Variant report

Variant	rs11720542
Chromosome Location	chr3:49357427-49357428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10154992	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155014	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs11130183	1.00[ASN][1000 genomes]
rs11130186	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130189	0.83[AFR][1000 genomes]
rs11130190	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11710434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719762	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11720657	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637346	0.83[AMR][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs1464569	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs2082923	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2099526	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs4384984	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4955413	0.83[EUR][1000 genomes]
rs4955414	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955417	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4955421	1.00[ASN][1000 genomes]
rs4955423	1.00[ASN][1000 genomes]
rs4955424	0.87[EUR][1000 genomes]
rs4955425	0.86[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127630	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57273516	0.81[AMR][1000 genomes]
rs62259933	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs6446256	1.00[ASN][1000 genomes]
rs6446257	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446262	0.88[EUR][1000 genomes]
rs6446275	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6769744	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6769821	1.00[ASN][1000 genomes]
rs6775069	0.87[EUR][1000 genomes]
rs6778080	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784203	0.87[EUR][1000 genomes]
rs6785045	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796147	0.84[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809204	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809851	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619789	0.81[AMR][1000 genomes]
rs7620024	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7626076	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.82[EUR][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9654010	0.83[AMR][1000 genomes]
rs974495	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9811047	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9812360	0.81[EUR][1000 genomes]
rs9817807	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	1.00[ASN][1000 genomes]
rs9834535	0.84[AMR][1000 genomes]
rs9842132	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867285	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	1.00[ASN][1000 genomes]
rs9881860	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11720542	AMT	cis	Artery Tibial	GTEx
rs11720542	AMT	cis	Thyroid	GTEx
rs11720542	AMT	cis	lung	GTEx
rs11720542	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs11720542	AMT	cis	Nerve Tibial	GTEx
rs11720542	AMT	cis	Muscle Skeletal	GTEx
rs11720542	NICN1	cis	Thyroid	GTEx
rs11720542	AMT	cis	Artery Aorta	GTEx
rs11720542	AMT	cis	Esophagus Mucosa	GTEx
rs11720542	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs11720542	AMT	cis	Whole Blood	GTEx
rs11720542	WDR6	cis	Muscle Skeletal	GTEx
rs11720542	NICN1-AS1	cis	Thyroid	GTEx
rs11720542	AMT	cis	Esophagus Muscularis	GTEx
rs11720542	AMT	cis	Adipose Subcutaneous	GTEx
rs11720542	PFKFB4	cis	Nerve Tibial	GTEx
rs11720542	WDR6	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
5	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
6	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
8	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:49320200-49375000	Strong transcription	Thymus	Thymus
13	chr3:49320800-49368000	Strong transcription	Primary T cells from cord blood	blood
14	chr3:49321800-49373600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:49326800-49373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:49326800-49375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:49333600-49369600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:49335000-49365200	Strong transcription	Spleen	Spleen
19	chr3:49335000-49369400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:49335000-49375000	Strong transcription	Placenta	Placenta
21	chr3:49335200-49365200	Strong transcription	Lung	lung
22	chr3:49335200-49369800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:49335200-49375200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:49335400-49365200	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:49336200-49365600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:49338200-49361600	Weak transcription	Stomach Mucosa	stomach
27	chr3:49338200-49375000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:49348200-49358200	Weak transcription	Psoas Muscle	Psoas
29	chr3:49348400-49361200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:49348600-49361800	Weak transcription	Fetal Brain Male	brain
31	chr3:49348800-49358200	Weak transcription	A549	lung
32	chr3:49349000-49358000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:49349000-49358000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:49349000-49359600	Weak transcription	Hela-S3	cervix
35	chr3:49349000-49362400	Weak transcription	Fetal Heart	heart
36	chr3:49350400-49367600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:49350400-49370200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:49350400-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:49350600-49365200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:49350600-49365200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:49350600-49365400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:49350600-49365400	Strong transcription	Fetal Intestine Large	intestine
43	chr3:49350600-49369800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:49350600-49370600	Strong transcription	Adipose Nuclei	Adipose
45	chr3:49350800-49368000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:49350800-49370400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:49351000-49365400	Strong transcription	Brain Angular Gyrus	brain
48	chr3:49351400-49365200	Strong transcription	Fetal Brain Female	brain
49	chr3:49351400-49365400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:49351400-49365600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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