Variant report

Variant	rs9861027
Chromosome Location	chr3:49436584-49436585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49433634..49436647-chr3:49437237..49441017,4	K562	blood:
2	chr3:49433245..49436928-chr3:49447117..49449989,7	K562	blood:
3	chr3:49435199..49436979-chr3:49506002..49508091,2	K562	blood:
4	chr3:49435715..49437316-chr3:49449738..49451282,2	MCF-7	breast:
5	chr3:49433690..49436598-chr3:49447912..49450850,3	K562	blood:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1009051	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10154992	1.00[ASN][1000 genomes]
rs10155014	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10452032	1.00[ASN][1000 genomes]
rs1078341	1.00[ASN][1000 genomes]
rs10865956	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130183	1.00[ASN][1000 genomes]
rs11130186	1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[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];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715060	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11719762	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720542	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923032	0.83[AMR][1000 genomes]
rs11928090	0.82[EUR][1000 genomes]
rs12583	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	0.82[EUR][1000 genomes]
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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	0.82[EUR][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs3866330	0.82[EUR][1000 genomes]
rs3870339	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3870341	0.82[EUR][1000 genomes]
rs3905330	0.85[EUR][1000 genomes]
rs4052546	0.83[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4241407	0.82[EUR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4855845	1.00[ASN][1000 genomes]
rs4855846	1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855858	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855869	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855885	1.00[ASN][1000 genomes]
rs4955413	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955421	1.00[ASN][1000 genomes]
rs4955423	1.00[ASN][1000 genomes]
rs4955424	0.90[EUR][1000 genomes]
rs4955425	0.89[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	1.00[ASN][1000 genomes]
rs4955443	1.00[ASN][1000 genomes]
rs56127630	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57273516	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62259933	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62261249	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446256	1.00[ASN][1000 genomes]
rs6446257	1.00[ASN][1000 genomes]
rs6446262	0.93[EUR][1000 genomes]
rs6446275	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6769744	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6769821	1.00[ASN][1000 genomes]
rs6775069	0.91[EUR][1000 genomes]
rs6778080	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6783003	0.87[EUR][1000 genomes]
rs6784203	0.90[EUR][1000 genomes]
rs6785045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790105	0.82[EUR][1000 genomes]
rs6796147	0.89[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809204	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934271	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7613491	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	1.00[ASN][1000 genomes]
rs7619789	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7620024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7622786	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7626076	1.00[ASN][1000 genomes]
rs7631586	1.00[ASN][1000 genomes]
rs7638750	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644148	0.84[EUR][1000 genomes]
rs7647973	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9654010	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs974495	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9757181	0.84[EUR][1000 genomes]
rs9809237	0.85[EUR][1000 genomes]
rs9812360	0.86[EUR][1000 genomes]
rs9817807	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	1.00[ASN][1000 genomes]
rs9842132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	0.82[EUR][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	1.00[ASN][1000 genomes]

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9861027	AMT	cis	Whole Blood	GTEx
rs9861027	AMT	cis	Esophagus Mucosa	GTEx
rs9861027	AMT	cis	lung	GTEx
rs9861027	WDR6	cis	Nerve Tibial	GTEx
rs9861027	WDR6	cis	Muscle Skeletal	GTEx
rs9861027	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs9861027	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9861027	AMT	cis	Muscle Skeletal	GTEx
rs9861027	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9861027	AMT	cis	Artery Tibial	GTEx
rs9861027	AMT	cis	Artery Aorta	GTEx
rs9861027	AMT	cis	Esophagus Muscularis	GTEx
rs9861027	WDR6	cis	Esophagus Muscularis	GTEx
rs9861027	AMT	cis	Adipose Subcutaneous	GTEx
rs9861027	AMT	cis	Nerve Tibial	GTEx
rs9861027	NICN1	cis	Thyroid	GTEx
rs9861027	NICN1-AS1	cis	Thyroid	GTEx
rs9861027	AMT	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:49413200-49441400	Weak transcription	Aorta	Aorta
5	chr3:49413200-49443000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:49413400-49439000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:49413600-49441000	Weak transcription	Fetal Brain Female	brain
9	chr3:49417800-49437800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:49422200-49443000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:49424200-49443400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:49425800-49437800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:49426000-49436600	Weak transcription	Gastric	stomach
14	chr3:49426000-49444000	Weak transcription	Esophagus	oesophagus
15	chr3:49426200-49437800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:49426200-49443000	Weak transcription	NHLF	lung
17	chr3:49427000-49448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:49428800-49438600	Strong transcription	Fetal Stomach	stomach
19	chr3:49429000-49437000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:49429000-49441800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:49429000-49447200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:49430800-49439200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:49431000-49437800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:49431200-49447200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:49431800-49439600	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr3:49432400-49436800	Weak transcription	NH-A	brain
27	chr3:49432400-49438000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:49433000-49436800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:49433800-49438600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:49433800-49438600	Weak transcription	HMEC	breast
31	chr3:49433800-49444000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:49433800-49447200	Weak transcription	Colonic Mucosa	Colon
33	chr3:49434000-49436800	Weak transcription	NHEK	skin
34	chr3:49434200-49436600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:49434200-49436800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:49434200-49438600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:49434200-49438800	Weak transcription	Fetal Intestine Large	intestine
38	chr3:49434200-49439400	Weak transcription	Fetal Lung	lung
39	chr3:49434200-49440800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:49434200-49442800	Weak transcription	Brain Germinal Matrix	brain
41	chr3:49434600-49437600	Weak transcription	Thymus	Thymus
42	chr3:49434600-49437800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:49434600-49437800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:49434600-49440000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:49434800-49439000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:49434800-49439000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:49434800-49441000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:49434800-49443000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:49435200-49438000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:49435200-49438200	Enhancers	Pancreas	Pancrea

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