Variant report

Variant	rs11720657
Chromosome Location	chr3:49392620-49392621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49376682..49378615-chr3:49390504..49394214,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1009051	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs10154992	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs10155014	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10865956	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs1106620	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130183	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs11130186	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11710434	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715060	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11719762	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11720542	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	0.86[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.86[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	0.86[CEU][hapmap]
rs2029591	1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	1.00[ASN][1000 genomes]
rs2131108	1.00[ASN][1000 genomes]
rs2140270	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329025	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3448	0.86[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs3866330	0.86[CEU][hapmap]
rs3870339	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs3905330	0.86[CEU][hapmap]
rs4052546	0.80[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855858	0.84[EUR][1000 genomes]
rs4855869	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4955413	0.93[EUR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955417	0.86[CEU][hapmap]
rs4955421	1.00[ASN][1000 genomes]
rs4955423	1.00[ASN][1000 genomes]
rs4955424	0.96[EUR][1000 genomes]
rs4955425	0.95[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs4955443	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs56127630	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57273516	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62259933	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446256	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs6446257	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs6446262	0.99[EUR][1000 genomes]
rs6446275	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6769744	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6769821	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs6775069	0.97[EUR][1000 genomes]
rs6778080	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs6783003	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs6784203	0.96[EUR][1000 genomes]
rs6785045	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790105	0.86[EUR][1000 genomes]
rs6796147	0.94[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809204	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809851	0.86[CEU][hapmap]
rs72934271	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.82[EUR][1000 genomes]
rs7429661	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs7613491	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617480	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs7619016	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs7619789	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7620024	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7622786	0.81[EUR][1000 genomes]
rs7626076	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs7631586	1.00[ASN][1000 genomes]
rs7638750	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644148	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs7647973	0.91[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9654010	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs974495	0.86[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9757181	0.87[CEU][hapmap]
rs9809237	0.82[EUR][1000 genomes]
rs9812360	0.91[EUR][1000 genomes]
rs9817807	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9831648	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs9834003	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs9834535	0.83[EUR][1000 genomes]
rs9842132	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847585	0.83[EUR][1000 genomes]
rs9860055	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	0.86[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.87[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	1.00[ASN][1000 genomes]

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11720657	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs11720657	AMT	cis	Whole Blood	GTEx
rs11720657	AMT	cis	Adipose Subcutaneous	GTEx
rs11720657	AMT	cis	Esophagus Mucosa	GTEx
rs11720657	AMT	cis	Artery Aorta	GTEx
rs11720657	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs11720657	AMT	cis	Muscle Skeletal	GTEx
rs11720657	WDR6	cis	Muscle Skeletal	GTEx
rs11720657	AMT	cis	Artery Tibial	GTEx
rs11720657	WDR6	cis	Nerve Tibial	GTEx
rs11720657	AMT	cis	Nerve Tibial	GTEx
rs11720657	AMT	cis	Thyroid	GTEx
rs11720657	AMT	cis	Esophagus Muscularis	GTEx
rs11720657	NICN1	cis	Thyroid	GTEx
rs11720657	AMT	cis	lung	GTEx
rs11720657	NICN1-AS1	cis	Thyroid	GTEx
rs11720657	WDR6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49379800-49392800	Weak transcription	Thymus	Thymus
2	chr3:49381600-49393000	Weak transcription	Right Atrium	heart
3	chr3:49383000-49393600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:49387000-49393000	Weak transcription	Aorta	Aorta
5	chr3:49387200-49392800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:49387400-49392800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:49387400-49393000	Weak transcription	Right Ventricle	heart
8	chr3:49387400-49393800	Weak transcription	Gastric	stomach
9	chr3:49387800-49393000	Weak transcription	Dnd41	blood
10	chr3:49388400-49393000	Weak transcription	Colonic Mucosa	Colon
11	chr3:49388800-49393600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:49389000-49392800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:49389200-49394600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:49389400-49392800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49389400-49392800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:49389400-49392800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:49389400-49392800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:49389400-49393000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:49389400-49393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:49389400-49393800	Weak transcription	Brain Angular Gyrus	brain
21	chr3:49389400-49393800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:49389400-49393800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:49389400-49393800	Weak transcription	Psoas Muscle	Psoas
24	chr3:49389400-49393800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:49389600-49392800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:49389600-49393000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:49389600-49393600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:49389600-49393600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:49389600-49393800	Weak transcription	Small Intestine	intestine
30	chr3:49389800-49392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:49389800-49392800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:49389800-49393600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:49389800-49393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:49390000-49392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:49390000-49392800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:49390000-49392800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:49390000-49393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:49390000-49393000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:49390200-49392800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:49390200-49393000	Weak transcription	Liver	Liver
41	chr3:49390200-49393800	Weak transcription	Brain Anterior Caudate	brain
42	chr3:49390400-49392800	Weak transcription	Fetal Brain Female	brain
43	chr3:49390400-49392800	Weak transcription	Placenta	Placenta
44	chr3:49390400-49392800	Weak transcription	Spleen	Spleen
45	chr3:49390400-49392800	Weak transcription	A549	lung
46	chr3:49390400-49392800	Weak transcription	HMEC	breast
47	chr3:49390400-49392800	Weak transcription	NH-A	brain
48	chr3:49390400-49393000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:49390400-49393600	Weak transcription	HepG2	liver
50	chr3:49390400-49393800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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