Variant report

Variant	rs12637313
Chromosome Location	chr3:49645458-49645459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10452032	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[CHD][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11130207	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11130208	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130217	0.82[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11709734	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs11720705	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11721148	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12583	1.00[CHD][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs12715437	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13096480	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[CHD][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs1352889	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1463728	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1491985	0.87[CEU][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs1532204	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586827	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]
rs1982861	1.00[CHD][hapmap];0.95[YRI][hapmap]
rs2029591	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][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]
rs2131108	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][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]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2312462	1.00[CHD][hapmap];0.95[YRI][hapmap]
rs2329021	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020779	0.86[CEU][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap]
rs3905330	1.00[CHD][hapmap]
rs4241405	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	1.00[CHD][hapmap];0.95[YRI][hapmap]
rs4855833	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855845	0.87[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs4855885	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];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	0.94[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446286	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805609	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6809204	1.00[ASN][1000 genomes]
rs6809879	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][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	0.88[CEU][hapmap]
rs7620848	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs7628207	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs7637711	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	1.00[CHD][hapmap];0.91[YRI][hapmap]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs7653505	1.00[CHD][hapmap]
rs8897	1.00[CHD][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs940045	1.00[CHD][hapmap]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs9830730	0.88[CEU][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs9842132	1.00[ASN][1000 genomes]
rs9849038	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs9860055	1.00[CHD][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9862534	1.00[CHD][hapmap]
rs9870755	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs9870858	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs9871024	1.00[CHD][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883000	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[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
rs12637313	AMT	cis	Nerve Tibial	GTEx
rs12637313	NICN1	cis	Thyroid	GTEx
rs12637313	AMT	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	chr3:49638000-49647200	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	chr3:49643800-49645800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:49644200-49645600	Enhancers	Hela-S3	cervix
9	chr3:49644200-49646800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:49644600-49648800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:49644800-49645600	Enhancers	Brain Angular Gyrus	brain
12	chr3:49644800-49645600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:49645000-49645800	Enhancers	Brain Substantia Nigra	brain
14	chr3:49645000-49646800	Weak transcription	Fetal Brain Female	brain
15	chr3:49645000-49646800	Weak transcription	Fetal Stomach	stomach
16	chr3:49645000-49647200	Weak transcription	Left Ventricle	heart
17	chr3:49645200-49646800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:49645200-49646800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:49645200-49646800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49645200-49647000	Weak transcription	Fetal Brain Male	brain
21	chr3:49645400-49645800	Enhancers	Fetal Lung	lung
22	chr3:49645400-49646600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:49645400-49646800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:49645400-49646800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:49645400-49646800	Weak transcription	Right Ventricle	heart
26	chr3:49645400-49647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:49645400-49647200	Weak transcription	Brain Germinal Matrix	brain
28	chr3:49645400-49648200	Weak transcription	Esophagus	oesophagus
29	chr3:49645400-49648200	Weak transcription	Stomach Mucosa	stomach

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