Variant report

Variant	rs1463728
Chromosome Location	chr3:49647404-49647405
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10452032	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130208	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130217	1.00[ASN][1000 genomes]
rs11709734	1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	1.00[ASN][1000 genomes]
rs11721148	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637313	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13096480	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs1352889	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1491983	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131108	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2329021	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs4241405	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855845	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855885	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262673	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262675	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6446285	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446286	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830730	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9871024	1.00[ASN][1000 genomes]
rs9883000	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1463728	AMT	cis	Nerve Tibial	GTEx
rs1463728	AMT	cis	Thyroid	GTEx
rs1463728	NICN1	cis	Thyroid	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:49644600-49648800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:49645400-49648200	Weak transcription	Esophagus	oesophagus
5	chr3:49645400-49648200	Weak transcription	Stomach Mucosa	stomach
6	chr3:49645800-49653600	Weak transcription	Fetal Lung	lung
7	chr3:49646600-49649200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:49646800-49647600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:49646800-49647600	Enhancers	Stomach Smooth Muscle	stomach
10	chr3:49646800-49647800	Enhancers	Fetal Heart	heart
11	chr3:49646800-49648400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:49646800-49648600	Enhancers	Brain Hippocampus Middle	brain
13	chr3:49646800-49648600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:49646800-49648600	Enhancers	Brain Substantia Nigra	brain
15	chr3:49646800-49648600	Enhancers	Fetal Stomach	stomach
16	chr3:49646800-49648800	Enhancers	Brain Angular Gyrus	brain
17	chr3:49646800-49649000	Enhancers	Brain Anterior Caudate	brain
18	chr3:49646800-49649000	Enhancers	Brain Cingulate Gyrus	brain
19	chr3:49646800-49649400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:49647000-49649400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:49647000-49649600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:49647200-49647600	Enhancers	Left Ventricle	heart
23	chr3:49647200-49648200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:49647200-49648200	Weak transcription	NHDF-Ad	bronchial
25	chr3:49647200-49648400	Enhancers	Brain Germinal Matrix	brain
26	chr3:49647400-49647600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:49647400-49648200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:49647400-49649000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:49647400-49653400	Weak transcription	Fetal Brain Female	brain

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