Variant report

Variant	rs4299453
Chromosome Location	chr3:55826780-55826781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12631767	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1495368	0.95[ASN][1000 genomes]
rs1495369	0.95[ASN][1000 genomes]
rs17272960	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17332241	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17714443	0.91[ASN][1000 genomes]
rs2168818	0.96[ASN][1000 genomes]
rs2315943	0.84[ASN][1000 genomes]
rs35664654	0.95[ASN][1000 genomes]
rs4129821	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4129822	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4129823	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4260395	0.89[ASN][1000 genomes]
rs4493400	0.96[ASN][1000 genomes]
rs4521190	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4955877	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs4955878	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap]
rs4955879	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4955880	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4955881	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4955883	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4974144	0.95[ASN][1000 genomes]
rs4974145	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4974146	0.89[ASN][1000 genomes]
rs56912263	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57802485	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60551886	0.95[ASN][1000 genomes]
rs61072124	0.95[ASN][1000 genomes]
rs72877116	0.87[ASN][1000 genomes]
rs73076938	0.95[ASN][1000 genomes]
rs73076939	0.95[ASN][1000 genomes]
rs73076947	0.97[ASN][1000 genomes]
rs7641474	0.92[ASN][1000 genomes]
rs9815001	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs9835091	0.85[CHB][hapmap]
rs9838012	0.89[ASN][1000 genomes]
rs9846380	0.91[ASN][1000 genomes]
rs9852746	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs9852888	0.82[CHB][hapmap]
rs9853067	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9854025	0.81[ASN][1000 genomes]
rs9854247	0.81[ASN][1000 genomes]
rs9857120	0.81[ASN][1000 genomes]
rs9866297	0.88[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4299453	HESX1	cis	cerebellum	SCAN
rs4299453	CCDC66	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55817200-55830600	Weak transcription	Pancreas	Pancrea
2	chr3:55823000-55826800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:55825200-55830400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:55825200-55831000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:55825400-55829200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:55826000-55827000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:55826200-55826800	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr3:55826400-55830600	Weak transcription	Fetal Lung	lung

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