Variant report

Variant	rs1470370
Chromosome Location	chr13:67038392-67038393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10507739	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs12859352	0.82[ASN][1000 genomes]
rs12866298	0.93[ASN][1000 genomes]
rs12867615	0.87[ASN][1000 genomes]
rs12868791	0.83[CHB][hapmap]
rs12868964	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs12870336	0.86[ASN][1000 genomes]
rs12877241	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17081420	0.87[ASN][1000 genomes]
rs1932881	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1932883	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1932886	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2324915	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs3843947	0.80[CHD][hapmap]
rs4144493	0.86[ASN][1000 genomes]
rs4379952	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4393452	0.92[CEU][hapmap];0.92[YRI][hapmap]
rs4883779	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4883780	0.81[ASN][1000 genomes]
rs4884677	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4884678	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9317591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs9317595	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9529073	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9529076	0.81[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9529077	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9529079	0.89[ASN][1000 genomes]
rs9529081	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs9529083	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9529084	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs9529087	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9540770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9540772	0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs9540776	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9540784	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs9540785	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9540786	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9540787	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9540788	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs9540789	0.86[ASN][1000 genomes]
rs9540790	0.86[ASN][1000 genomes]
rs9540791	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9540792	0.82[ASN][1000 genomes]
rs9540793	0.82[ASN][1000 genomes]
rs9540796	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs9540799	0.83[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs9540800	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9540803	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9540804	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9540809	0.84[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs9540812	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9540813	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9540817	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs9564317	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9564319	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9564320	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9564321	0.80[JPT][hapmap]
rs9571587	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9571588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs9571595	0.84[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs9571596	0.84[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1470370	GCA	trans	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67036400-67038400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:67036600-67038800	Enhancers	Brain Substantia Nigra	brain
3	chr13:67037000-67038400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:67037200-67038400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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