Variant report

Variant	rs10961040
Chromosome Location	chr9:13397944-13397945
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10115277	0.84[EUR][1000 genomes]
rs10961035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10961038	0.85[EUR][1000 genomes]
rs10961041	0.82[EUR][1000 genomes]
rs10961042	0.84[EUR][1000 genomes]
rs10961043	0.84[EUR][1000 genomes]
rs12000439	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12339589	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339756	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12340743	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12343381	0.84[EUR][1000 genomes]
rs12348720	0.85[EUR][1000 genomes]
rs12348887	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12349249	0.85[EUR][1000 genomes]
rs12351125	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12352551	0.83[EUR][1000 genomes]
rs12352741	0.85[EUR][1000 genomes]
rs12353283	0.84[EUR][1000 genomes]
rs17190837	0.85[EUR][1000 genomes]
rs17191126	0.84[EUR][1000 genomes]
rs1927649	0.85[EUR][1000 genomes]
rs2017195	0.84[EUR][1000 genomes]
rs34776649	0.84[ASN][1000 genomes]
rs57935015	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59092758	0.84[EUR][1000 genomes]
rs6474770	0.83[EUR][1000 genomes]
rs7027951	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7045055	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7048018	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7048309	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73410180	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73410188	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73410195	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7849940	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7857179	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs880023	0.83[EUR][1000 genomes]
rs9987546	0.83[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	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2752281	chr9:13284600-13405072	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831515	chr9:13333205-13517308	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10961040	RP11-536O18.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13395400-13409600	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:13395600-13398000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:13396600-13399200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:13397200-13398200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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