Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:157188238-157188643	T-47D	breast:	n/a	n/a
2	GATA2	chr3:157188268-157188590	HUVEC	blood vessel:	n/a	n/a
3	GATA3	chr3:157188173-157188667	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
VEPH1	TF binding region

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12635273	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1350149	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2165873	0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2316337	0.81[ASN][1000 genomes]
rs4258914	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4611770	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679796	0.96[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680371	0.82[CHB][hapmap]
rs4680372	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs62280977	0.81[ASN][1000 genomes]
rs62280978	0.81[ASN][1000 genomes]
rs62280979	0.81[ASN][1000 genomes]
rs62280980	0.81[ASN][1000 genomes]
rs62280981	0.81[ASN][1000 genomes]
rs62280982	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67118252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67228252	0.81[ASN][1000 genomes]
rs6779693	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73158530	0.81[ASN][1000 genomes]
rs9682174	0.82[CHB][hapmap]
rs988757	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1011060	VEPH1	cis	cerebellum	SCAN
rs1011060	C3orf55	cis	parietal	SCAN
rs1011060	RAD9A	trans	cerebellum	SCAN

Chromatin state (count:18 , 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	chr3:157182800-157190400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:157183000-157188400	Weak transcription	Fetal Stomach	stomach
4	chr3:157184400-157190400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:157185600-157189600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:157185600-157211400	Weak transcription	HSMM	muscle
7	chr3:157186000-157193400	Weak transcription	NHLF	lung
8	chr3:157187000-157189400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:157187200-157189800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:157187400-157193600	Weak transcription	NH-A	brain
11	chr3:157187600-157210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:157187800-157188400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr3:157187800-157193400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:157188000-157188800	Genic enhancers	HUVEC	blood vessel
15	chr3:157188000-157203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:157188200-157193600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:157188200-157193600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:157188200-157193800	Weak transcription	Osteobl	bone

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