Variant report

Variant	rs13097450
Chromosome Location	chr3:48267825-48267826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48261134..48262894-chr3:48267767..48269966,2	K562	blood:

Extended variants
information (count: 151 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1045482	0.84[EUR][1000 genomes]
rs11130162	0.84[EUR][1000 genomes]
rs11130163	0.84[EUR][1000 genomes]
rs11130164	0.92[EUR][1000 genomes]
rs11706221	0.91[EUR][1000 genomes]
rs11706277	0.93[EUR][1000 genomes]
rs11707606	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707997	0.91[EUR][1000 genomes]
rs11709691	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710257	0.91[EUR][1000 genomes]
rs11710861	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714176	0.93[EUR][1000 genomes]
rs11714944	0.90[EUR][1000 genomes]
rs11715776	0.89[EUR][1000 genomes]
rs11715799	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715876	0.83[EUR][1000 genomes]
rs11716371	0.91[EUR][1000 genomes]
rs11716848	0.91[EUR][1000 genomes]
rs11717716	0.91[EUR][1000 genomes]
rs11718329	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718350	0.92[EUR][1000 genomes]
rs11719365	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11928691	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13059037	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060020	0.91[EUR][1000 genomes]
rs13061269	0.91[EUR][1000 genomes]
rs13066044	0.91[EUR][1000 genomes]
rs13066758	0.94[EUR][1000 genomes]
rs13067450	0.94[EUR][1000 genomes]
rs13068265	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13068288	0.81[EUR][1000 genomes]
rs13069029	0.93[EUR][1000 genomes]
rs13070210	0.93[EUR][1000 genomes]
rs13071960	0.92[EUR][1000 genomes]
rs13072018	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13079728	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13081169	0.93[EUR][1000 genomes]
rs13081633	0.93[EUR][1000 genomes]
rs13082158	0.90[EUR][1000 genomes]
rs13082859	0.94[EUR][1000 genomes]
rs13084616	0.94[EUR][1000 genomes]
rs13085251	0.94[EUR][1000 genomes]
rs13087929	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090538	0.92[EUR][1000 genomes]
rs13094727	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13095983	0.93[EUR][1000 genomes]
rs13100815	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17647717	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17786132	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125482	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2361685	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2541	0.94[EUR][1000 genomes]
rs3197223	0.94[EUR][1000 genomes]
rs34076262	0.92[EUR][1000 genomes]
rs34225441	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34523942	0.94[EUR][1000 genomes]
rs34589064	0.94[EUR][1000 genomes]
rs34630841	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34728236	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34749846	0.94[EUR][1000 genomes]
rs34946886	0.94[EUR][1000 genomes]
rs35190747	0.94[EUR][1000 genomes]
rs35297395	0.94[EUR][1000 genomes]
rs35297486	0.88[EUR][1000 genomes]
rs35411187	0.93[EUR][1000 genomes]
rs35414021	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35456569	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778847	0.94[EUR][1000 genomes]
rs35802497	0.94[EUR][1000 genomes]
rs35944878	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36020562	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36064160	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36075665	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36092070	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36121690	0.94[EUR][1000 genomes]
rs3729577	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731487	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731489	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731497	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731513	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731515	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731534	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731550	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731555	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3937	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4130522	0.93[EUR][1000 genomes]
rs4131361	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131362	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4371540	0.93[EUR][1000 genomes]
rs4392440	0.94[EUR][1000 genomes]
rs4404473	0.88[EUR][1000 genomes]
rs4420898	0.91[EUR][1000 genomes]
rs4479622	0.94[EUR][1000 genomes]
rs4511915	0.94[EUR][1000 genomes]
rs4511916	0.94[EUR][1000 genomes]
rs4541431	0.92[EUR][1000 genomes]
rs4619808	0.92[EUR][1000 genomes]
rs4632568	0.92[EUR][1000 genomes]
rs6442110	0.84[EUR][1000 genomes]
rs6442111	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775179	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6782166	0.93[EUR][1000 genomes]
rs6787500	0.84[EUR][1000 genomes]
rs6791930	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793150	0.93[EUR][1000 genomes]
rs6793223	0.92[EUR][1000 genomes]
rs6793239	0.93[EUR][1000 genomes]
rs6794644	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796343	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800492	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6801801	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6804986	0.92[EUR][1000 genomes]
rs6806112	0.86[EUR][1000 genomes]
rs71323391	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71323394	0.93[EUR][1000 genomes]
rs71323395	0.91[EUR][1000 genomes]
rs71323396	0.90[EUR][1000 genomes]
rs71323397	0.91[EUR][1000 genomes]
rs745116	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614532	0.94[EUR][1000 genomes]
rs7621785	0.94[EUR][1000 genomes]
rs7624450	0.94[EUR][1000 genomes]
rs7632297	0.93[EUR][1000 genomes]
rs7636461	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644414	0.85[EUR][1000 genomes]
rs7645425	0.92[EUR][1000 genomes]
rs7647817	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7648720	0.96[EUR][1000 genomes]
rs7652233	0.92[EUR][1000 genomes]
rs7653152	0.90[EUR][1000 genomes]
rs7653336	0.92[EUR][1000 genomes]
rs9311421	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936426	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936427	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9818937	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819094	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9825637	0.92[EUR][1000 genomes]
rs9830016	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9831531	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9833309	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9834095	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9837228	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9847953	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850672	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9853804	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9862131	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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:36)

