Variant report

Variant	rs590240
Chromosome Location	chr11:57024830-57024831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10736682	0.86[YRI][hapmap]
rs10792083	0.81[JPT][hapmap]
rs10896595	0.87[ASN][1000 genomes]
rs10896596	0.94[EUR][1000 genomes]
rs10896597	0.95[ASN][1000 genomes]
rs10896599	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896601	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11228968	0.89[ASN][1000 genomes]
rs11228971	0.94[EUR][1000 genomes]
rs11228975	0.89[ASN][1000 genomes]
rs11228976	0.89[ASN][1000 genomes]
rs11228978	0.89[ASN][1000 genomes]
rs11228980	0.89[ASN][1000 genomes]
rs11228982	0.83[ASN][1000 genomes]
rs11228984	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11228985	0.87[ASN][1000 genomes]
rs11602501	0.96[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs11604560	0.89[ASN][1000 genomes]
rs11605053	0.87[ASN][1000 genomes]
rs11607817	0.89[ASN][1000 genomes]
rs12419065	0.81[ASN][1000 genomes]
rs12421633	0.89[ASN][1000 genomes]
rs12421755	0.89[ASN][1000 genomes]
rs12792781	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12797769	0.88[ASN][1000 genomes]
rs17572970	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17573746	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs17651610	0.89[ASN][1000 genomes]
rs17652078	0.89[ASN][1000 genomes]
rs1892963	0.89[ASN][1000 genomes]
rs1892964	0.95[ASN][1000 genomes]
rs1893675	0.86[YRI][hapmap]
rs1939489	0.87[ASN][1000 genomes]
rs1939495	0.89[ASN][1000 genomes]
rs1939496	0.85[EUR][1000 genomes]
rs2155230	0.89[ASN][1000 genomes]
rs2155231	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226613	0.86[ASN][1000 genomes]
rs2276038	0.82[JPT][hapmap]
rs2511026	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511029	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511030	0.95[ASN][1000 genomes]
rs2846042	0.95[ASN][1000 genomes]
rs2846049	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2846050	0.95[ASN][1000 genomes]
rs2846051	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2851722	0.95[ASN][1000 genomes]
rs35610294	0.88[ASN][1000 genomes]
rs3935068	0.85[ASN][1000 genomes]
rs4384399	0.89[ASN][1000 genomes]
rs4565915	0.87[ASN][1000 genomes]
rs479949	0.95[ASN][1000 genomes]
rs4938855	0.89[ASN][1000 genomes]
rs4938857	0.89[ASN][1000 genomes]
rs4938859	0.88[ASN][1000 genomes]
rs4938861	0.84[ASN][1000 genomes]
rs4939129	0.84[EUR][1000 genomes]
rs4939131	0.83[EUR][1000 genomes]
rs4939132	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs499318	0.95[ASN][1000 genomes]
rs5012051	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs519277	0.95[ASN][1000 genomes]
rs522656	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528101	0.95[ASN][1000 genomes]
rs58295319	0.81[ASN][1000 genomes]
rs599947	1.00[ASN][1000 genomes]
rs625565	0.95[ASN][1000 genomes]
rs652016	0.92[ASN][1000 genomes]
rs654635	0.95[ASN][1000 genomes]
rs6591413	0.89[ASN][1000 genomes]
rs6591415	0.89[ASN][1000 genomes]
rs6591416	0.87[ASN][1000 genomes]
rs6591417	0.87[ASN][1000 genomes]
rs7102963	0.89[ASN][1000 genomes]
rs7120644	0.89[ASN][1000 genomes]
rs7128371	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7130020	0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs7130252	0.89[ASN][1000 genomes]
rs72921992	0.86[ASN][1000 genomes]
rs7931298	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7935236	0.83[ASN][1000 genomes]
rs7936545	0.91[EUR][1000 genomes]
rs7948723	0.83[EUR][1000 genomes]
rs948844	0.86[YRI][hapmap]

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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs590240	OR4C6	cis	parietal	SCAN
rs590240	OR5M9	cis	cerebellum	SCAN
rs590240	GLYATL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57017200-57026000	Weak transcription	Fetal Brain Male	brain
2	chr11:57018200-57028800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:57023600-57028400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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