Variant report

Variant	rs6809204
Chromosome Location	chr3:49369383-49369384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1009051	0.80[EUR][1000 genomes]
rs10154992	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155014	0.87[EUR][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs1106620	0.83[EUR][1000 genomes]
rs11130183	1.00[ASN][1000 genomes]
rs11130186	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11710434	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715060	0.83[EUR][1000 genomes]
rs11719762	0.93[EUR][1000 genomes]
rs11720542	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	0.87[EUR][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.87[EUR][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs2029591	1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329025	0.82[EUR][1000 genomes]
rs3448	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs3870339	0.80[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4384984	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855858	0.80[EUR][1000 genomes]
rs4855869	0.80[EUR][1000 genomes]
rs4955413	0.87[EUR][1000 genomes]
rs4955414	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955417	0.83[EUR][1000 genomes]
rs4955421	1.00[ASN][1000 genomes]
rs4955423	1.00[ASN][1000 genomes]
rs4955424	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4955425	0.90[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127630	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57273516	0.82[EUR][1000 genomes]
rs62259933	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.81[EUR][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	0.92[EUR][1000 genomes]
rs6446275	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6769744	0.93[EUR][1000 genomes]
rs6769821	1.00[ASN][1000 genomes]
rs6775069	0.91[EUR][1000 genomes]
rs6778080	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783003	0.81[EUR][1000 genomes]
rs6784203	0.91[EUR][1000 genomes]
rs6785045	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796147	0.88[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809851	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72934271	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7613491	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619789	0.82[EUR][1000 genomes]
rs7620024	0.86[EUR][1000 genomes]
rs7626076	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	1.00[ASN][1000 genomes]
rs7638750	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647973	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.86[EUR][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs974495	0.93[EUR][1000 genomes]
rs9811047	0.82[EUR][1000 genomes]
rs9812360	0.85[EUR][1000 genomes]
rs9817807	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	1.00[ASN][1000 genomes]
rs9842132	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.88[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	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6809204	ARIH2	cis	Thyroid	GTEx
rs6809204	AMT	cis	lung	GTEx
rs6809204	AMT	cis	Nerve Tibial	GTEx
rs6809204	AMT	cis	Artery Tibial	GTEx
rs6809204	AMT	cis	Adipose Subcutaneous	GTEx
rs6809204	AMT	cis	Muscle Skeletal	GTEx
rs6809204	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs6809204	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs6809204	WDR6	cis	Muscle Skeletal	GTEx
rs6809204	AMT	cis	Esophagus Muscularis	GTEx
rs6809204	AMT	cis	Artery Aorta	GTEx
rs6809204	AMT	cis	Whole Blood	GTEx
rs6809204	AMT	cis	Esophagus Mucosa	GTEx
rs6809204	NICN1	cis	Thyroid	GTEx
rs6809204	AMT	cis	Thyroid	GTEx
rs6809204	NICN1-AS1	cis	Thyroid	GTEx
rs6809204	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	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
4	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
5	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
7	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:49320200-49375000	Strong transcription	Thymus	Thymus
12	chr3:49321800-49373600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:49326800-49373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:49326800-49375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49333600-49369600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:49335000-49369400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:49335000-49375000	Strong transcription	Placenta	Placenta
18	chr3:49335200-49369800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:49335200-49375200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr3:49338200-49375000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:49350400-49370200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:49350400-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:49350600-49369800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:49350600-49370600	Strong transcription	Adipose Nuclei	Adipose
25	chr3:49350800-49370400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:49351400-49373000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr3:49351400-49374200	Strong transcription	Dnd41	blood
28	chr3:49351600-49373400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:49352000-49375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:49352000-49375000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:49352200-49375000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:49352800-49374800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:49354200-49369600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:49354800-49376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:49355000-49370200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:49357400-49374800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:49362600-49372000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:49362600-49374400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:49362600-49376800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:49362800-49370400	Weak transcription	Fetal Heart	heart
41	chr3:49363200-49376800	Weak transcription	Small Intestine	intestine
42	chr3:49363400-49369800	Weak transcription	HSMM	muscle
43	chr3:49363400-49371000	Weak transcription	Hela-S3	cervix
44	chr3:49363400-49371800	Weak transcription	Psoas Muscle	Psoas
45	chr3:49363400-49376600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:49363400-49376800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:49365000-49370600	Weak transcription	Aorta	Aorta
48	chr3:49365200-49369800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:49365200-49370800	Weak transcription	Brain Anterior Caudate	brain
50	chr3:49365200-49371000	Weak transcription	Pancreas	Pancrea

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