Variant report

Variant	rs3017858
Chromosome Location	chr18:12210278-12210279
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11080549	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11080550	0.80[AFR][1000 genomes]
rs12454161	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12604417	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12605163	0.84[EUR][1000 genomes]
rs12605170	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12607481	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276369	0.88[EUR][1000 genomes]
rs2276370	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2851905	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2851907	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34185303	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4261610	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4347689	0.84[EUR][1000 genomes]
rs4528645	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4569357	0.83[EUR][1000 genomes]
rs56101236	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57801464	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs60401418	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62099061	0.80[EUR][1000 genomes]
rs62099085	0.85[EUR][1000 genomes]
rs6505725	0.82[EUR][1000 genomes]
rs7226400	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7239448	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8083709	0.82[EUR][1000 genomes]
rs8084532	0.81[EUR][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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1055343	chr18:12107012-12226356	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv960252	chr18:12161216-12220798	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3017858	RP11-64C12.3	cis	lung	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12209200-12217400	Weak transcription	NHEK	skin
2	chr18:12209400-12218600	Weak transcription	Hela-S3	cervix

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