Variant report

Variant	rs61958118
Chromosome Location	chr13:53170226-53170227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53169737..53172275-chr13:53234901..53237385,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11148260	0.85[ASN][1000 genomes]
rs11616261	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11617331	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811894	0.88[ASN][1000 genomes]
rs1811895	0.88[ASN][1000 genomes]
rs2038826	0.86[ASN][1000 genomes]
rs2147692	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2575960	0.82[ASN][1000 genomes]
rs342768	0.82[ASN][1000 genomes]
rs342770	0.82[ASN][1000 genomes]
rs3742297	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4301905	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4335671	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4885325	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55688428	0.85[ASN][1000 genomes]
rs61959716	0.84[ASN][1000 genomes]
rs6561671	0.84[ASN][1000 genomes]
rs6561675	0.80[ASN][1000 genomes]
rs7139495	0.87[ASN][1000 genomes]
rs7334137	0.80[ASN][1000 genomes]
rs7334677	0.80[ASN][1000 genomes]
rs7336771	0.80[ASN][1000 genomes]
rs7399901	0.83[ASN][1000 genomes]
rs7997186	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7999849	0.83[ASN][1000 genomes]
rs9526950	0.81[EUR][1000 genomes]
rs9526951	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526968	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526974	0.84[ASN][1000 genomes]
rs9526975	0.84[ASN][1000 genomes]
rs9526982	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9536185	0.80[EUR][1000 genomes]
rs9536190	0.80[EUR][1000 genomes]
rs9536197	0.84[ASN][1000 genomes]
rs9536202	0.85[ASN][1000 genomes]
rs9536211	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536212	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536217	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9536219	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536223	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536236	0.84[ASN][1000 genomes]
rs9536247	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9536262	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
5	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
6	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
7	nsv1038132	chr13:53057359-53190994	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	esv2760295	chr13:53071152-53178504	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv900087	chr13:53119704-53208030	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv976118	chr13:53120951-53171671	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv13738	chr13:53159859-53177755	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61958118	CKAP2	cis	Artery Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53161000-53173000	Weak transcription	Fetal Heart	heart
2	chr13:53167600-53171400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr13:53168400-53173000	Weak transcription	Osteobl	bone
4	chr13:53168800-53172800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:53169000-53171400	Weak transcription	HepG2	liver
6	chr13:53169000-53174000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:53169400-53173200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:53169800-53171000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:53170200-53172800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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