Variant report

Variant	rs12599931
Chromosome Location	chr16:58826531-58826532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11076263	0.84[EUR][1000 genomes]
rs11076270	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11643969	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11646756	0.84[EUR][1000 genomes]
rs12325054	0.81[EUR][1000 genomes]
rs12595974	0.88[JPT][hapmap]
rs12596434	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12598527	0.84[EUR][1000 genomes]
rs12600201	0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12600206	0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12709013	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12926993	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928733	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12930298	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12935488	0.83[EUR][1000 genomes]
rs1364346	0.82[EUR][1000 genomes]
rs1615326	0.92[CHD][hapmap];0.89[JPT][hapmap]
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	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62064940	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62066381	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62066382	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62066815	0.82[EUR][1000 genomes]
rs62066843	0.83[EUR][1000 genomes]
rs6499983	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6993	0.84[JPT][hapmap]
rs7185513	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8046667	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046998	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8049572	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8054482	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs863944	0.84[CHD][hapmap];0.84[JPT][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12599931	CETP	cis	parietal	SCAN
rs12599931	IRX5	cis	cerebellum	SCAN
rs12599931	GOT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58825600-58827400	Enhancers	Fetal Heart	heart
2	chr16:58826000-58826600	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr16:58826200-58826600	Active TSS	K562	blood
4	chr16:58826200-58826800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr16:58826200-58827200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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