Variant report

Variant	rs2575794
Chromosome Location	chr3:87085213-87085214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1370040	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1370042	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436647	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1821750	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1836918	0.84[CEU][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs1898274	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2043663	0.84[MEX][hapmap]
rs2118078	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2262594	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2262595	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2575775	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs2575780	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2575782	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2575783	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2575792	0.84[EUR][1000 genomes]
rs2575799	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2575800	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2660767	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2660769	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2660772	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2660773	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2660774	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2660777	0.81[CEU][hapmap]
rs2660779	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2660796	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2660798	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs990159	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1000548	chr3:87034157-87331360	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv834754	chr3:87055161-87216408	ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2575794	CGGBP1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87084200-87085600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:87084400-87085600	Weak transcription	Placenta	Placenta

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