Variant report

Variant	rs12890771
Chromosome Location	chr14:39455806-39455807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10133362	0.82[EUR][1000 genomes]
rs10134230	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10134654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140949	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10141255	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10141471	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10148623	0.84[EUR][1000 genomes]
rs1061583	1.00[ASW][hapmap]
rs11157041	0.89[CEU][hapmap];0.91[CHD][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12050319	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12147991	1.00[ASW][hapmap]
rs12434593	0.82[ASN][1000 genomes]
rs12434847	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437346	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878139	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12878789	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879229	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12882868	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12885242	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHD][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1555257	0.94[CHD][hapmap]
rs17108728	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17108846	1.00[ASW][hapmap]
rs17677562	0.84[EUR][1000 genomes]
rs1957064	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2003740	0.82[EUR][1000 genomes]
rs2025064	0.82[ASN][1000 genomes]
rs2415522	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28367031	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34676226	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34702834	0.83[EUR][1000 genomes]
rs34875314	0.83[EUR][1000 genomes]
rs34985331	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35287240	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35712728	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35807641	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36161173	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3742354	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHD][hapmap];0.89[MEX][hapmap]
rs3742355	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4899137	0.83[EUR][1000 genomes]
rs4902259	0.95[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902285	0.81[EUR][1000 genomes]
rs4902308	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4902418	1.00[ASW][hapmap]
rs71407775	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7150092	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7151246	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7152746	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8018842	0.84[EUR][1000 genomes]
rs8019028	0.84[EUR][1000 genomes]
rs9322992	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9743575	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs975521	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv901657	chr14:39410706-39460072	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12890771	FIBP	trans	parietal	SCAN
rs12890771	TRAPPC6B	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39450000-39465000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr14:39455600-39464800	Weak transcription	Psoas Muscle	Psoas
3	chr14:39455800-39465200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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