Variant report

Variant	rs56127630
Chromosome Location	chr3:49438036-49438037
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49433634..49436647-chr3:49437237..49441017,4	K562	blood:

Extended variants
information (count: 138 )
Associated
traits (count: 17 )

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	0.85[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	0.94[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	0.86[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.98[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	0.89[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	0.84[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]
rs57273516	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62259933	0.95[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	0.93[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	0.98[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	0.81[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	0.83[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	0.98[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	0.90[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	0.98[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	0.96[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	0.89[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	0.96[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.85[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]
rs9861027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	0.82[EUR][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs56127630	NICN1-AS1	cis	Thyroid	GTEx
rs56127630	AMT	cis	Adipose Subcutaneous	GTEx
rs56127630	WDR6	cis	Esophagus Muscularis	GTEx
rs56127630	AMT	cis	Nerve Tibial	GTEx
rs56127630	AMT	cis	Artery Tibial	GTEx
rs56127630	NICN1	cis	Thyroid	GTEx
rs56127630	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs56127630	AMT	cis	Whole Blood	GTEx
rs56127630	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs56127630	AMT	cis	Muscle Skeletal	GTEx
rs56127630	AMT	cis	Esophagus Mucosa	GTEx
rs56127630	WDR6	cis	Nerve Tibial	GTEx
rs56127630	AMT	cis	Thyroid	GTEx
rs56127630	WDR6	cis	Muscle Skeletal	GTEx
rs56127630	AMT	cis	Esophagus Muscularis	GTEx
rs56127630	AMT	cis	Artery Aorta	GTEx
rs56127630	AMT	cis	lung	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	chr3:49422200-49443000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:49424200-49443400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:49426000-49444000	Weak transcription	Esophagus	oesophagus
12	chr3:49426200-49443000	Weak transcription	NHLF	lung
13	chr3:49427000-49448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:49428800-49438600	Strong transcription	Fetal Stomach	stomach
15	chr3:49429000-49441800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:49429000-49447200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:49430800-49439200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:49431200-49447200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:49431800-49439600	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr3:49433800-49438600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:49433800-49438600	Weak transcription	HMEC	breast
22	chr3:49433800-49444000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:49433800-49447200	Weak transcription	Colonic Mucosa	Colon
24	chr3:49434200-49438600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:49434200-49438800	Weak transcription	Fetal Intestine Large	intestine
26	chr3:49434200-49439400	Weak transcription	Fetal Lung	lung
27	chr3:49434200-49440800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:49434200-49442800	Weak transcription	Brain Germinal Matrix	brain
29	chr3:49434600-49440000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:49434800-49439000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:49434800-49439000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:49434800-49441000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:49434800-49443000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:49435200-49438200	Enhancers	Pancreas	Pancrea
35	chr3:49435200-49439000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:49435400-49438400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:49435400-49438600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:49435400-49438800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:49435400-49439200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:49435400-49441200	Weak transcription	Stomach Mucosa	stomach
41	chr3:49435400-49442400	Strong transcription	Fetal Intestine Small	intestine
42	chr3:49435400-49445600	Weak transcription	Fetal Brain Male	brain
43	chr3:49435400-49447000	Weak transcription	HSMMtube	muscle
44	chr3:49435400-49447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:49435600-49438600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:49435600-49438800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:49435600-49439200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:49435600-49439200	Weak transcription	Fetal Heart	heart
49	chr3:49435600-49439600	Weak transcription	HUVEC	blood vessel
50	chr3:49435600-49443000	Weak transcription	NHDF-Ad	bronchial

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