Variant report

Variant	rs7981732
Chromosome Location	chr13:52912217-52912218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1815669	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3886077	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4884452	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4885953	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6561664	0.86[EUR][1000 genomes]
rs6561665	0.89[ASN][1000 genomes]
rs6561666	0.83[EUR][1000 genomes]
rs7334583	0.83[EUR][1000 genomes]
rs7399631	0.82[EUR][1000 genomes]
rs7400602	0.82[EUR][1000 genomes]
rs7987115	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7993748	0.81[EUR][1000 genomes]
rs9526913	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9536006	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568728	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9596643	0.94[ASN][1000 genomes]
rs9596648	0.82[ASN][1000 genomes]
rs9596649	0.83[EUR][1000 genomes]
rs9596651	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv819887	chr13:52772113-52926921	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7981732	CKAP2	cis	Artery Tibial	GTEx
rs7981732	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs7981732	CKAP2	cis	Thyroid	GTEx
rs7981732	CKAP2	cis	Adipose Subcutaneous	GTEx
rs7981732	CKAP2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52911800-52913400	Enhancers	HepG2	liver
2	chr13:52912000-52912400	Enhancers	HMEC	breast
3	chr13:52912000-52913000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:52912200-52913000	Enhancers	HSMM	muscle
5	chr13:52912200-52913400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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Input of quick search could be:

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

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