Variant report

Variant	rs12225299
Chromosome Location	chr11:60084465-60084466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1020288	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10431136	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10750932	0.86[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs10750933	0.86[EUR][1000 genomes]
rs10750934	0.85[EUR][1000 genomes]
rs10750935	0.83[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs10792264	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10792265	0.82[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs10792267	0.86[EUR][1000 genomes]
rs10792268	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10897027	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10897028	0.85[EUR][1000 genomes]
rs10897030	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10897031	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10897032	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10897033	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10897044	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs10897045	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs10897046	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs10897047	0.83[CEU][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs10897048	0.83[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10897049	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11230239	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11230240	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11230243	0.84[EUR][1000 genomes]
rs11230248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230275	0.90[JPT][hapmap]
rs11230276	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs11230280	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605188	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11605235	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12792791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12798157	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12802385	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1443250	0.95[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1899571	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1899572	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289614	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2304933	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304935	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304936	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2868118	0.84[EUR][1000 genomes]
rs2868119	0.84[EUR][1000 genomes]
rs2868120	0.84[EUR][1000 genomes]
rs2868121	0.83[CEU][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs35905922	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4477457	0.86[EUR][1000 genomes]
rs4506675	0.83[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes]
rs61900468	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7103808	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7108879	0.85[EUR][1000 genomes]
rs7116069	0.85[EUR][1000 genomes]
rs7924433	0.83[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs7931525	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7950431	0.83[CEU][hapmap];0.90[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	esv3449168	chr11:60084417-60085198	Weak transcription Flanking Active TSS Enhancers	lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12225299	OR8J1	cis	cerebellum	SCAN
rs12225299	MS4A4A	cis	cerebellum	SCAN
rs12225299	ZP1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:60083800-60084600	Flanking Active TSS	GM12878-XiMat	blood
2	chr11:60083800-60086200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:60084400-60086400	Weak transcription	Placenta	Placenta

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