Variant report

Variant	rs36020562
Chromosome Location	chr3:48258638-48258639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48257660..48261585-chr3:48263263..48266797,5	MCF-7	breast:
2	chr3:48257167..48259114-chr3:48263972..48266066,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164047	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1045482	0.82[EUR][1000 genomes]
rs11130162	0.82[EUR][1000 genomes]
rs11130163	0.82[EUR][1000 genomes]
rs11130164	0.90[EUR][1000 genomes]
rs11706221	0.89[EUR][1000 genomes]
rs11706277	0.91[EUR][1000 genomes]
rs11707606	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707997	0.89[EUR][1000 genomes]
rs11709691	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710257	0.89[EUR][1000 genomes]
rs11710861	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714176	0.91[EUR][1000 genomes]
rs11714944	0.89[EUR][1000 genomes]
rs11715776	0.87[EUR][1000 genomes]
rs11715799	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715876	0.81[EUR][1000 genomes]
rs11716371	0.89[EUR][1000 genomes]
rs11716848	0.89[EUR][1000 genomes]
rs11717716	0.89[EUR][1000 genomes]
rs11718329	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718350	0.90[EUR][1000 genomes]
rs11719365	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11928691	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13059037	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060020	0.89[EUR][1000 genomes]
rs13061269	0.89[EUR][1000 genomes]
rs13066044	0.89[EUR][1000 genomes]
rs13066758	0.92[EUR][1000 genomes]
rs13067450	0.92[EUR][1000 genomes]
rs13068265	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069029	0.91[EUR][1000 genomes]
rs13070210	0.91[EUR][1000 genomes]
rs13071960	0.90[EUR][1000 genomes]
rs13072018	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13079728	0.92[EUR][1000 genomes]
rs13081169	0.91[EUR][1000 genomes]
rs13081633	0.91[EUR][1000 genomes]
rs13082158	0.89[EUR][1000 genomes]
rs13082859	0.92[EUR][1000 genomes]
rs13084616	0.92[EUR][1000 genomes]
rs13085251	0.92[EUR][1000 genomes]
rs13087929	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090538	0.90[EUR][1000 genomes]
rs13094727	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13095983	0.91[EUR][1000 genomes]
rs13097450	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100815	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17647717	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17786132	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125482	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2361685	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2541	0.92[EUR][1000 genomes]
rs3197223	0.92[EUR][1000 genomes]
rs34076262	0.90[EUR][1000 genomes]
rs34225441	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34523942	0.92[EUR][1000 genomes]
rs34589064	0.92[EUR][1000 genomes]
rs34630841	0.92[EUR][1000 genomes]
rs34728236	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34749846	0.92[EUR][1000 genomes]
rs34946886	0.92[EUR][1000 genomes]
rs35190747	0.92[EUR][1000 genomes]
rs35297395	0.92[EUR][1000 genomes]
rs35297486	0.86[EUR][1000 genomes]
rs35411187	0.91[EUR][1000 genomes]
rs35414021	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35456569	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778847	0.92[EUR][1000 genomes]
rs35802497	0.92[EUR][1000 genomes]
rs35944878	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36064160	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36075665	0.92[EUR][1000 genomes]
rs36092070	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36121690	0.92[EUR][1000 genomes]
rs3729577	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731487	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731489	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731497	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731513	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731515	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731534	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731550	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731555	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3937	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4130522	0.91[EUR][1000 genomes]
rs4131361	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131362	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4371540	0.91[EUR][1000 genomes]
rs4392440	0.92[EUR][1000 genomes]
rs4404473	0.86[EUR][1000 genomes]
rs4420898	0.89[EUR][1000 genomes]
rs4479622	0.92[EUR][1000 genomes]
rs4511915	0.92[EUR][1000 genomes]
rs4511916	0.92[EUR][1000 genomes]
rs4541431	0.90[EUR][1000 genomes]
rs4619808	0.90[EUR][1000 genomes]
rs4632568	0.90[EUR][1000 genomes]
rs6442110	0.82[EUR][1000 genomes]
rs6442111	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775179	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6782166	0.91[EUR][1000 genomes]
rs6787500	0.82[EUR][1000 genomes]
rs6791930	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793150	0.91[EUR][1000 genomes]
rs6793223	0.90[EUR][1000 genomes]
rs6793239	0.91[EUR][1000 genomes]
