Variant report

Variant	rs28692915
Chromosome Location	chr21:47074224-47074225
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47062875..47065834-chr21:47073386..47075636,2	MCF-7	breast:
2	chr21:47058472..47062802-chr21:47073375..47076804,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1029014	0.83[EUR][1000 genomes]
rs12151963	0.80[EUR][1000 genomes]
rs1467758	0.88[EUR][1000 genomes]
rs17004799	0.80[EUR][1000 genomes]
rs1964928	0.83[EUR][1000 genomes]
rs1989537	0.87[EUR][1000 genomes]
rs2150460	0.81[EUR][1000 genomes]
rs2183601	0.88[EUR][1000 genomes]
rs2838973	0.89[EUR][1000 genomes]
rs2838974	0.89[EUR][1000 genomes]
rs2838976	0.88[EUR][1000 genomes]
rs2838978	0.82[EUR][1000 genomes]
rs2838981	0.83[EUR][1000 genomes]
rs2838982	0.83[EUR][1000 genomes]
rs2838983	0.81[EUR][1000 genomes]
rs2838985	0.82[EUR][1000 genomes]
rs2838988	0.80[EUR][1000 genomes]
rs28625750	0.81[EUR][1000 genomes]
rs3920695	0.86[EUR][1000 genomes]
rs4347938	0.87[EUR][1000 genomes]
rs4434082	0.87[EUR][1000 genomes]
rs4818795	0.82[EUR][1000 genomes]
rs4818797	0.81[EUR][1000 genomes]
rs4819144	0.81[EUR][1000 genomes]
rs55912508	0.80[EUR][1000 genomes]
rs55923134	0.83[EUR][1000 genomes]
rs55957843	0.81[EUR][1000 genomes]
rs56213918	0.87[EUR][1000 genomes]
rs56288252	0.87[EUR][1000 genomes]
rs57057834	0.82[EUR][1000 genomes]
rs57282159	0.83[EUR][1000 genomes]
rs57328058	0.81[EUR][1000 genomes]
rs57501220	0.88[EUR][1000 genomes]
rs57990579	0.86[EUR][1000 genomes]
rs58368336	0.80[EUR][1000 genomes]
rs58925015	0.83[EUR][1000 genomes]
rs60988006	0.83[EUR][1000 genomes]
rs61329313	0.83[EUR][1000 genomes]
rs62213277	0.80[EUR][1000 genomes]
rs62215031	0.89[EUR][1000 genomes]
rs62215035	0.89[EUR][1000 genomes]
rs62215040	0.87[EUR][1000 genomes]
rs62215047	0.83[EUR][1000 genomes]
rs62215048	0.83[EUR][1000 genomes]
rs67565220	0.88[EUR][1000 genomes]
rs725358	0.83[EUR][1000 genomes]
rs7279909	0.85[EUR][1000 genomes]
rs7280560	0.83[EUR][1000 genomes]
rs7283803	0.89[EUR][1000 genomes]
rs7410008	0.82[EUR][1000 genomes]
rs744506	0.82[EUR][1000 genomes]
rs767137	0.84[EUR][1000 genomes]
rs8133966	0.82[EUR][1000 genomes]
rs9306139	0.85[EUR][1000 genomes]
rs9637169	0.80[EUR][1000 genomes]
rs9647229	0.81[EUR][1000 genomes]
rs9976878	0.87[EUR][1000 genomes]
rs9978158	0.83[EUR][1000 genomes]
rs9978882	0.83[EUR][1000 genomes]
rs9981586	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
5	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
7	nsv914077	chr21:46998548-47091361	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
9	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28692915	PCBP3	cis	lung	GTEx
rs28692915	PCBP3	cis	Muscle Skeletal	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47068400-47082200	Weak transcription	Fetal Thymus	thymus
2	chr21:47072200-47075600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr21:47072800-47074600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:47074200-47074600	Weak transcription	NHDF-Ad	bronchial

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