Variant report

Variant	rs11229439
Chromosome Location	chr11:58192611-58192612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10896734	0.84[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs11229369	0.88[EUR][1000 genomes]
rs11229371	0.80[ASN][1000 genomes]
rs11229438	0.84[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229440	0.84[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs11229479	0.97[ASN][1000 genomes]
rs11229532	0.91[ASN][1000 genomes]
rs11229535	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11229537	0.91[ASN][1000 genomes]
rs11229544	0.91[ASN][1000 genomes]
rs11229552	0.88[ASN][1000 genomes]
rs11541682	0.90[ASN][1000 genomes]
rs12361887	0.97[ASN][1000 genomes]
rs12362065	0.84[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12365107	0.92[GIH][hapmap]
rs12365551	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17473544	0.90[ASN][1000 genomes]
rs17489568	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17568220	0.88[ASN][1000 genomes]
rs1800169	1.00[ASW][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[TSI][hapmap];0.88[ASN][1000 genomes]
rs1938601	0.87[ASN][1000 genomes]
rs1944051	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2096558	0.88[GIH][hapmap]
rs2298607	0.88[ASN][1000 genomes]
rs3829218	0.84[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs60767173	0.88[ASN][1000 genomes]
rs60998298	0.94[ASN][1000 genomes]
rs7111679	0.92[GIH][hapmap]
rs7112350	0.94[ASN][1000 genomes]
rs73470773	0.87[ASN][1000 genomes]
rs73470778	0.87[ASN][1000 genomes]
rs7481388	0.91[ASN][1000 genomes]
rs7482383	0.91[ASN][1000 genomes]
rs7484263	0.87[ASN][1000 genomes]
rs7945889	0.84[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs948562	0.84[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv517849	chr11:58129053-58264181	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1042491	chr11:58134936-58263639	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11229439	OR4C6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58191200-58192800	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr11:58191200-58193000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr11:58191600-58192800	Enhancers	HUES48 Cell Line	embryonic stem cell

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