Variant report

Variant	rs6786490
Chromosome Location	chr3:134613588-134613589
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10935140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706968	0.85[JPT][hapmap]
rs12489360	0.88[JPT][hapmap]
rs12630436	0.83[JPT][hapmap]
rs13068347	0.81[JPT][hapmap]
rs13073341	0.83[JPT][hapmap]
rs13078906	0.88[JPT][hapmap]
rs1399706	0.88[JPT][hapmap]
rs1399707	0.81[JPT][hapmap]
rs1515359	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1515364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1515366	0.88[JPT][hapmap]
rs2280157	0.83[JPT][hapmap]
rs2895696	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs4955458	0.93[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4955508	0.94[JPT][hapmap]
rs4955510	0.87[JPT][hapmap]
rs4955511	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6439530	0.81[JPT][hapmap]
rs6439535	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762621	0.81[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs6779978	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789449	0.81[JPT][hapmap]
rs6793377	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs6796514	0.81[JPT][hapmap]
rs6802089	0.81[JPT][hapmap]
rs7639520	0.93[JPT][hapmap]
rs7639843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643782	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs7645886	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs7653227	0.81[JPT][hapmap]
rs868130	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs884381	0.94[JPT][hapmap]
rs938382	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs9814692	0.93[JPT][hapmap]
rs9819889	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs9825632	0.83[JPT][hapmap]
rs9825687	0.88[JPT][hapmap]
rs9839573	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846488	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9851596	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs9868348	0.84[ASW][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9874291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874607	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	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
rs6786490	EPHB1	cis	cerebellum	SCAN
rs6786490	RAB6B	cis	cerebellum	SCAN
rs6786490	EPHB1	cis	parietal	SCAN
rs6786490	KY	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134610800-134617400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:134611200-134616200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:134611400-134619600	Weak transcription	GM12878-XiMat	blood
4	chr3:134612200-134622000	Weak transcription	Brain Germinal Matrix	brain
5	chr3:134612400-134614200	Enhancers	Brain Cingulate Gyrus	brain
6	chr3:134612400-134614400	Enhancers	Dnd41	blood
7	chr3:134612800-134613800	Enhancers	Brain Substantia Nigra	brain
8	chr3:134612800-134614000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr3:134612800-134615000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:134613200-134614600	Enhancers	Brain Anterior Caudate	brain
11	chr3:134613400-134613800	Enhancers	Fetal Brain Female	brain
12	chr3:134613400-134614000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:134613400-134614000	Enhancers	Brain Hippocampus Middle	brain

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