Variant report

Variant	rs60221109
Chromosome Location	chr2:114537300-114537301
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10209330	0.81[AFR][1000 genomes]
rs11685086	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11692142	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3870303	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3982388	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849276	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56884727	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57489086	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58511785	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59123894	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62170104	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62170106	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62170136	0.83[EUR][1000 genomes]
rs72946678	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs60221109	DDX11L2	cis	Esophagus Mucosa	GTEx
rs60221109	DDX11L2	cis	Whole Blood	GTEx
rs60221109	RPL23AP7	cis	Artery Tibial	GTEx
rs60221109	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs60221109	DDX11L2	cis	Artery Tibial	GTEx
rs60221109	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs60221109	DDX11L2	cis	Heart Left Ventricle	GTEx
rs60221109	DDX11L2	cis	lung	GTEx
rs60221109	DDX11L2	cis	Muscle Skeletal	GTEx
rs60221109	RPL23AP7	cis	Muscle Skeletal	GTEx
rs60221109	RPL23AP7	cis	Whole Blood	GTEx
rs60221109	RPL23AP7	cis	lung	GTEx
rs60221109	RPL23AP7	cis	Artery Aorta	GTEx
rs60221109	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs60221109	DDX11L2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114534800-114537800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:114537000-114538400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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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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