Variant report

Variant	rs12239085
Chromosome Location	chr1:186541360-186541361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10489394	0.87[AMR][1000 genomes]
rs10489395	0.87[AMR][1000 genomes]
rs12239322	1.00[AMR][1000 genomes]
rs12239327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374242	0.87[AMR][1000 genomes]
rs13376114	0.87[AMR][1000 genomes]
rs13376658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825448	0.87[AMR][1000 genomes]
rs16825457	0.87[AMR][1000 genomes]
rs1929094	0.87[AMR][1000 genomes]
rs3934201	0.87[AMR][1000 genomes]
rs56158125	1.00[AMR][1000 genomes]
rs56888492	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57020506	1.00[AMR][1000 genomes]
rs57488115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58300321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58336827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58410196	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60957652	0.87[AMR][1000 genomes]
rs6425029	0.87[AMR][1000 genomes]
rs6673816	0.87[AMR][1000 genomes]
rs6679283	1.00[AMR][1000 genomes]
rs6688055	0.87[AMR][1000 genomes]
rs7355201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7355203	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7530502	0.87[AMR][1000 genomes]
rs9803910	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186535800-186544400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:186539600-186544000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:186539600-186544000	Weak transcription	Osteobl	bone
4	chr1:186540000-186544400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:186541000-186546200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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