Variant report

Variant	rs61959711
Chromosome Location	chr13:53054276-53054277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs56249382	0.99[AFR][1000 genomes]
rs659848	0.86[ASN][1000 genomes]
rs664827	0.86[ASN][1000 genomes]
rs9536044	0.86[ASN][1000 genomes]
rs9536090	1.00[ASN][1000 genomes]
rs9536097	0.86[ASN][1000 genomes]
rs9536098	0.93[AFR][1000 genomes]
rs9536153	1.00[ASN][1000 genomes]
rs9536167	1.00[ASN][1000 genomes]
rs9536168	1.00[ASN][1000 genomes]
rs9536169	1.00[ASN][1000 genomes]
rs9536170	1.00[ASN][1000 genomes]
rs9536172	0.86[ASN][1000 genomes]
rs9536173	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv900085	chr13:53022518-53216622	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv900086	chr13:53030565-53208030	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	14 gene(s)	inside rSNPs	diseases
9	nsv976117	chr13:53051476-53058376	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2421964	chr13:53051526-53160234	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61959711	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53030400-53055800	Weak transcription	Lung	lung
2	chr13:53034400-53054400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr13:53038200-53055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:53042800-53054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:53050000-53055400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:53050000-53058800	Weak transcription	HepG2	liver
7	chr13:53051000-53055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr13:53051400-53054800	Weak transcription	Osteobl	bone
9	chr13:53051400-53055200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr13:53051400-53055400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr13:53051400-53055400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr13:53051800-53055000	Weak transcription	HMEC	breast
13	chr13:53052000-53055200	Weak transcription	HSMM	muscle

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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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