Variant report

Variant	rs4545703
Chromosome Location	chr13:52802822-52802823
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1056335	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs11620062	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1327323	0.90[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap]
rs1815348	0.82[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap]
rs1815349	0.82[ASN][1000 genomes]
rs1815350	0.82[ASN][1000 genomes]
rs1865877	0.82[ASN][1000 genomes]
rs2760772	0.80[ASN][1000 genomes]
rs3803264	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs3866534	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3886077	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4369550	0.81[ASN][1000 genomes]
rs4884452	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs4885953	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4886018	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap]
rs4886077	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs4941727	0.81[GIH][hapmap]
rs6561665	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap]
rs7981050	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap]
rs7983971	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7987115	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap]
rs7993748	0.88[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap]
rs9526913	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9535895	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs9535914	0.96[CEU][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9536046	0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs9536048	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs9536052	0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap]
rs9536066	0.88[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap]
rs9568732	0.88[ASW][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs9596643	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs9596648	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs9596651	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv983588	chr13:52772461-52833538	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
8	nsv900083	chr13:52783120-52885838	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4545703	CKAP2	cis	parietal	SCAN
rs4545703	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs4545703	CKAP2	cis	Adipose Subcutaneous	GTEx
rs4545703	CKAP2	cis	Nerve Tibial	GTEx
rs4545703	CKAP2	cis	Artery Tibial	GTEx
rs4545703	CKAP2	cis	Thyroid	GTEx
rs4545703	CKAP2	cis	cerebellum	SCAN
rs4545703	LECT1	cis	parietal	SCAN
rs4545703	CKAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs4545703	ALG11	cis	cerebellum	SCAN
rs4545703	HNRNPA1L2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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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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