Variant report

Variant	rs2590665
Chromosome Location	chr8:125955401-125955402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2382999	0.88[JPT][hapmap]
rs2555724	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555725	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2590667	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2725878	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]
rs28455785	0.94[ASN][1000 genomes]
rs28558480	0.94[ASN][1000 genomes]
rs28870400	0.94[ASN][1000 genomes]
rs3866472	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3909714	0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3909715	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4006739	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4099573	0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2590665	ATAD2	cis	cerebellum	SCAN
rs2590665	LINC00964	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125950000-125958200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:125953200-125955600	Enhancers	Fetal Heart	heart
3	chr8:125954200-125956600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr8:125954600-125956600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr8:125955000-125955600	Enhancers	Psoas Muscle	Psoas
6	chr8:125955000-125956200	Enhancers	Skeletal Muscle Male	skeletal muscle

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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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