Variant report

Variant	rs9294806
Chromosome Location	chr6:69439486-69439487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:69438284..69440310-chr6:69450555..69453510,2	K562	blood:
2	chr6:69399809..69401625-chr6:69437402..69440315,2	K562	blood:
3	chr6:69438379..69440553-chr6:69446567..69448077,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10945140	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs1357618	0.89[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap]
rs1357619	0.83[JPT][hapmap]
rs1403927	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1523937	0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs1523947	1.00[JPT][hapmap];0.94[MEX][hapmap]
rs1523948	0.85[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap]
rs1983623	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs2024562	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2064389	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2140510	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2177448	1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2204285	0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2206834	1.00[JPT][hapmap]
rs2206836	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2223724	0.80[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2257875	0.86[EUR][1000 genomes]
rs2585601	0.89[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs2585603	0.89[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2746128	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs2746133	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs4708243	0.83[JPT][hapmap]
rs562010	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[ASN][1000 genomes]
rs6455295	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6455298	1.00[JPT][hapmap]
rs6455302	1.00[JPT][hapmap]
rs6455303	1.00[JPT][hapmap]
rs6911395	0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs6920537	0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs6928142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6929378	1.00[JPT][hapmap]
rs6932940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738291	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7739996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7746943	0.98[GIH][hapmap];0.82[TSI][hapmap]
rs7747313	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7747314	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754795	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755356	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7769724	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9294807	1.00[JPT][hapmap]
rs9294810	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs9294811	1.00[JPT][hapmap]
rs9346239	1.00[JPT][hapmap]
rs9346240	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs9346243	1.00[JPT][hapmap]
rs9346245	1.00[JPT][hapmap]
rs9346246	0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9354796	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9360357	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs9360361	0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs9363961	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9363963	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446057	1.00[JPT][hapmap];0.94[MEX][hapmap]
rs9446058	1.00[JPT][hapmap]
rs9454611	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9454616	0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9454621	0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs9454622	1.00[JPT][hapmap]
rs992784	0.92[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9294806	BAI3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69436600-69444200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:69436800-69440200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:69438000-69441000	Enhancers	Fetal Lung	lung
4	chr6:69438600-69440400	Weak transcription	Fetal Brain Male	brain
5	chr6:69439200-69439600	Flanking Active TSS	Brain Cingulate Gyrus	brain
6	chr6:69439200-69439600	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr6:69439200-69440800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr6:69439200-69441000	Active TSS	Brain Angular Gyrus	brain
9	chr6:69439200-69441000	Active TSS	Brain Anterior Caudate	brain
10	chr6:69439400-69440200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:69439400-69441000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:69439400-69441000	Active TSS	Brain Substantia Nigra	brain
13	chr6:69439400-69442400	Weak transcription	K562	blood

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