Variant report

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1016306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1248858	0.81[CHB][hapmap]
rs1248860	0.80[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs13081745	0.85[CHB][hapmap]
rs1694977	0.81[CHB][hapmap]
rs1872553	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1872556	0.86[CHB][hapmap]
rs2035561	0.81[CHB][hapmap]
rs2035562	0.81[CHB][hapmap]
rs2326123	0.86[CHB][hapmap]
rs4301023	0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4499618	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4856559	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6549009	0.85[CHB][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.86[MKK][hapmap]
rs7651996	0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs765461	0.85[CHB][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap]
rs9816652	0.82[ASN][1000 genomes]
rs9831123	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs9834688	0.81[ASN][1000 genomes]
rs9840607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1016305	GJB4	trans	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85068600-85090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85079600-85083200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:85079600-85083600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:85079600-85086400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:85080000-85083400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:85081400-85088800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:85082200-85086400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:85082200-85088800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:85082400-85083800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:85082600-85083600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr3:85082600-85090000	Weak transcription	Fetal Brain Female	brain
12	chr3:85082600-85090400	Weak transcription	Fetal Brain Male	brain
13	chr3:85082600-85091600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:85082800-85083000	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:85082800-85083200	Enhancers	Brain Anterior Caudate	brain
16	chr3:85082800-85083600	Enhancers	Brain Angular Gyrus	brain
17	chr3:85082800-85083600	Enhancers	Brain Hippocampus Middle	brain
18	chr3:85082800-85083800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:85082800-85083800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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