Variant report

Variant	rs28367031
Chromosome Location	chr14:39427080-39427081
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39409994..39412907-chr14:39426330..39428595,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10133362	0.82[EUR][1000 genomes]
rs10134230	0.89[ASN][1000 genomes]
rs10134654	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137988	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140949	0.88[ASN][1000 genomes]
rs10141255	0.90[ASN][1000 genomes]
rs10141471	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10148623	0.81[EUR][1000 genomes]
rs11157041	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12050319	0.90[ASN][1000 genomes]
rs12434593	0.82[ASN][1000 genomes]
rs12434847	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437031	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437346	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878139	0.88[ASN][1000 genomes]
rs12878789	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879229	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12882868	0.86[ASN][1000 genomes]
rs12885242	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12890771	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108728	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17677562	0.81[EUR][1000 genomes]
rs1957064	0.87[ASN][1000 genomes]
rs2025064	0.82[ASN][1000 genomes]
rs2415522	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34676226	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34985331	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35287240	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35712728	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35807641	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36161173	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3742355	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4902259	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902308	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71407775	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7150092	0.87[ASN][1000 genomes]
rs7151246	0.87[ASN][1000 genomes]
rs7152746	0.84[AMR][1000 genomes]
rs8018842	0.81[EUR][1000 genomes]
rs8019028	0.81[EUR][1000 genomes]
rs9322992	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9743575	0.90[ASN][1000 genomes]
rs975521	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28367031	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39414200-39433600	Weak transcription	Brain Angular Gyrus	brain
2	chr14:39418000-39428000	Weak transcription	Brain Hippocampus Middle	brain
3	chr14:39425400-39428800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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