Variant report

Variant	rs2555724
Chromosome Location	chr8:125955586-125955587
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2555725	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2590665	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590667	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2725878	0.91[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28455785	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28558480	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28870400	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3866472	0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs3909714	0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs3909715	0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4006739	0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4099573	0.94[ASN][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2555724	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

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

what's new

Quick links