Variant report

Variant	rs12422789
Chromosome Location	chr12:66469850-66469851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10506479	0.82[CHB][hapmap]
rs10748036	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784515	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784516	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10878384	0.82[CHB][hapmap]
rs10878388	0.82[CHB][hapmap]
rs11176031	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176047	0.82[CHB][hapmap]
rs11176051	0.82[CHB][hapmap]
rs11176058	0.82[CHB][hapmap]
rs12230800	0.82[CHB][hapmap]
rs12298245	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12301212	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423372	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12426813	0.83[ASN][1000 genomes]
rs12578754	0.81[ASN][1000 genomes]
rs12581033	0.82[CHB][hapmap]
rs12825992	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12827665	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370129	0.82[CHB][hapmap]
rs1921080	0.82[CHB][hapmap]
rs2870786	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs35085853	0.87[ASN][1000 genomes]
rs56788341	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135814	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7294608	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73315943	0.83[ASN][1000 genomes]
rs7397481	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954873	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961011	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv976723	chr12:66465896-66471495	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12422789	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs12422789	LEMD3	cis	brain	seeQTL
rs12422789	TMBIM4	cis	cerebellum	SCAN
rs12422789	XPOT	cis	parietal	SCAN
rs12422789	TMBIM4	cis	parietal	SCAN
rs12422789	MDM1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66468800-66486000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:66469200-66472200	Enhancers	HepG2	liver

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