Variant report

Variant	rs4459870
Chromosome Location	chr3:55829060-55829061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1008	0.81[EUR][1000 genomes]
rs1495365	0.83[CHB][hapmap]
rs1495366	0.83[CHB][hapmap]
rs2315942	0.93[EUR][1000 genomes]
rs2315944	0.87[EUR][1000 genomes]
rs4246673	0.86[EUR][1000 genomes]
rs4542991	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4572738	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4592994	0.81[EUR][1000 genomes]
rs4955877	0.82[CHB][hapmap]
rs4955882	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955884	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4974113	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4974147	0.87[ASN][1000 genomes]
rs4974148	0.85[EUR][1000 genomes]
rs55665761	0.82[EUR][1000 genomes]
rs6445754	0.89[EUR][1000 genomes]
rs6790618	0.81[EUR][1000 genomes]
rs7615473	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7616709	0.85[EUR][1000 genomes]
rs7617962	0.81[EUR][1000 genomes]
rs7641474	0.82[ASN][1000 genomes]
rs9809248	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9815001	0.89[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9815091	0.80[EUR][1000 genomes]
rs9828807	0.87[EUR][1000 genomes]
rs9835091	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9840522	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9846380	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9852746	0.89[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9852888	0.89[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9853067	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs9854025	0.86[ASN][1000 genomes]
rs9854247	0.86[ASN][1000 genomes]
rs9857120	0.88[ASN][1000 genomes]
rs9860951	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9866297	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9874792	0.85[ASN][1000 genomes]
rs9879933	0.93[EUR][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	nsv876814	chr3:55802749-55860526	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4459870	CCDC66	cis	parietal	SCAN
rs4459870	TWF2	cis	parietal	SCAN
rs4459870	RRP9	cis	cerebellum	SCAN
rs4459870	HESX1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55817200-55830600	Weak transcription	Pancreas	Pancrea
2	chr3:55825200-55830400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:55825200-55831000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:55825400-55829200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:55826400-55830600	Weak transcription	Fetal Lung	lung
6	chr3:55826800-55830800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:55827000-55830200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links