Variant report

Variant	rs9568713
Chromosome Location	chr13:52699834-52699835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52699126..52701652-chr13:52702989..52705135,2	K562	blood:

Variant related genes	Relation type
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1004576	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1055062	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1060631	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11616964	0.86[ASN][1000 genomes]
rs11620583	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs12146904	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12431310	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12584961	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12585654	0.91[AFR][1000 genomes]
rs1571189	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1801243	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs1801244	0.82[CEU][hapmap]
rs1886538	0.81[CHB][hapmap]
rs1886542	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]
rs1886543	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886544	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1886547	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924611	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs1998696	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2004866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs2181891	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs2274202	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2277448	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2296347	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2296348	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2296349	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2296350	0.99[ASN][1000 genomes]
rs2408544	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2408549	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408551	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2408552	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2408554	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2408609	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.99[ASN][1000 genomes]
rs2408611	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.99[ASN][1000 genomes]
rs28393037	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2897964	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2897976	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2897977	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.99[ASN][1000 genomes]
rs3368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]
rs35895576	0.88[ASN][1000 genomes]
rs3742288	0.82[CEU][hapmap]
rs3742289	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3783242	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3818422	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3825527	0.82[CEU][hapmap]
rs3825528	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs4297592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4497567	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4941727	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs55772266	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61958812	0.95[ASN][1000 genomes]
rs6561656	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6650383	0.90[ASN][1000 genomes]
rs723102	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs723103	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs732071	0.81[CHB][hapmap]
rs7320831	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7321120	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7321435	0.81[CHB][hapmap]
rs7324458	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7327634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs7337430	0.88[ASN][1000 genomes]
rs747781	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs755363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7981904	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7991237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs7993492	0.81[ASN][1000 genomes]
rs7995946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998770	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7999812	0.84[CEU][hapmap]
rs9316563	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9526819	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9526821	0.85[ASN][1000 genomes]
rs9526823	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526825	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526832	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526841	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9526842	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9535812	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535822	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9535825	0.81[CHB][hapmap]
rs9535826	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9535828	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[YRI][hapmap]
rs9535829	0.85[ASN][1000 genomes]
rs9535832	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9535833	0.86[ASN][1000 genomes]
rs9535836	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9535849	0.91[ASN][1000 genomes]
rs9535851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535856	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs9535858	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535860	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535861	0.82[CHB][hapmap]
rs9535862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535867	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535872	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535873	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9535878	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]
rs9535879	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9535880	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.99[ASN][1000 genomes]
rs9535882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs9535885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[ASN][1000 genomes]
rs9535887	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.97[ASN][1000 genomes]
rs9563084	0.86[ASN][1000 genomes]
rs9563089	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs9563091	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9563093	0.97[ASN][1000 genomes]
rs9568682	0.81[CHB][hapmap]
rs9568693	0.91[ASN][1000 genomes]
rs9568695	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568708	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9568713	CKAP2	cis	cerebellum	SCAN
rs9568713	CKAP2	cis	parietal	SCAN
rs9568713	LOC440138	cis	multi-tissue	Pritchard
rs9568713	NCRNA00282	cis	cerebellum	SCAN
rs9568713	CKAP2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52694400-52701600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr13:52699000-52701800	Enhancers	K562	blood

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