Variant report

Variant	rs489458
Chromosome Location	chr6:101742573-101742574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1160258	0.83[ASN][1000 genomes]
rs17658674	0.83[ASN][1000 genomes]
rs1948050	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518173	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518319	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629982	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283186	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2852497	0.81[EUR][1000 genomes]
rs2852500	1.00[ASN][1000 genomes]
rs2852502	1.00[ASN][1000 genomes]
rs2852503	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs2852504	1.00[ASN][1000 genomes]
rs2852506	1.00[ASN][1000 genomes]
rs2852507	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs2852509	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs2852511	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2852512	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs471631	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473846	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480221	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484819	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485947	0.94[AFR][1000 genomes]
rs493123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496596	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs500305	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503387	0.81[EUR][1000 genomes]
rs504406	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528879	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542820	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542923	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546327	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550690	0.94[AFR][1000 genomes]
rs566507	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570556	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs577503	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579069	1.00[ASN][1000 genomes]
rs584655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594870	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597750	0.85[AFR][1000 genomes]
rs600842	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608847	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636796	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638255	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649828	0.94[AFR][1000 genomes]
rs661064	0.81[EUR][1000 genomes]
rs662916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668267	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683830	0.94[AFR][1000 genomes]
rs684160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687497	0.82[EUR][1000 genomes]
rs697440	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697441	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808952	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs489458	SNX7	trans	lymphoblastoid	seeQTL
rs489458	TOX3	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101741400-101743800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:101742000-101742600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:101742000-101743200	Enhancers	NHEK	skin
4	chr6:101742000-101745000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr6:101742200-101742600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:101742200-101742600	Enhancers	HMEC	breast
7	chr6:101742400-101742600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:101742400-101744000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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