Variant report

Variant	rs9536098
Chromosome Location	chr13:53058891-53058892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr13:53058865-53059328	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TPTE2P3	TF binding region
ENSG00000244471	TF binding region
LINC00345	TF binding region

Extended variants
information (count: 150 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1053245	0.81[EUR][1000 genomes]
rs11148250	0.81[EUR][1000 genomes]
rs11148262	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12184815	0.81[EUR][1000 genomes]
rs1436728	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1925135	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2118093	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2760780	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2760801	0.82[CEU][hapmap]
rs342774	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs342777	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs34355831	0.84[AMR][1000 genomes]
rs35975091	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3809374	1.00[JPT][hapmap]
rs41292810	0.81[EUR][1000 genomes]
rs4539485	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4542538	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4884223	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4884629	1.00[CEU][hapmap]
rs4885804	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4885887	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4885910	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs55850688	0.81[EUR][1000 genomes]
rs56173235	0.81[EUR][1000 genomes]
rs56249382	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57412438	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57831032	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57904860	0.81[EUR][1000 genomes]
rs58655347	0.94[EUR][1000 genomes]
rs61011708	0.81[EUR][1000 genomes]
rs61677410	0.81[EUR][1000 genomes]
rs617660	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs61957307	0.84[AMR][1000 genomes]
rs61957983	0.84[AMR][1000 genomes]
rs61957987	0.84[AMR][1000 genomes]
rs61957988	0.84[AMR][1000 genomes]
rs61957995	0.81[EUR][1000 genomes]
rs61957997	0.81[EUR][1000 genomes]
rs61958009	0.84[AMR][1000 genomes]
rs61958011	0.81[EUR][1000 genomes]
rs61958012	0.84[AMR][1000 genomes]
rs61958017	0.81[EUR][1000 genomes]
rs61958018	0.84[AMR][1000 genomes]
rs61958019	0.81[EUR][1000 genomes]
rs61958020	0.81[EUR][1000 genomes]
rs61958026	0.81[EUR][1000 genomes]
rs61958052	0.81[EUR][1000 genomes]
rs61958053	0.81[EUR][1000 genomes]
rs61959660	0.81[EUR][1000 genomes]
rs61959668	0.81[EUR][1000 genomes]
rs61959673	0.81[EUR][1000 genomes]
rs61959674	0.81[EUR][1000 genomes]
rs61959679	0.81[EUR][1000 genomes]
rs61959707	0.87[EUR][1000 genomes]
rs61959711	0.93[AFR][1000 genomes]
rs630892	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs646498	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6561673	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6561674	1.00[CEU][hapmap]
rs6561676	1.00[JPT][hapmap]
rs6561677	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs676306	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs693991	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7319451	0.82[CEU][hapmap]
rs7325840	1.00[JPT][hapmap]
rs7330193	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7330361	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7335270	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7987405	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7995188	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7996692	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7999466	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs8000715	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9316581	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9316583	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9526882	0.81[EUR][1000 genomes]
rs9526908	0.81[EUR][1000 genomes]
rs9526909	0.84[AMR][1000 genomes]
rs9526910	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9526915	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9526916	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9526924	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9526926	0.87[EUR][1000 genomes]
rs9526957	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9526958	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9526966	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9526970	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9526976	1.00[JPT][hapmap]
rs9526978	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9535968	1.00[CEU][hapmap]
rs9536004	0.81[EUR][1000 genomes]
rs9536009	0.81[EUR][1000 genomes]
rs9536018	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536019	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536025	0.84[AMR][1000 genomes]
rs9536026	0.84[AMR][1000 genomes]
rs9536028	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536029	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs9536034	0.84[AMR][1000 genomes]
rs9536040	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9536041	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536042	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536044	0.81[EUR][1000 genomes]
rs9536047	0.84[AMR][1000 genomes]
rs9536049	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs9536050	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9536053	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs9536056	0.84[AMR][1000 genomes]
rs9536057	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9536058	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536060	0.81[EUR][1000 genomes]
rs9536061	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9536062	0.84[AMR][1000 genomes]
rs9536064	0.81[EUR][1000 genomes]
rs9536067	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536070	0.81[EUR][1000 genomes]
rs9536072	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536073	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536075	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9536076	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536077	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536078	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536080	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536083	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536084	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9536085	0.81[EUR][1000 genomes]
rs9536087	0.87[EUR][1000 genomes]
rs9536090	0.87[EUR][1000 genomes]
rs9536097	0.87[EUR][1000 genomes]
rs9536099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9536184	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs9536222	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536228	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536232	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9536235	1.00[CEU][hapmap]
rs9536238	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9568747	1.00[JPT][hapmap]
rs971513	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs973198	1.00[CEU][hapmap];1.00[JPT][hapmap]

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	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9536098	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53058800-53059600	Enhancers	HepG2	liver

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