Variant report

Variant	rs11229438
Chromosome Location	chr11:58191203-58191204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10896734	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap]
rs11229350	0.85[EUR][1000 genomes]
rs11229358	0.85[EUR][1000 genomes]
rs11229359	0.85[EUR][1000 genomes]
rs11229371	0.88[EUR][1000 genomes]
rs11229385	0.81[EUR][1000 genomes]
rs11229439	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11229479	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229532	0.94[ASN][1000 genomes]
rs11229535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11229537	0.94[ASN][1000 genomes]
rs11229544	0.94[ASN][1000 genomes]
rs11229552	0.91[ASN][1000 genomes]
rs11494130	0.85[EUR][1000 genomes]
rs11494131	0.85[EUR][1000 genomes]
rs11541682	0.92[ASN][1000 genomes]
rs12361789	0.85[EUR][1000 genomes]
rs12361887	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362065	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs12365107	0.85[GIH][hapmap]
rs12365551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17473544	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17489568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17568220	0.91[ASN][1000 genomes]
rs1800169	0.91[ASN][1000 genomes]
rs1938601	0.89[ASN][1000 genomes]
rs1944051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2096558	0.81[GIH][hapmap]
rs2298607	0.91[ASN][1000 genomes]
rs3829218	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[TSI][hapmap];0.97[ASN][1000 genomes]
rs4482047	0.82[EUR][1000 genomes]
rs57106977	0.85[EUR][1000 genomes]
rs57922517	0.86[EUR][1000 genomes]
rs58085299	0.85[EUR][1000 genomes]
rs60767173	0.91[ASN][1000 genomes]
rs60998298	0.97[ASN][1000 genomes]
rs7111679	0.85[GIH][hapmap]
rs7112350	0.97[ASN][1000 genomes]
rs73470773	0.89[ASN][1000 genomes]
rs73470778	0.89[ASN][1000 genomes]
rs734777	0.88[EUR][1000 genomes]
rs73481989	0.85[EUR][1000 genomes]
rs73484144	0.88[EUR][1000 genomes]
rs7481388	0.94[ASN][1000 genomes]
rs7482383	0.94[ASN][1000 genomes]
rs7484263	0.89[ASN][1000 genomes]
rs7945889	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs948562	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[TSI][hapmap];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11229438	OR4C6	cis	parietal	SCAN
rs11229438	CD5	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58191200-58191600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr11:58191200-58192400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr11:58191200-58192600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr11:58191200-58192800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr11:58191200-58193000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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