Variant report

Variant	rs35802497
Chromosome Location	chr3:48345449-48345450
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48343201..48345959-chr3:48358674..48361429,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1045482	0.83[EUR][1000 genomes]
rs11130162	0.83[EUR][1000 genomes]
rs11130163	0.83[EUR][1000 genomes]
rs11130164	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134867	0.84[EUR][1000 genomes]
rs11706221	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706277	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707606	0.84[EUR][1000 genomes]
rs11707997	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709691	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11710257	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710861	0.97[EUR][1000 genomes]
rs11713476	0.85[EUR][1000 genomes]
rs11714176	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714944	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715776	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715799	0.92[EUR][1000 genomes]
rs11715876	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716371	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716848	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717716	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718329	0.97[EUR][1000 genomes]
rs11718350	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719365	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11928691	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13059037	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13060020	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061269	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066044	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066758	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13067450	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068265	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13068288	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13069029	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070210	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071960	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072018	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081169	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081633	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082158	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082859	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084616	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085251	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087929	0.84[EUR][1000 genomes]
rs13090538	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094727	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13095983	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097450	0.94[EUR][1000 genomes]
rs13100815	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17647717	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17786132	0.89[EUR][1000 genomes]
rs2125482	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2361685	0.84[EUR][1000 genomes]
rs2541	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3197223	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34076262	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34225441	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34523942	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34589064	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34630841	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34728236	0.93[EUR][1000 genomes]
rs34749846	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34946886	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35190747	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35297395	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35297486	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35411187	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35414021	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35456569	0.89[EUR][1000 genomes]
rs35778847	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35944878	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36020562	0.92[EUR][1000 genomes]
rs36064160	0.84[EUR][1000 genomes]
rs36075665	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36092070	0.97[EUR][1000 genomes]
rs36121690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729577	0.84[EUR][1000 genomes]
rs3731487	0.84[EUR][1000 genomes]
rs3731489	0.84[EUR][1000 genomes]
rs3731497	0.84[EUR][1000 genomes]
rs3731513	0.84[EUR][1000 genomes]
rs3731515	0.84[EUR][1000 genomes]
rs3731534	0.84[EUR][1000 genomes]
rs3731550	0.83[EUR][1000 genomes]
rs3731555	0.83[EUR][1000 genomes]
rs3937	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4130522	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130995	0.83[EUR][1000 genomes]
rs4131361	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4131362	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4371540	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392440	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4404473	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4420898	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479622	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4511915	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4511916	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4541431	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4619808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632568	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442110	0.83[EUR][1000 genomes]
rs6442111	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775179	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782166	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787500	0.83[EUR][1000 genomes]
rs6791930	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793150	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793223	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793239	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794644	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6796343	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6800492	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6801801	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804986	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806112	0.81[EUR][1000 genomes]
rs71323391	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71323394	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71323395	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71323396	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71323397	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs745116	0.94[EUR][1000 genomes]
rs7614532	0.96[EUR][1000 genomes]
rs7619865	0.82[EUR][1000 genomes]
rs7621785	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624450	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636461	0.94[EUR][1000 genomes]
rs7644414	0.84[EUR][1000 genomes]
rs7645425	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647817	0.84[EUR][1000 genomes]
rs7648720	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7652233	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653152	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653336	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311421	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs936426	0.84[EUR][1000 genomes]
rs936427	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9818937	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9819094	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9825637	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830016	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831531	0.84[EUR][1000 genomes]
rs9833309	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9834095	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9837228	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9846818	0.81[EUR][1000 genomes]
rs9847953	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9850672	0.97[EUR][1000 genomes]
rs9853804	0.97[EUR][1000 genomes];0.88[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	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs35802497	CDC25A	cis	Adipose Subcutaneous	GTEx
rs35802497	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs35802497	SPINK8	cis	Whole Blood	GTEx
rs35802497	ZNF589	cis	Esophagus Mucosa	GTEx
rs35802497	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs35802497	ZNF589	cis	Artery Aorta	GTEx
rs35802497	ZNF589	cis	Stomach	GTEx
rs35802497	ZNF589	cis	Thyroid	GTEx
rs35802497	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs35802497	MRPS18AP1	cis	Nerve Tibial	GTEx
rs35802497	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs35802497	MRPS18AP1	cis	Artery Aorta	GTEx
rs35802497	ZNF589	cis	Artery Tibial	GTEx
rs35802497	NME6	cis	Esophagus Muscularis	GTEx
rs35802497	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs35802497	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs35802497	CDC25A	cis	Muscle Skeletal	GTEx
rs35802497	ZNF589	cis	Nerve Tibial	GTEx
rs35802497	ZNF589	cis	Adipose Subcutaneous	GTEx
rs35802497	FCF1P2	cis	Artery Tibial	GTEx
rs35802497	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs35802497	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs35802497	CDC25A	cis	Thyroid	GTEx
rs35802497	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs35802497	ZNF589	cis	Esophagus Muscularis	GTEx
rs35802497	ZNF589	cis	lung	GTEx
rs35802497	CDC25A	cis	Artery Tibial	GTEx
rs35802497	MRPS18AP1	cis	Artery Tibial	GTEx
rs35802497	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs35802497	NME6	cis	Muscle Skeletal	GTEx
rs35802497	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs35802497	MRPS18AP1	cis	Stomach	GTEx
rs35802497	MRPS18AP1	cis	Thyroid	GTEx
rs35802497	NME6	cis	Artery Tibial	GTEx
rs35802497	NME6	cis	Nerve Tibial	GTEx
rs35802497	MRPS18AP1	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48343800-48345600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:48343800-48345800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:48343800-48346400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:48343800-48346800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:48343800-48346800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:48344000-48345800	Weak transcription	Fetal Intestine Small	intestine
7	chr3:48344000-48346000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:48344000-48346600	Weak transcription	Fetal Brain Female	brain
9	chr3:48344000-48347600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:48344000-48347800	Weak transcription	Primary B cells from cord blood	blood
11	chr3:48344000-48348000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr3:48344000-48348000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:48344000-48348200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:48344000-48348200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:48344200-48347000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:48344200-48348000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:48344200-48348000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:48344800-48345800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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