Variant report

Variant	rs2725878
Chromosome Location	chr8:125959054-125959055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000255313	TF binding region
ENSG00000147684	Chromatin interaction
ENSG00000249816	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1427086	0.93[YRI][hapmap]
rs2382999	0.88[JPT][hapmap]
rs2555724	0.91[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555725	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590665	0.87[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2590667	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28455785	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28558480	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28870400	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3866472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3909714	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3909715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4006739	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4099573	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6651232	0.84[JPT][hapmap]

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	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030803	chr8:125868684-125969635	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1024405	chr8:125868684-125971035	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1020502	chr8:125868684-125972572	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2725878	LINC00964	cis	Skin Sun Exposed Lower leg	GTEx
rs2725878	WDR67	cis	parietal	SCAN
rs2725878	ATAD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125958600-125959800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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