Variant report

Variant	rs6561665
Chromosome Location	chr13:52917592-52917593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52917176..52917696-chr13:53382727..53383690,2	K562	blood:
2	chr13:52917213..52918202-chr13:53024381..53024988,3	K562	blood:
3	chr13:52917157..52919301-chr13:53024221..53025626,7	MCF-7	breast:
4	chr13:52917335..52918274-chr13:53024499..53025207,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136100	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1056335	0.89[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs11148252	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs11618716	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs11620062	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1327323	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13431	0.81[ASN][1000 genomes]
rs1815348	0.90[CHB][hapmap]
rs1815669	0.81[ASN][1000 genomes]
rs2296347	0.87[MEX][hapmap]
rs3783242	0.87[MEX][hapmap]
rs3803262	0.81[ASN][1000 genomes]
rs3803264	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3818422	0.95[MEX][hapmap]
rs3886077	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3892337	0.86[CHB][hapmap]
rs4286007	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4545703	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap]
rs4884320	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4884354	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs4884452	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs4885953	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4886018	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs4886077	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs61958050	0.83[ASN][1000 genomes]
rs7321964	0.86[CHB][hapmap]
rs7323666	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs7333451	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7336679	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs7981050	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7981732	0.89[ASN][1000 genomes]
rs7983971	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7985262	0.83[ASN][1000 genomes]
rs7987115	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[ASN][1000 genomes]
rs7990581	0.86[CHB][hapmap]
rs7993748	0.90[CHB][hapmap]
rs8001624	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs9379	0.89[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs9526913	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs9526914	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535895	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9535914	0.82[CEU][hapmap]
rs9536046	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536048	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs9536052	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536066	0.86[CHB][hapmap]
rs9536069	0.81[ASN][1000 genomes]
rs9536079	0.86[CHB][hapmap]
rs9568728	0.83[ASN][1000 genomes]
rs9568732	0.86[CHB][hapmap]
rs9568734	0.80[CHB][hapmap]
rs9596643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9596648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9596651	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[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	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
7	nsv977243	chr13:52915464-52918841	Active TSS Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6561665	CKAP2	cis	Artery Tibial	GTEx
rs6561665	VPS36	cis	cerebellum	SCAN
rs6561665	LECT1	cis	parietal	SCAN
rs6561665	CKAP2	cis	parietal	SCAN
rs6561665	ATP7B	cis	cerebellum	SCAN
rs6561665	CKAP2	cis	Adipose Subcutaneous	GTEx
rs6561665	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs6561665	HNRNPA1L2	cis	cerebellum	SCAN
rs6561665	CKAP2	cis	Thyroid	GTEx
rs6561665	CKAP2	cis	cerebellum	SCAN
rs6561665	CKAP2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52913000-52918000	Weak transcription	HSMM	muscle
2	chr13:52913000-52918200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:52913400-52918200	Weak transcription	HepG2	liver
4	chr13:52913400-52918800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:52917400-52917600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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