Variant report

Variant	rs6472078
Chromosome Location	chr8:49745347-49745348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10103815	0.96[ASN][1000 genomes]
rs10108018	0.96[ASN][1000 genomes]
rs1023769	0.94[JPT][hapmap]
rs11779318	0.94[ASN][1000 genomes]
rs11783791	0.97[ASN][1000 genomes]
rs1482261	0.83[ASW][hapmap]
rs28620290	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891648	0.83[ASW][hapmap]
rs4873087	0.87[ASN][1000 genomes]
rs4873290	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6989076	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7007780	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7831003	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv890854	chr8:49738821-49838908	Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6472078	EFCAB1	cis	cerebellum	SCAN
rs6472078	KIAA0146	cis	parietal	SCAN
rs6472078	EFCAB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:49734000-49748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:49734600-49747800	Weak transcription	NHEK	skin
3	chr8:49737600-49747800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:49740800-49746000	Weak transcription	Fetal Lung	lung
5	chr8:49744800-49746600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr8:49745000-49745400	Enhancers	HSMMtube	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