Variant report

Variant	rs17016260
Chromosome Location	chr3:25392580-25392581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11707139	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11709169	0.96[ASN][1000 genomes]
rs11709623	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11709732	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714481	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11716065	0.93[EUR][1000 genomes]
rs11717848	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718046	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718836	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720675	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11721271	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1436251	0.83[ASN][1000 genomes]
rs17016187	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs17588596	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1905465	0.85[ASN][1000 genomes]
rs2164476	1.00[JPT][hapmap]
rs57697446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550961	0.85[ASN][1000 genomes]
rs6550962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6550966	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771956	0.96[ASN][1000 genomes]
rs6774199	0.96[ASN][1000 genomes]
rs6799363	0.96[ASN][1000 genomes]
rs7615094	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615609	0.96[ASN][1000 genomes]
rs7623030	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649070	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9822411	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9877461	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17016260	AZI2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25386800-25396200	Weak transcription	Fetal Stomach	stomach
2	chr3:25388600-25395200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:25390400-25392600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:25390400-25393200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:25390800-25392800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:25391200-25393400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:25391400-25393400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:25392400-25392800	Enhancers	Fetal Brain Male	brain
9	chr3:25392400-25396800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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