Variant report

Variant	rs2158123
Chromosome Location	chr7:79931904-79931905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10081383	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10215570	0.86[ASN][1000 genomes]
rs10224409	0.86[ASN][1000 genomes]
rs10226374	0.90[ASN][1000 genomes]
rs10235376	0.96[ASN][1000 genomes]
rs10245039	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10246790	0.86[ASN][1000 genomes]
rs10249625	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10265717	0.81[JPT][hapmap]
rs10267427	0.81[JPT][hapmap]
rs10269645	0.86[ASN][1000 genomes]
rs10480799	0.81[JPT][hapmap]
rs10954137	0.97[ASN][1000 genomes]
rs13222182	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13224358	0.96[EUR][1000 genomes]
rs13226877	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13229096	0.90[ASN][1000 genomes]
rs13230620	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13233772	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13234088	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13237208	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13237302	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13237312	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13238619	0.91[ASN][1000 genomes]
rs13243724	0.97[ASN][1000 genomes]
rs1878214	0.80[JPT][hapmap]
rs1995971	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2048474	0.97[ASN][1000 genomes]
rs28584961	0.90[ASN][1000 genomes]
rs28875814	0.86[ASN][1000 genomes]
rs304773	0.93[JPT][hapmap]
rs304774	0.87[JPT][hapmap]
rs304775	0.93[JPT][hapmap]
rs3914181	0.86[ASN][1000 genomes]
rs4731318	0.93[EUR][1000 genomes]
rs56186526	0.82[AFR][1000 genomes]
rs67417372	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966532	0.93[JPT][hapmap]
rs7782930	0.95[ASN][1000 genomes]
rs7785183	0.97[ASN][1000 genomes]
rs7788512	0.82[JPT][hapmap]
rs7788673	0.81[EUR][1000 genomes]
rs7792873	0.81[EUR][1000 genomes]
rs7797587	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7798039	0.97[ASN][1000 genomes]
rs9656355	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs979425	0.97[ASN][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	nsv429785	chr7:79589749-80177049	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1024312	chr7:79832637-80004812	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1029180	chr7:79832637-80017560	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2158123	GNAI1	cis	parietal	SCAN
rs2158123	RPL13AP17	cis	parietal	SCAN
rs2158123	RPS6KA5	trans	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79923800-79932400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:79930800-79933000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:79930800-79933600	Enhancers	Fetal Brain Male	brain
4	chr7:79931600-79934000	Enhancers	Fetal Brain Female	brain
5	chr7:79931800-79936400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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