Variant report

Variant	rs62262672
Chromosome Location	chr3:49655927-49655928
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49654340..49656120-chr3:49672426..49675250,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10452032	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11130211	0.82[AMR][1000 genomes];0.87[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	0.86[EUR][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637313	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13096480	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs1352889	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463728	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131108	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2329021	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4855833	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855845	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855885	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	1.00[ASN][1000 genomes]
rs55754265	0.81[EUR][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]
rs62262671	0.81[EUR][1000 genomes]
rs62262673	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262675	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446285	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6446286	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	0.98[EUR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	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	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830730	1.00[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	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62262672	AMT	cis	Thyroid	GTEx
rs62262672	AMT	cis	lung	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49648400-49662000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49652800-49656600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:49654000-49662400	Weak transcription	Fetal Brain Female	brain
4	chr3:49654200-49657000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:49654200-49662600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:49654400-49656000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49654400-49656800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:49654400-49656800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:49654400-49656800	Weak transcription	HSMM	muscle
10	chr3:49654400-49657000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:49654400-49657000	Weak transcription	HSMMtube	muscle
12	chr3:49654400-49657000	Weak transcription	NH-A	brain
13	chr3:49654400-49668200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:49654600-49656000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:49654600-49657000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:49654600-49662200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:49654600-49662400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:49654600-49662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:49654600-49662600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:49654600-49663600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:49654600-49664200	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:49655000-49668800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:49655400-49656000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:49655600-49656000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:49655600-49676200	Weak transcription	HepG2	liver

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