Variant report

Variant	rs2099526
Chromosome Location	chr3:49269758-49269759
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10154992	0.82[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130183	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720542	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs12637346	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs2082923	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs4384984	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955414	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955417	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4955421	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs6446256	0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778080	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809851	0.92[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7429661	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432077	0.83[EUR][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7619016	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9860285	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9867285	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.80[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	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2099526	AMT	cis	Artery Tibial	GTEx
rs2099526	AMT	cis	Adipose Subcutaneous	GTEx
rs2099526	WDR6	cis	Nerve Tibial	GTEx
rs2099526	AMT	cis	lung	GTEx
rs2099526	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs2099526	NICN1-AS1	cis	Thyroid	GTEx
rs2099526	NICN1	cis	Thyroid	GTEx
rs2099526	AMT	cis	Whole Blood	GTEx
rs2099526	AMT	cis	Esophagus Mucosa	GTEx
rs2099526	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs2099526	AMT	cis	Artery Aorta	GTEx
rs2099526	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs2099526	AMT	cis	Nerve Tibial	GTEx
rs2099526	AMT	cis	Thyroid	GTEx
rs2099526	AMT	cis	Muscle Skeletal	GTEx
rs2099526	WDR6	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49250200-49274000	Weak transcription	Osteobl	bone
2	chr3:49256600-49275800	Weak transcription	NHLF	lung
3	chr3:49266200-49292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:49266600-49270200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:49266800-49270000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:49267000-49270000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:49268400-49269800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:49268800-49270600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:49269400-49270200	Strong transcription	Ovary	ovary
10	chr3:49269600-49271600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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