Variant report

Variant	rs10133362
Chromosome Location	chr14:39433580-39433581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10134654	0.82[EUR][1000 genomes]
rs10137988	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs10141471	0.80[EUR][1000 genomes]
rs10148623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12147991	1.00[ASW][hapmap]
rs12164875	0.82[CEU][hapmap]
rs12434847	0.82[EUR][1000 genomes]
rs12437031	0.81[EUR][1000 genomes]
rs12437346	0.83[EUR][1000 genomes]
rs12878789	0.84[EUR][1000 genomes]
rs12885242	1.00[ASW][hapmap]
rs12889064	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12890771	1.00[ASW][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs17108846	1.00[ASW][hapmap]
rs17677562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2003740	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28367031	0.82[EUR][1000 genomes]
rs34702834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34875314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35287240	0.82[EUR][1000 genomes]
rs35712728	0.81[EUR][1000 genomes]
rs35807641	0.80[EUR][1000 genomes]
rs3742354	1.00[ASW][hapmap]
rs4899137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4902418	1.00[ASW][hapmap]
rs8018842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8019028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs975521	0.83[EUR][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	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10133362	TRAPPC6B	cis	multi-tissue	Pritchard
rs10133362	MIA2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39414200-39433600	Weak transcription	Brain Angular Gyrus	brain
2	chr14:39428600-39435400	Weak transcription	Left Ventricle	heart
3	chr14:39428800-39433600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr14:39429000-39434000	Weak transcription	Brain Anterior Caudate	brain
5	chr14:39430200-39433800	Weak transcription	Fetal Stomach	stomach
6	chr14:39431200-39433600	Weak transcription	Brain Substantia Nigra	brain
7	chr14:39431600-39433600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:39431600-39433600	Weak transcription	Fetal Kidney	kidney
9	chr14:39433000-39433600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr14:39433400-39434400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr14:39433400-39434600	Enhancers	HepG2	liver

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