Variant report

Variant	rs35456569
Chromosome Location	chr3:48250899-48250900
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs11130164	0.87[EUR][1000 genomes]
rs11706221	0.86[EUR][1000 genomes]
rs11706277	0.88[EUR][1000 genomes]
rs11707606	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707997	0.86[EUR][1000 genomes]
rs11709691	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710257	0.86[EUR][1000 genomes]
rs11710861	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714176	0.88[EUR][1000 genomes]
rs11714944	0.86[EUR][1000 genomes]
rs11715776	0.84[EUR][1000 genomes]
rs11715799	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716371	0.86[EUR][1000 genomes]
rs11716848	0.86[EUR][1000 genomes]
rs11717716	0.86[EUR][1000 genomes]
rs11718329	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718350	0.87[EUR][1000 genomes]
rs11719365	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11928691	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13059037	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060020	0.86[EUR][1000 genomes]
rs13061269	0.86[EUR][1000 genomes]
rs13066044	0.86[EUR][1000 genomes]
rs13066758	0.89[EUR][1000 genomes]
rs13067450	0.89[EUR][1000 genomes]
rs13068265	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069029	0.88[EUR][1000 genomes]
rs13070210	0.88[EUR][1000 genomes]
rs13071960	0.87[EUR][1000 genomes]
rs13072018	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13079728	0.89[EUR][1000 genomes]
rs13081169	0.88[EUR][1000 genomes]
rs13081633	0.88[EUR][1000 genomes]
rs13082158	0.86[EUR][1000 genomes]
rs13082859	0.89[EUR][1000 genomes]
rs13084616	0.89[EUR][1000 genomes]
rs13085251	0.89[EUR][1000 genomes]
rs13087929	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090538	0.87[EUR][1000 genomes]
rs13094727	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13095983	0.88[EUR][1000 genomes]
rs13097450	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099560	0.81[EUR][1000 genomes]
rs13100815	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17647717	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17786132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125482	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2361685	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2541	0.89[EUR][1000 genomes]
rs3197223	0.89[EUR][1000 genomes]
rs34076262	0.87[EUR][1000 genomes]
rs34225441	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34523942	0.89[EUR][1000 genomes]
rs34589064	0.89[EUR][1000 genomes]
rs34630841	0.89[EUR][1000 genomes]
rs34728236	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34749846	0.89[EUR][1000 genomes]
rs34946886	0.89[EUR][1000 genomes]
rs35190747	0.89[EUR][1000 genomes]
rs35297395	0.89[EUR][1000 genomes]
rs35297486	0.83[EUR][1000 genomes]
rs35411187	0.88[EUR][1000 genomes]
rs35414021	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35778847	0.89[EUR][1000 genomes]
rs35802497	0.89[EUR][1000 genomes]
rs35944878	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36020562	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36064160	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36075665	0.89[EUR][1000 genomes]
rs36092070	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36121690	0.89[EUR][1000 genomes]
rs3729577	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731487	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731489	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731497	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731513	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731515	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731534	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731550	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731555	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3937	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4130522	0.88[EUR][1000 genomes]
rs4131361	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131362	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4371540	0.88[EUR][1000 genomes]
rs4392440	0.89[EUR][1000 genomes]
rs4404473	0.84[EUR][1000 genomes]
rs4420898	0.86[EUR][1000 genomes]
rs4479622	0.89[EUR][1000 genomes]
rs4511915	0.89[EUR][1000 genomes]
rs4511916	0.89[EUR][1000 genomes]
rs4541431	0.87[EUR][1000 genomes]
rs4619808	0.87[EUR][1000 genomes]
rs4632568	0.87[EUR][1000 genomes]
rs6442111	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775179	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6782166	0.88[EUR][1000 genomes]
rs6791930	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793150	0.88[EUR][1000 genomes]
rs6793223	0.87[EUR][1000 genomes]
rs6793239	0.88[EUR][1000 genomes]
rs6794644	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796343	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796490	0.81[EUR][1000 genomes]
rs6800492	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6801801	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6804986	0.87[EUR][1000 genomes]
rs6806112	0.80[EUR][1000 genomes]
rs71323391	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71323394	0.88[EUR][1000 genomes]
rs71323395	0.86[EUR][1000 genomes]
rs71323396	0.86[EUR][1000 genomes]
rs71323397	0.86[EUR][1000 genomes]
rs745116	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614532	0.87[EUR][1000 genomes]
rs7621785	0.89[EUR][1000 genomes]
rs7624450	0.89[EUR][1000 genomes]
rs7632297	0.88[EUR][1000 genomes]
rs7636461	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644414	0.80[EUR][1000 genomes]
rs7645425	0.87[EUR][1000 genomes]
rs7647817	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7648720	0.90[EUR][1000 genomes]
rs7652233	0.87[EUR][1000 genomes]
rs7653152	0.86[EUR][1000 genomes]
rs7653336	0.87[EUR][1000 genomes]
rs9311421	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936426	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936427	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9818937	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819094	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9825637	0.87[EUR][1000 genomes]
rs9830016	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9831531	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9833309	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9834095	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9837228	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9847953	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850672	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9853804	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9862131	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs35456569	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs35456569	MRPS18AP1	cis	Thyroid	GTEx
rs35456569	ZNF589	cis	Thyroid	GTEx
rs35456569	ZNF589	cis	Stomach	GTEx
rs35456569	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs35456569	MRPS18AP1	cis	Stomach	GTEx
rs35456569	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs35456569	FCF1P2	cis	Artery Tibial	GTEx
rs35456569	NME6	cis	multi-tissue	Pritchard
rs35456569	CDC25A	cis	Muscle Skeletal	GTEx
rs35456569	MRPS18AP1	cis	Nerve Tibial	GTEx
rs35456569	SPINK8	cis	Whole Blood	GTEx
rs35456569	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs35456569	NME6	cis	Muscle Skeletal	GTEx
rs35456569	NME6	cis	Artery Tibial	GTEx
rs35456569	ZNF589	cis	Nerve Tibial	GTEx
rs35456569	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs35456569	ZNF589	cis	Adipose Subcutaneous	GTEx
rs35456569	MRPS18AP1	cis	lung	GTEx
rs35456569	ZNF589	cis	Esophagus Muscularis	GTEx
rs35456569	MRPS18AP1	cis	Artery Aorta	GTEx
rs35456569	MRPS18AP1	cis	Artery Tibial	GTEx
rs35456569	CDC25A	cis	Artery Tibial	GTEx
rs35456569	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs35456569	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs35456569	CDC25A	cis	Thyroid	GTEx
rs35456569	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs35456569	CDC25A	cis	Adipose Subcutaneous	GTEx
rs35456569	ZNF589	cis	Esophagus Mucosa	GTEx
rs35456569	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs35456569	ZNF589	cis	lung	GTEx
rs35456569	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs35456569	ZNF589	cis	Artery Aorta	GTEx
rs35456569	NME6	cis	Nerve Tibial	GTEx
rs35456569	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs35456569	ZNF589	cis	Artery Tibial	GTEx
rs35456569	NME6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48248400-48255800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:48250800-48251800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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