Variant report

Variant	rs12709013
Chromosome Location	chr16:58829790-58829791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11076263	0.84[EUR][1000 genomes]
rs11076270	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11643969	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11646756	0.84[EUR][1000 genomes]
rs12325054	0.81[EUR][1000 genomes]
rs12596434	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12598527	0.80[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs12599931	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12600201	0.81[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12600206	0.81[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12926993	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12928733	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12930298	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12935488	0.83[EUR][1000 genomes]
rs1364346	0.82[EUR][1000 genomes]
rs1627257	0.83[EUR][1000 genomes]
rs1628029	0.83[EUR][1000 genomes]
rs1646262	0.83[EUR][1000 genomes]
rs1646277	0.81[EUR][1000 genomes]
rs1646283	0.82[EUR][1000 genomes]
rs1646289	0.82[EUR][1000 genomes]
rs1646290	0.82[EUR][1000 genomes]
rs1657175	0.82[EUR][1000 genomes]
rs257623	0.83[EUR][1000 genomes]
rs257625	0.83[EUR][1000 genomes]
rs257626	0.83[EUR][1000 genomes]
rs36098613	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62064940	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62066381	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62066382	0.81[EUR][1000 genomes]
rs62066815	0.82[EUR][1000 genomes]
rs62066843	0.83[EUR][1000 genomes]
rs6499983	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7185513	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8046667	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8046998	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8049572	0.85[EUR][1000 genomes]
rs8054482	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
4	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv520998	chr16:58807542-58834219	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	esv3393800	chr16:58812500-58840628	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite ratios	24816252	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12709013	CETP	cis	parietal	SCAN
rs12709013	GOT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58828400-58830200	Weak transcription	K562	blood

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