Variant report

Variant	rs4369534
Chromosome Location	chr13:67091273-67091274
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:67090368..67092830-chr13:67094169..67095769,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs17410188	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17494498	0.91[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs17583099	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1932880	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1932892	0.89[YRI][hapmap]
rs1932893	0.82[YRI][hapmap]
rs2152741	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2152742	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2184839	0.91[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2210927	0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2210928	0.85[ASW][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324909	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs2324911	0.83[YRI][hapmap]
rs2324914	0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324916	0.89[YRI][hapmap]
rs3922753	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315244	0.93[GIH][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403934	1.00[ASN][1000 genomes]
rs4884673	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4884679	0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4884680	0.88[YRI][hapmap]
rs6562458	0.82[YRI][hapmap]
rs73194772	1.00[ASN][1000 genomes]
rs73194773	1.00[ASN][1000 genomes]
rs73196691	1.00[ASN][1000 genomes]
rs73196694	1.00[ASN][1000 genomes]
rs7321336	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321696	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323944	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324673	0.91[CEU][hapmap]
rs7326921	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334257	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7339194	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7991352	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998429	0.80[AMR][1000 genomes]
rs7998682	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002783	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920863	0.91[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9317592	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9317593	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529075	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9529100	0.82[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs9540778	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9540779	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9540780	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9571591	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530416	chr13:66198235-67126195	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1053763	chr13:66210166-67184972	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541811	chr13:66210166-67184972	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv932195	chr13:66215786-67215733	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv530723	chr13:66219650-67200316	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1052017	chr13:66232288-67213033	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv534503	chr13:66287963-67126195	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv915828	chr13:66544825-67212201	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1041133	chr13:66723731-67530595	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv1051051	chr13:66948744-67126296	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv900390	chr13:66990736-67094634	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv2757538	chr13:67005812-67119200	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv2759943	chr13:67005812-67119200	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv2422196	chr13:67041890-67295480	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv832639	chr13:67049800-67223701	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv900391	chr13:67080274-67133203	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv900392	chr13:67080274-67166073	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv900393	chr13:67080274-67180045	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv900394	chr13:67090292-67180045	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4369534	CCDC59	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67088600-67094600	Weak transcription	Brain Substantia Nigra	brain
2	chr13:67089000-67094600	Weak transcription	Brain Angular Gyrus	brain
3	chr13:67089000-67096600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:67089200-67095000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr13:67089200-67095000	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:67091000-67092000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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