Variant report

Variant	rs2082923
Chromosome Location	chr3:49255172-49255173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs10154992	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130183	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11720542	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs12637346	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs2099526	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	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955414	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955417	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4955421	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[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	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778080	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809851	0.90[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7429661	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432077	0.85[EUR][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.92[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	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9860285	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9867285	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2082923	AMT	cis	Nerve Tibial	GTEx
rs2082923	WDR6	cis	Nerve Tibial	GTEx
rs2082923	AMT	cis	lung	GTEx
rs2082923	AMT	cis	Artery Aorta	GTEx
rs2082923	AMT	cis	Muscle Skeletal	GTEx
rs2082923	NICN1-AS1	cis	Thyroid	GTEx
rs2082923	NICN1	cis	Thyroid	GTEx
rs2082923	PFKFB4	cis	Nerve Tibial	GTEx
rs2082923	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs2082923	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs2082923	AMT	cis	Adipose Subcutaneous	GTEx
rs2082923	ARIH2	cis	Thyroid	GTEx
rs2082923	AMT	cis	Whole Blood	GTEx
rs2082923	AMT	cis	Esophagus Mucosa	GTEx
rs2082923	AMT	cis	Thyroid	GTEx
rs2082923	AMT	cis	Esophagus Muscularis	GTEx
rs2082923	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs2082923	AMT	cis	Artery Tibial	GTEx
rs2082923	WDR6	cis	Muscle Skeletal	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49237600-49255600	Weak transcription	Left Ventricle	heart
2	chr3:49238200-49255400	Weak transcription	Right Ventricle	heart
3	chr3:49243200-49255200	Weak transcription	Fetal Heart	heart
4	chr3:49245800-49255200	Weak transcription	Right Atrium	heart
5	chr3:49246800-49255200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:49247400-49255400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:49249200-49255400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:49250200-49274000	Weak transcription	Osteobl	bone
9	chr3:49250800-49255200	Weak transcription	NHDF-Ad	bronchial
10	chr3:49251000-49255400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:49251400-49255200	Weak transcription	Aorta	Aorta
12	chr3:49251400-49255200	Weak transcription	Spleen	Spleen
13	chr3:49251600-49255200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:49251600-49255200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:49251600-49255400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:49251600-49265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:49251800-49255200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:49251800-49255200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:49251800-49255200	Weak transcription	Adipose Nuclei	Adipose
20	chr3:49251800-49255200	Weak transcription	Fetal Stomach	stomach
21	chr3:49251800-49255200	Weak transcription	Pancreas	Pancrea
22	chr3:49251800-49255400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:49251800-49255400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:49251800-49255600	Weak transcription	NHLF	lung
25	chr3:49252000-49255200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:49252000-49265600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:49253000-49255200	Weak transcription	HUVEC	blood vessel
28	chr3:49253200-49255200	Weak transcription	Ovary	ovary
29	chr3:49253200-49256600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:49253400-49255200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:49253400-49255200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:49253400-49255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:49253400-49255200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:49255000-49256800	Enhancers	Fetal Muscle Leg	muscle

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