Variant report

Variant	rs6446286
Chromosome Location	chr3:49681704-49681705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49673401..49676066-chr3:49680626..49682586,2	MCF-7	breast:
2	chr3:49663253..49665357-chr3:49680487..49682256,2	K562	blood:
3	chr3:49594418..49597323-chr3:49680831..49683098,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10452032	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];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	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130217	1.00[ASN][1000 genomes]
rs11709734	1.00[ASN][1000 genomes]
rs11720705	1.00[ASN][1000 genomes]
rs11721148	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637313	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13096480	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs1352889	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463728	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491983	0.82[AMR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029591	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131108	1.00[AFR][1000 genomes];0.93[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[AFR][1000 genomes];0.98[AMR][1000 genomes];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	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855833	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855845	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855885	0.84[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	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]
rs6446285	1.00[ASN][1000 genomes]
rs6774202	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];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	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830730	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];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	1.00[AFR][1000 genomes];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6446286	AMT	cis	Thyroid	GTEx
rs6446286	AMT	cis	lung	GTEx
rs6446286	RNF123	cis	Artery Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:49660800-49682600	Weak transcription	Liver	Liver
3	chr3:49661600-49692400	Weak transcription	Ovary	ovary
4	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
5	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
6	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
7	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:49673800-49692400	Weak transcription	Gastric	stomach
9	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:49676000-49686400	Weak transcription	Spleen	Spleen
11	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
12	chr3:49676400-49687000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:49679000-49682400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:49679400-49683000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:49679600-49687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:49679800-49683000	Strong transcription	Fetal Brain Female	brain
17	chr3:49679800-49683200	Strong transcription	Brain Germinal Matrix	brain
18	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:49680000-49682000	Strong transcription	Brain Hippocampus Middle	brain
20	chr3:49680000-49682200	Strong transcription	Brain Cingulate Gyrus	brain
21	chr3:49680000-49682600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:49680000-49684800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:49680200-49682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:49680200-49682400	Strong transcription	Brain Anterior Caudate	brain
25	chr3:49680200-49684400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:49680400-49684800	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:49680600-49682600	Weak transcription	Psoas Muscle	Psoas
28	chr3:49681000-49682800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:49681000-49685400	Weak transcription	Fetal Stomach	stomach
30	chr3:49681200-49684800	Weak transcription	HepG2	liver
31	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:49681400-49682000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:49681600-49683200	Weak transcription	Brain Angular Gyrus	brain

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