Variant report

Variant	rs10853221
Chromosome Location	chr18:12160297-12160298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10853218	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10853220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11080540	0.83[EUR][1000 genomes]
rs11662286	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11662304	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11663207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11664969	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12605611	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12606540	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12607922	0.84[EUR][1000 genomes]
rs16972943	0.81[EUR][1000 genomes]
rs35578149	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4528646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56032100	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56153833	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56250185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56966010	0.84[EUR][1000 genomes]
rs57902247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9966458	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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10853221	RP11-64C12.3	cis	lung	GTEx
rs10853221	RP11-64C12.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12154200-12183800	Weak transcription	Pancreas	Pancrea
2	chr18:12160200-12160600	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr18:12160200-12160800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr18:12160200-12160800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr18:12160200-12160800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr18:12160200-12160800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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