SNP	Gene	Cis/trans	Tissue	Source
rs13097450	CDC25A	cis	Muscle Skeletal	GTEx
rs13097450	ZNF589	cis	Artery Tibial	GTEx
rs13097450	NME6	cis	Esophagus Muscularis	GTEx
rs13097450	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs13097450	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs13097450	SPINK8	cis	Whole Blood	GTEx
rs13097450	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs13097450	ZNF589	cis	lung	GTEx
rs13097450	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs13097450	FCF1P2	cis	Artery Tibial	GTEx
rs13097450	MRPS18AP1	cis	Artery Tibial	GTEx
rs13097450	CDC25A	cis	Artery Tibial	GTEx
rs13097450	MRPS18AP1	cis	Artery Aorta	GTEx
rs13097450	NME6	cis	Nerve Tibial	GTEx
rs13097450	MRPS18AP1	cis	lung	GTEx
rs13097450	ZNF589	cis	Stomach	GTEx
rs13097450	ZNF589	cis	Nerve Tibial	GTEx
rs13097450	MRPS18AP1	cis	Nerve Tibial	GTEx
rs13097450	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs13097450	ZNF589	cis	Esophagus Mucosa	GTEx
rs13097450	ZNF589	cis	Thyroid	GTEx
rs13097450	MRPS18AP1	cis	Stomach	GTEx
rs13097450	NME6	cis	Muscle Skeletal	GTEx
rs13097450	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs13097450	ZNF589	cis	Artery Aorta	GTEx
rs13097450	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs13097450	MRPS18AP1	cis	Thyroid	GTEx
rs13097450	CDC25A	cis	Thyroid	GTEx
rs13097450	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs13097450	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs13097450	ZNF589	cis	Esophagus Muscularis	GTEx
rs13097450	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs13097450	CDC25A	cis	Adipose Subcutaneous	GTEx
rs13097450	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs13097450	NME6	cis	Artery Tibial	GTEx
rs13097450	ZNF589	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48257800-48272400	Weak transcription	Stomach Mucosa	stomach
2	chr3:48260000-48274400	Weak transcription	Right Atrium	heart
3	chr3:48262200-48269200	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:48265200-48268200	Enhancers	GM12878-XiMat	blood
5	chr3:48265400-48268400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:48265400-48274000	Weak transcription	Hela-S3	cervix
7	chr3:48265600-48274400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:48265800-48268200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:48265800-48273400	Weak transcription	Esophagus	oesophagus
10	chr3:48265800-48277600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:48266000-48268400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:48266000-48274200	Weak transcription	Spleen	Spleen
13	chr3:48266400-48268600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:48266400-48269600	Enhancers	Fetal Thymus	thymus
15	chr3:48266600-48268600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:48266600-48269200	Enhancers	Primary B cells from cord blood	blood
17	chr3:48267000-48268000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:48267000-48269000	Enhancers	Thymus	Thymus
19	chr3:48267200-48268800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:48267400-48269200	Enhancers	Primary neutrophils fromperipheralblood	blood

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