Variant report

Variant	rs9454616
Chromosome Location	chr6:69486291-69486292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:69473849..69476721-chr6:69483757..69486701,2	K562	blood:
2	chr6:69484056..69486437-chr6:69489948..69492199,2	K562	blood:
3	chr6:69449624..69452933-chr6:69485444..69489658,4	K562	blood:
4	chr6:69479313..69481691-chr6:69485193..69486882,2	K562	blood:
5	chr6:69479313..69482227-chr6:69485193..69487773,3	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1015152	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10945140	0.95[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs11965496	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357618	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1357619	0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs1403927	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1523937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1523947	0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.92[ASN][1000 genomes]
rs1523948	0.90[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1983623	0.84[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs2024562	0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs2064389	0.84[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2140510	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2140511	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177448	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.98[ASN][1000 genomes]
rs2204285	0.85[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206834	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2206836	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2223724	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585601	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs2585603	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs2746128	0.84[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs2746133	0.85[JPT][hapmap]
rs4434435	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4708243	0.83[JPT][hapmap]
rs562010	0.95[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs644877	0.91[EUR][1000 genomes]
rs6455295	0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6455296	1.00[JPT][hapmap]
rs6455298	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6455299	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6455302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6455303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6903692	0.85[ASN][1000 genomes]
rs6907661	0.98[ASN][1000 genomes]
rs6911395	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.98[ASN][1000 genomes]
rs6919103	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6920537	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6924533	0.89[ASN][1000 genomes]
rs6928142	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6929378	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6932940	1.00[JPT][hapmap]
rs7738131	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7738291	1.00[JPT][hapmap]
rs7746943	0.87[GIH][hapmap]
rs7747314	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7751539	0.94[ASN][1000 genomes]
rs7754795	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7755356	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758017	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765583	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771494	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7775093	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9294806	0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9294807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294810	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9294811	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9346239	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9346240	0.88[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs9346241	1.00[ASN][1000 genomes]
rs9346243	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9346245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9346246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs9354800	0.94[ASN][1000 genomes]
rs9360357	0.83[JPT][hapmap]
rs9360360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9360361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9363963	0.84[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9446057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9446058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454621	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9454622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs992784	0.88[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv886131	chr6:69480628-69545903	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9454616	BAI3	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69484600-69487600	Enhancers	Brain Anterior Caudate	brain
2	chr6:69484800-69490000	Enhancers	Fetal Brain Female	brain
3	chr6:69485000-69486400	Enhancers	Fetal Brain Male	brain
4	chr6:69485000-69487600	Enhancers	Brain Cingulate Gyrus	brain
5	chr6:69485000-69490400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:69485400-69487200	Enhancers	Brain Germinal Matrix	brain
7	chr6:69485600-69486400	Weak transcription	Brain Angular Gyrus	brain
8	chr6:69485600-69486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:69485600-69487600	Enhancers	Brain Hippocampus Middle	brain
10	chr6:69485600-69487600	Enhancers	Brain Substantia Nigra	brain
11	chr6:69485600-69488400	Weak transcription	K562	blood
12	chr6:69485800-69487600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr6:69486000-69487600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:69486200-69489600	Enhancers	Fetal Lung	lung

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