Variant report

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11712475	0.91[ASN][1000 genomes]
rs11716284	1.00[JPT][hapmap]
rs11716674	1.00[JPT][hapmap]
rs11718407	0.91[ASN][1000 genomes]
rs12489940	0.91[ASN][1000 genomes]
rs12493260	1.00[JPT][hapmap]
rs12493623	0.95[ASN][1000 genomes]
rs12630117	1.00[JPT][hapmap]
rs1449336	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4076707	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4076709	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4373100	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4408898	0.95[ASN][1000 genomes]
rs4428220	0.95[ASN][1000 genomes]
rs4428221	0.95[ASN][1000 genomes]
rs4927998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4928001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6445630	0.91[ASN][1000 genomes]
rs6809942	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73085903	0.91[ASN][1000 genomes]
rs73085927	0.82[ASN][1000 genomes]
rs7623444	0.85[EUR][1000 genomes]
rs7639142	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9880023	SPATA12	cis	cerebellum	SCAN
rs9880023	MANF	cis	cerebellum	SCAN
rs9880023	POC1A	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54159800-54180400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:54160000-54180200	Weak transcription	Hela-S3	cervix
3	chr3:54170800-54180200	Weak transcription	Right Atrium	heart
4	chr3:54174000-54180400	Weak transcription	Brain Anterior Caudate	brain
5	chr3:54174800-54180200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:54177000-54180200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:54177000-54180200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:54177000-54180200	Weak transcription	Ovary	ovary
9	chr3:54177200-54180200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:54177200-54183000	Weak transcription	H9 Cell Line	embryonic stem cell

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