rs6794644	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796343	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800492	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6801801	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6804986	0.90[EUR][1000 genomes]
rs6806112	0.84[EUR][1000 genomes]
rs71323391	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71323394	0.91[EUR][1000 genomes]
rs71323395	0.89[EUR][1000 genomes]
rs71323396	0.89[EUR][1000 genomes]
rs71323397	0.89[EUR][1000 genomes]
rs745116	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614532	0.92[EUR][1000 genomes]
rs7621785	0.92[EUR][1000 genomes]
rs7624450	0.92[EUR][1000 genomes]
rs7632297	0.91[EUR][1000 genomes]
rs7636461	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7644414	0.83[EUR][1000 genomes]
rs7645425	0.90[EUR][1000 genomes]
rs7647817	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7648720	0.94[EUR][1000 genomes]
rs7652233	0.90[EUR][1000 genomes]
rs7653152	0.89[EUR][1000 genomes]
rs7653336	0.90[EUR][1000 genomes]
rs9311421	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936426	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs936427	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9818937	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819094	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9825637	0.90[EUR][1000 genomes]
rs9830016	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9831531	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9833309	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9834095	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9837228	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9847953	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850672	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9853804	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9862131	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
rs36020562	NME6	cis	Artery Tibial	GTEx
rs36020562	ZNF589	cis	Thyroid	GTEx
rs36020562	MRPS18AP1	cis	lung	GTEx
rs36020562	MRPS18AP1	cis	Thyroid	GTEx
rs36020562	SPINK8	cis	Whole Blood	GTEx
rs36020562	ZNF589	cis	Nerve Tibial	GTEx
rs36020562	CDC25A	cis	Thyroid	GTEx
rs36020562	NME6	cis	Muscle Skeletal	GTEx
rs36020562	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs36020562	MRPS18AP1	cis	Artery Aorta	GTEx
rs36020562	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs36020562	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs36020562	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs36020562	CDC25A	cis	Artery Tibial	GTEx
rs36020562	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs36020562	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs36020562	ZNF589	cis	Adipose Subcutaneous	GTEx
rs36020562	CDC25A	cis	Adipose Subcutaneous	GTEx
rs36020562	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs36020562	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs36020562	ZNF589	cis	Artery Aorta	GTEx
rs36020562	FCF1P2	cis	Artery Tibial	GTEx
rs36020562	MRPS18AP1	cis	Stomach	GTEx
rs36020562	ZNF589	cis	Esophagus Muscularis	GTEx
rs36020562	ZNF589	cis	lung	GTEx
rs36020562	ZNF589	cis	Artery Tibial	GTEx
rs36020562	ZNF589	cis	Esophagus Mucosa	GTEx
rs36020562	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs36020562	CDC25A	cis	Muscle Skeletal	GTEx
rs36020562	MRPS18AP1	cis	Artery Tibial	GTEx
rs36020562	NME6	cis	Esophagus Muscularis	GTEx
rs36020562	MRPS18AP1	cis	Nerve Tibial	GTEx
rs36020562	ZNF589	cis	Stomach	GTEx
rs36020562	NME6	cis	Nerve Tibial	GTEx
rs36020562	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs36020562	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48251800-48264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:48255800-48259400	Enhancers	Pancreas	Pancrea
3	chr3:48255800-48260000	Enhancers	Spleen	Spleen
4	chr3:48255800-48261600	Enhancers	Adipose Nuclei	Adipose
5	chr3:48256200-48261600	Enhancers	Ovary	ovary
6	chr3:48256400-48259400	Enhancers	Right Ventricle	heart
7	chr3:48256400-48260600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:48256600-48258800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:48256600-48260000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:48257000-48259000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:48257000-48259000	Weak transcription	Brain Substantia Nigra	brain
12	chr3:48257400-48263400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:48257600-48259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:48257600-48264800	Weak transcription	Hela-S3	cervix
15	chr3:48257800-48272400	Weak transcription	Stomach Mucosa	stomach
16	chr3:48258000-48259000	Weak transcription	Lung	lung
17	chr3:48258000-48259000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:48258200-48259000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:48258200-48259600	Weak transcription	Gastric	stomach
20	chr3:48258200-48262800	Weak transcription	Left Ventricle	heart
21	chr3:48258200-48263800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:48258200-48264000	Weak transcription	Esophagus	oesophagus
23	chr3:48258400-48258800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:48258400-48258800	Weak transcription	Right Atrium	heart
25	chr3:48258400-48259000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links