Variant report

Variant	rs6445639
Chromosome Location	chr3:54330010-54330011
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs3934631	0.88[GIH][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes]
rs3934632	0.88[GIH][hapmap]
rs3934633	1.00[YRI][hapmap]
rs4078006	0.88[GIH][hapmap]
rs4078007	0.88[GIH][hapmap]
rs55719584	0.83[EUR][1000 genomes]
rs56034762	0.82[AFR][1000 genomes]
rs56208940	0.84[EUR][1000 genomes]
rs56271940	0.85[AFR][1000 genomes]
rs56362821	0.85[AFR][1000 genomes]
rs57836319	0.85[AFR][1000 genomes]
rs57945354	0.82[AFR][1000 genomes]
rs58682581	0.83[EUR][1000 genomes]
rs58976292	0.82[AFR][1000 genomes]
rs59461034	0.82[AFR][1000 genomes]
rs59771874	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59804657	0.82[AFR][1000 genomes]
rs59965289	0.83[EUR][1000 genomes]
rs61200778	0.85[AFR][1000 genomes]
rs61444952	0.82[AFR][1000 genomes]
rs6445641	0.85[AFR][1000 genomes]
rs6445643	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs6769501	0.84[EUR][1000 genomes]
rs6792199	1.00[YRI][hapmap]
rs6804595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6807491	1.00[YRI][hapmap]
rs73081630	0.85[EUR][1000 genomes]
rs7427601	0.85[AFR][1000 genomes]
rs7428712	0.84[AFR][1000 genomes]
rs7430091	0.84[AFR][1000 genomes]
rs7432978	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7434141	1.00[YRI][hapmap]
rs7434171	0.84[AFR][1000 genomes]
rs7626696	0.83[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7627905	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7632823	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs7649860	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9714322	0.82[AFR][1000 genomes]
rs9863855	0.87[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876806	chr3:54256648-54330010	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6445639	CACNA2D2	cis	cerebellum	SCAN
rs6445639	MANF	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54328600-54331000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:54328800-54330800	Weak transcription	H9 Cell Line	embryonic stem cell

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