Variant report

Variant	rs1586827
Chromosome Location	chr3:49671224-49671225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130208	0.94[CEU][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130217	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12583	0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs12637313	0.88[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096480	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463728	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.94[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs1491985	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs1532204	0.94[CEU][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.95[YRI][hapmap]
rs2029591	0.94[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131108	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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]
rs2312462	0.95[YRI][hapmap]
rs2329021	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap]
rs4241405	0.94[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	0.95[YRI][hapmap]
rs4855833	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855845	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	1.00[CEU][hapmap]
rs4855885	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];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]
rs62262672	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262673	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262675	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446284	0.84[AMR][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809879	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap]
rs7620848	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7628207	1.00[CEU][hapmap]
rs7637711	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.91[YRI][hapmap]
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	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9830730	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	1.00[CEU][hapmap]
rs9860055	0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9870755	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9870858	1.00[CEU][hapmap]
rs9871024	0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv3812	chr3:49669773-49680587	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1586827	AMT	cis	lung	GTEx
rs1586827	RNF123	cis	Artery Tibial	GTEx
rs1586827	AMT	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49655600-49676200	Weak transcription	HepG2	liver
2	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49660800-49682600	Weak transcription	Liver	Liver
4	chr3:49661600-49692400	Weak transcription	Ovary	ovary
5	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
6	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
7	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
9	chr3:49664600-49674000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:49665000-49672400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:49665600-49673800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:49667200-49674000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:49667600-49679800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:49668000-49673800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:49669400-49674200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:49669600-49679400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:49669600-49679800	Weak transcription	Fetal Brain Female	brain
20	chr3:49669600-49680000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:49670000-49680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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