Variant report

Variant	rs62259933
Chromosome Location	chr3:49469703-49469704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:49469670-49469827	K562	blood:	n/a	n/a
2	FOXA1	chr3:49469428-49469719	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:49469421-49469777	HepG2	liver:	n/a	n/a
4	FOXA1	chr3:49469414-49469769	HepG2	liver:	n/a	n/a
5	FOXA1	chr3:49469405-49469808	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49463674..49466648-chr3:49468773..49471558,2	K562	blood:
2	chr3:49375307..49378183-chr3:49467814..49470350,2	K562	blood:
3	chr3:49458231..49460313-chr3:49468054..49470360,2	MCF-7	breast:

Variant related genes	Relation type
NICN1	TF binding region
ENSG00000145020	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1009051	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10154992	1.00[ASN][1000 genomes]
rs10155014	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10452032	1.00[ASN][1000 genomes]
rs1078341	1.00[ASN][1000 genomes]
rs10865956	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130183	1.00[ASN][1000 genomes]
rs11130186	1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11130217	1.00[ASN][1000 genomes]
rs11709734	1.00[ASN][1000 genomes]
rs11710434	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715060	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11719762	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11720542	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720705	1.00[ASN][1000 genomes]
rs11923032	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11928090	0.86[EUR][1000 genomes]
rs12583	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs12715437	1.00[ASN][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1491985	1.00[ASN][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	0.86[EUR][1000 genomes]
rs2029591	1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	1.00[ASN][1000 genomes]
rs2131108	1.00[ASN][1000 genomes]
rs2140270	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	0.86[EUR][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866330	0.86[EUR][1000 genomes]
rs3870339	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3870341	0.86[EUR][1000 genomes]
rs3905330	0.89[EUR][1000 genomes]
rs4052546	0.87[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4241407	0.86[EUR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4855837	0.84[EUR][1000 genomes]
rs4855845	1.00[ASN][1000 genomes]
rs4855846	1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855858	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4855869	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4855885	1.00[ASN][1000 genomes]
rs4955413	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955421	1.00[ASN][1000 genomes]
rs4955423	1.00[ASN][1000 genomes]
rs4955424	0.86[EUR][1000 genomes]
rs4955425	0.85[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	1.00[ASN][1000 genomes]
rs4955443	1.00[ASN][1000 genomes]
rs56127630	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57273516	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62259943	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62261249	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446256	1.00[ASN][1000 genomes]
rs6446257	1.00[ASN][1000 genomes]
rs6446262	0.89[EUR][1000 genomes]
rs6446275	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6769744	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6769821	1.00[ASN][1000 genomes]
rs6775069	0.87[EUR][1000 genomes]
rs6778080	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6783003	0.91[EUR][1000 genomes]
rs6784203	0.86[EUR][1000 genomes]
rs6785045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796147	0.85[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809204	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934271	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073004	0.80[EUR][1000 genomes]
rs73088137	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7613491	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	1.00[ASN][1000 genomes]
rs7619789	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620024	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7622786	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7625857	0.84[EUR][1000 genomes]
rs7626076	1.00[ASN][1000 genomes]
rs7631586	1.00[ASN][1000 genomes]
rs7638750	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644148	0.89[EUR][1000 genomes]
rs7647973	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9654010	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs974495	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9809237	0.89[EUR][1000 genomes]
rs9812360	0.82[EUR][1000 genomes]
rs9817807	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	1.00[ASN][1000 genomes]
rs9842132	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	0.86[EUR][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs62259933	AMT	cis	Artery Tibial	GTEx
rs62259933	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs62259933	WDR6	cis	Esophagus Muscularis	GTEx
rs62259933	NICN1-AS1	cis	Thyroid	GTEx
rs62259933	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs62259933	AMT	cis	lung	GTEx
rs62259933	AMT	cis	Whole Blood	GTEx
rs62259933	AMT	cis	Esophagus Muscularis	GTEx
rs62259933	AMT	cis	Artery Aorta	GTEx
rs62259933	AMT	cis	Esophagus Mucosa	GTEx
rs62259933	WDR6	cis	Nerve Tibial	GTEx
rs62259933	AMT	cis	Thyroid	GTEx
rs62259933	WDR6	cis	Muscle Skeletal	GTEx
rs62259933	AMT	cis	Nerve Tibial	GTEx
rs62259933	AMT	cis	Muscle Skeletal	GTEx
rs62259933	NICN1	cis	Thyroid	GTEx
rs62259933	AMT	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49467400-49486400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49467600-49470400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:49467800-49470200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:49467800-49481000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:49467800-49481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:49469200-49470200	Weak transcription	HepG2	liver

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