Variant report

Variant	rs11721148
Chromosome Location	chr3:49646669-49646670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009051	1.00[ASN][1000 genomes]
rs10452032	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1078341	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130207	0.82[AMR][1000 genomes]
rs11130208	0.84[AMR][1000 genomes]
rs11130211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13096480	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1352889	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1491983	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532204	0.84[AMR][1000 genomes]
rs1586827	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2029591	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2131108	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2329021	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4241405	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4855833	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855845	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855846	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855848	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855849	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855885	0.85[EUR][1000 genomes]
rs62262672	0.86[EUR][1000 genomes]
rs62262673	0.83[EUR][1000 genomes]
rs62262675	0.84[EUR][1000 genomes]
rs6446284	0.84[AMR][1000 genomes]
rs6446286	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6774202	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6797299	0.84[AMR][1000 genomes]
rs7622786	1.00[ASN][1000 genomes]
rs7653505	1.00[ASN][1000 genomes]
rs9824435	0.86[EUR][1000 genomes]
rs9830730	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9883000	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11721148	NICN1-AS1	cis	Thyroid	GTEx
rs11721148	AMT	cis	Nerve Tibial	GTEx
rs11721148	AMT	cis	Thyroid	GTEx
rs11721148	NICN1	cis	Thyroid	GTEx

Chromatin state (count:27 , 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	chr3:49638000-49647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:49640400-49646800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:49640600-49647000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:49640800-49646800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:49644200-49646800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:49644600-49648800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:49645000-49646800	Weak transcription	Fetal Brain Female	brain
10	chr3:49645000-49646800	Weak transcription	Fetal Stomach	stomach
11	chr3:49645000-49647200	Weak transcription	Left Ventricle	heart
12	chr3:49645200-49646800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:49645200-49646800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:49645200-49646800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:49645200-49647000	Weak transcription	Fetal Brain Male	brain
16	chr3:49645400-49646800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:49645400-49646800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:49645400-49646800	Weak transcription	Right Ventricle	heart
19	chr3:49645400-49647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:49645400-49647200	Weak transcription	Brain Germinal Matrix	brain
21	chr3:49645400-49648200	Weak transcription	Esophagus	oesophagus
22	chr3:49645400-49648200	Weak transcription	Stomach Mucosa	stomach
23	chr3:49645600-49646800	Weak transcription	Brain Angular Gyrus	brain
24	chr3:49645800-49646800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:49645800-49647400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:49645800-49653600	Weak transcription	Fetal Lung	lung
27	chr3:49646600-49649200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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