Variant report

Variant	rs6786886
Chromosome Location	chr3:118681862-118681863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10934470	0.88[JPT][hapmap]
rs11919143	0.84[EUR][1000 genomes]
rs12491833	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1369580	0.89[JPT][hapmap]
rs1369581	0.87[JPT][hapmap]
rs1369582	0.89[JPT][hapmap]
rs1435662	0.89[JPT][hapmap]
rs1435667	0.89[JPT][hapmap]
rs2160052	0.93[ASW][hapmap]
rs2866317	0.86[ASW][hapmap]
rs4687835	0.89[JPT][hapmap]
rs4687959	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438481	0.86[JPT][hapmap]
rs6773729	0.80[EUR][1000 genomes]
rs6792805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613076	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7641626	0.89[JPT][hapmap];0.81[YRI][hapmap]
rs9289117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824063	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848979	0.86[ASW][hapmap]
rs9861978	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872674	0.89[JPT][hapmap]
rs9878706	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6786886	UPK1B	cis	parietal	SCAN
rs6786886	OR52E8	trans	cerebellum	SCAN
rs6786886	IGSF11	cis	parietal	SCAN
rs6786886	EBLN2	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118675600-118684800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:118676800-118684000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:118679000-118688200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:118680000-118683800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:118680200-118684600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:118680200-118684600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:118680200-118684800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:118680200-118686600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:118680200-118686600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:118680200-118688200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:118680200-118688200	Weak transcription	Ovary	ovary
12	chr3:118681200-118694000	Enhancers	Brain Substantia Nigra	brain
13	chr3:118681400-118683400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:118681400-118683400	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:118681400-118684000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:118681400-118690000	Enhancers	Brain Hippocampus Middle	brain
17	chr3:118681600-118682200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:118681600-118683400	Enhancers	Brain Angular Gyrus	brain
19	chr3:118681800-118683400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:118681800-118692800	Enhancers	Brain Anterior Caudate	brain

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