Variant report

Variant	rs4679796
Chromosome Location	chr3:157186678-157186679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1011060	0.96[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12635273	0.88[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4258914	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4611770	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62280982	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67118252	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6779693	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs988757	0.89[AMR][1000 genomes];0.91[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv963283	chr3:157183446-157186979	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4679796	RAD9A	trans	cerebellum	SCAN
rs4679796	VEPH1	cis	cerebellar cortex	BrainEAC
rs4679796	PTX3	cis	cerebellum	SCAN
rs4679796	BCAR3	trans	lymphoblastoid	seeQTL
rs4679796	C3orf55	cis	parietal	SCAN
rs4679796	VEPH1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157160400-157195000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:157170200-157187000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:157182800-157190400	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr3:157183000-157188400	Weak transcription	Fetal Stomach	stomach
5	chr3:157184200-157187000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr3:157184400-157190400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:157185400-157187200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:157185600-157186800	Weak transcription	NH-A	brain
9	chr3:157185600-157187000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:157185600-157187200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:157185600-157189600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:157185600-157211400	Weak transcription	HSMM	muscle
13	chr3:157186000-157187000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:157186000-157187000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:157186000-157187200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:157186000-157188000	Strong transcription	Osteobl	bone
17	chr3:157186000-157193400	Weak transcription	NHLF	lung
18	chr3:157186200-157187000	Weak transcription	HUVEC	blood vessel
19	chr3:157186400-157186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:157186600-157187000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:157186600-157187600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:157186600-157188200	Enhancers	Primary monocytes fromperipheralblood	blood

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