Variant report

Variant	rs1957064
Chromosome Location	chr14:39379670-39379671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10134158	0.83[EUR][1000 genomes]
rs10134168	0.83[EUR][1000 genomes]
rs10134230	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10134654	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10135961	0.85[EUR][1000 genomes]
rs10137988	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10140949	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10141045	0.84[EUR][1000 genomes]
rs10141200	0.84[EUR][1000 genomes]
rs10141255	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10141471	0.87[AMR][1000 genomes]
rs10149957	0.85[EUR][1000 genomes]
rs11157041	0.85[CHD][hapmap];0.81[AMR][1000 genomes]
rs12050319	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12431829	0.80[EUR][1000 genomes]
rs12434847	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12437031	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12437346	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12717274	0.85[EUR][1000 genomes]
rs12878139	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12878789	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12879229	0.81[AMR][1000 genomes]
rs12882686	0.83[EUR][1000 genomes]
rs12882868	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12885242	0.88[CHD][hapmap]
rs12890268	0.85[EUR][1000 genomes]
rs12890771	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1555257	0.88[CHD][hapmap]
rs17108552	0.85[EUR][1000 genomes]
rs17108728	0.87[AMR][1000 genomes]
rs1951227	0.85[EUR][1000 genomes]
rs2093268	0.84[EUR][1000 genomes]
rs2145606	0.85[EUR][1000 genomes]
rs2208467	0.85[EUR][1000 genomes]
rs2415522	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28367031	0.87[ASN][1000 genomes]
rs35160151	0.83[EUR][1000 genomes]
rs35287240	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35712728	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35807641	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35924435	0.81[EUR][1000 genomes]
rs36128129	0.83[EUR][1000 genomes]
rs36161173	0.81[AMR][1000 genomes]
rs3742354	0.81[CHD][hapmap]
rs4902235	0.85[EUR][1000 genomes]
rs4902236	0.85[EUR][1000 genomes]
rs4902239	0.81[EUR][1000 genomes]
rs4902259	0.85[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4902308	0.81[AMR][1000 genomes]
rs59719953	0.83[EUR][1000 genomes]
rs60779326	0.82[EUR][1000 genomes]
rs66588760	0.80[EUR][1000 genomes]
rs7150092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152746	0.81[AMR][1000 genomes]
rs8008205	0.85[EUR][1000 genomes]
rs9322992	0.81[AMR][1000 genomes]
rs9743575	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs975521	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564416	chr14:39140536-39440106	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv470631	chr14:39153764-39440106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	nsv932194	chr14:39173578-39411337	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv901656	chr14:39370726-39423339	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1957064	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39379000-39379800	Enhancers	Brain Hippocampus Middle	brain
2	chr14:39379200-39379800	Flanking Active TSS	GM12878-XiMat	blood
3	chr14:39379600-39380000	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr14:39379600-39380000	Enhancers	Brain Substantia Nigra	brain
5	chr14:39379600-39380600	Enhancers	Spleen	Spleen

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