Variant report

Variant	rs12361887
Chromosome Location	chr11:58255678-58255679
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11229438	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229439	0.97[ASN][1000 genomes]
rs11229440	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap]
rs11229479	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229532	0.94[ASN][1000 genomes]
rs11229535	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11229537	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11229544	0.94[ASN][1000 genomes]
rs11229552	0.92[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11541682	0.92[ASN][1000 genomes]
rs12365107	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs12365551	0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17473544	0.92[ASN][1000 genomes]
rs17489568	0.91[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs17568220	0.92[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1800169	0.92[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1938601	0.89[ASN][1000 genomes]
rs1944051	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2298607	0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs3829218	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60767173	0.91[ASN][1000 genomes]
rs60998298	0.97[ASN][1000 genomes]
rs7112350	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73470773	0.89[ASN][1000 genomes]
rs73470778	0.89[ASN][1000 genomes]
rs7481388	0.94[ASN][1000 genomes]
rs7482383	0.94[ASN][1000 genomes]
rs7484263	0.89[ASN][1000 genomes]
rs7945889	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs948562	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv976518	chr11:58247628-58271109	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12361887	OR4C6	cis	parietal	SCAN
rs12361887	DAK	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58252400-58265200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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