Variant report

Variant	rs10239799
Chromosome Location	chr7:120405335-120405336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10225453	0.81[CHB][hapmap]
rs10231690	0.82[EUR][1000 genomes]
rs10266755	0.82[ASW][hapmap]
rs12673992	0.93[ASW][hapmap];0.91[GIH][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3823861	0.87[ASW][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs41624	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs41629	0.82[ASW][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs41632	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6466759	0.81[CHB][hapmap]
rs6466760	0.81[CHB][hapmap]
rs6466761	0.81[CHB][hapmap]
rs6953454	0.81[CHB][hapmap]
rs6968447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978494	0.82[EUR][1000 genomes]
rs727228	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73425858	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73425863	0.86[EUR][1000 genomes]
rs7791571	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs996903	0.80[ASW][hapmap];0.81[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10239799	TSPAN12	cis	Artery Tibial	GTEx
rs10239799	SPAM1	cis	parietal	SCAN
rs10239799	WASL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120401600-120407000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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