Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:25396590-25397140	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr3:25396603-25397151	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RNA5SP126	TF binding region

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11707139	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709169	0.89[ASN][1000 genomes]
rs11709623	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11709732	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714481	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11716065	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11717848	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11718046	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11718836	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720675	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11721271	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17016187	0.96[GIH][hapmap];0.88[JPT][hapmap]
rs17016260	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164476	0.84[JPT][hapmap]
rs57697446	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6550962	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6550963	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6550966	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771956	0.89[ASN][1000 genomes]
rs6774199	0.89[ASN][1000 genomes]
rs6799363	0.89[ASN][1000 genomes]
rs7615094	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7615609	0.89[ASN][1000 genomes]
rs7623030	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7649070	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9822411	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs9877461	1.00[CEU][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap]

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	nsv949035	chr3:25194301-26084890	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
2	nsv834645	chr3:25363723-25555107	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17588596	AZI2	cis	cerebellum	SCAN
rs17588596	UBE2D3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25395200-25397000	Enhancers	Osteobl	bone
2	chr3:25395200-25397400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:25395800-25397200	Enhancers	Fetal Lung	lung
4	chr3:25395800-25397400	Enhancers	NHDF-Ad	bronchial
5	chr3:25396000-25397400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:25396200-25397000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:25396200-25397000	Enhancers	Fetal Stomach	stomach
8	chr3:25396200-25398000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:25396400-25397000	Weak transcription	NH-A	brain
10	chr3:25396600-25397000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:25396800-25397000	Enhancers	Aorta	Aorta
12	chr3:25396800-25397200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:25396800-25397800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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