Variant report

Variant	rs7429094
Chromosome Location	chr3:54337874-54337875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11130416	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[EUR][1000 genomes]
rs11130417	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4928040	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]
rs6445645	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6445648	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[EUR][1000 genomes]
rs6784315	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6810202	0.85[EUR][1000 genomes]
rs7427630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7431577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7434239	0.86[EUR][1000 genomes]
rs7618315	0.85[EUR][1000 genomes]
rs7618850	0.91[ASW][hapmap]
rs7627905	1.00[CEU][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7632823	0.89[CHD][hapmap];0.80[TSI][hapmap]
rs7634811	0.85[EUR][1000 genomes]
rs7652209	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9683195	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9849660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863855	0.94[CEU][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9879885	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7429094	CACNA2D3	cis	brain	BrainEAC
rs7429094	CCDC66	cis	parietal	SCAN
rs7429094	TUSC2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54332200-54343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54333600-54338200	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:54334000-54338000	Weak transcription	Liver	Liver
4	chr3:54334000-54343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:54335800-54338600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:54336800-54340600	Weak transcription	Aorta	Aorta
7	chr3:54337000-54338400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:54337600-54338400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:54337600-54338400	Enhancers	Fetal Lung	lung
10	chr3:54337600-54338400	Enhancers	Left Ventricle	heart
11	chr3:54337600-54338800	Enhancers	Fetal Muscle Leg	muscle
12	chr3:54337600-54339800	Enhancers	Fetal Stomach	stomach
13	chr3:54337800-54338800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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