397481	0.83[ASN][1000 genomes]
rs7954873	0.84[ASN][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12578754	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66494200-66495000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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