Variant report

Variant	rs2669425
Chromosome Location	chr8:105395583-105395584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr8:105395544-105395956	GM12878	blood:	n/a	chr8:105395746-105395755 chr8:105395746-105395755

Variant related genes	Relation type
DPYS	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1317380	0.83[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs1317472	0.94[CEU][hapmap];0.89[GIH][hapmap];0.87[EUR][1000 genomes]
rs1325	0.83[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs1327	0.85[EUR][1000 genomes]
rs13282328	0.81[EUR][1000 genomes]
rs1513025	0.83[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1513026	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2246650	0.86[GIH][hapmap];0.87[EUR][1000 genomes]
rs2669423	0.87[EUR][1000 genomes]
rs2853154	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853155	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2853158	0.94[CEU][hapmap];0.89[GIH][hapmap];0.83[EUR][1000 genomes]
rs3737535	0.83[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs3793360	0.87[EUR][1000 genomes]
rs3793361	0.87[EUR][1000 genomes]
rs4734793	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs58596729	0.87[EUR][1000 genomes]
rs58903502	0.87[EUR][1000 genomes]
rs6989353	0.87[EUR][1000 genomes]
rs6989484	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs6989588	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs6994791	0.83[EUR][1000 genomes]
rs6994920	0.83[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7000266	0.83[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7012566	0.83[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7012764	0.83[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs870789	0.94[CEU][hapmap];0.86[EUR][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	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1032775	chr8:105311364-105409972	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2669425	DCAF13	cis	cerebellum	SCAN
rs2669425	DPYS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105390400-105421000	Strong transcription	Liver	Liver
2	chr8:105393400-105395600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:105394800-105395600	Enhancers	GM12878-XiMat	blood

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