Variant report

Variant	rs12599245
Chromosome Location	chr16:70656171-70656172
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11865702	0.86[ASN][1000 genomes]
rs12051132	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596022	0.87[ASN][1000 genomes]
rs12596821	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12596851	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12596861	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12596931	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12599982	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12708905	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917749	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12924106	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12928124	0.86[ASN][1000 genomes]
rs12932251	0.92[EUR][1000 genomes]
rs13330163	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34538878	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34878593	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813904	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985412	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985539	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985540	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985541	0.83[ASN][1000 genomes]
rs4985544	0.84[ASN][1000 genomes]
rs4985548	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499328	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6499329	0.89[ASN][1000 genomes]
rs6499330	0.88[ASN][1000 genomes]
rs7193968	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72792838	0.88[ASN][1000 genomes]
rs8053536	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8061569	0.86[ASN][1000 genomes]
rs8061854	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14380	chr16:70650573-70660117	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12599245	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs12599245	CLEC18A	cis	Whole Blood	GTEx
rs12599245	PDXDC2P	cis	Artery Aorta	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70647400-70669200	Weak transcription	Right Atrium	heart
2	chr16:70647800-70664800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr16:70652400-70656800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr16:70655200-70657000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr16:70655400-70656200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr16:70655600-70656800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr16:70656000-70656200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr16:70656000-70656200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr16:70656000-70656200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr16:70656000-70656200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr16:70656000-70656200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr16:70656000-70656400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr16:70656000-70656400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr16:70656000-70656800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr16:70656000-70657000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr16:70656000-70657400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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