Variant report

Variant	rs12828309
Chromosome Location	chr12:48641160-48641161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1061986	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10875763	0.83[ASN][1000 genomes]
rs1107654	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168460	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168464	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168468	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168474	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168484	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829841	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387259	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1387260	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1489108	0.87[AMR][1000 genomes]
rs1542707	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552550	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054905	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409003	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2409004	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2450994	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634676	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2634678	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2634680	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2634681	0.84[EUR][1000 genomes]
rs2634682	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2634684	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634686	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634688	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2634689	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2634691	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2634692	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2634693	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2634694	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634697	1.00[ASN][1000 genomes]
rs2732441	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2732445	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732448	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2732453	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2732454	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2732457	0.87[AMR][1000 genomes]
rs2732461	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732462	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732466	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2732479	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2732481	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2732484	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2732486	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2956703	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2956710	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087716	0.83[ASN][1000 genomes]
rs34286639	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580662	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297824	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307566	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315820	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486941	0.83[ASN][1000 genomes]
rs7966829	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923397	0.89[AMR][1000 genomes];0.87[EUR][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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12828309	H1FNT	cis	Muscle Skeletal	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48640600-48641800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48640600-48641800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr12:48640800-48641200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48640800-48641400	Enhancers	Psoas Muscle	Psoas
5	chr12:48640800-48641600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:48641000-48641400	ZNF genes & repeats	Aorta	Aorta

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