Variant report

Variant	rs7636461
Chromosome Location	chr3:48270955-48270956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 155 )
Associated
traits (count: 37 )

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

rs_ID	r²[population]
rs1045482	0.88[CEU][hapmap];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	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs11707606	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707997	0.91[EUR][1000 genomes]
rs11709691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710257	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs11710861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714176	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs11714944	0.90[EUR][1000 genomes]
rs11715776	0.89[EUR][1000 genomes]
rs11715799	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715876	0.83[EUR][1000 genomes]
rs11716371	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs11716848	0.91[EUR][1000 genomes]
rs11717716	0.91[EUR][1000 genomes]
rs11718329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718350	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes]
rs11719365	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11928691	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12486935	0.91[JPT][hapmap]
rs12486944	0.90[JPT][hapmap]
rs13059037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13060020	0.91[EUR][1000 genomes]
rs13061269	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs13066044	0.91[EUR][1000 genomes]
rs13066758	0.90[CEU][hapmap];0.89[CHB][hapmap];0.94[EUR][1000 genomes]
rs13067450	0.94[EUR][1000 genomes]
rs13068265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.83[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	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13079728	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs13081169	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13081633	0.93[EUR][1000 genomes]
rs13082158	0.90[EUR][1000 genomes]
rs13082859	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs13084616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs13085251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs13087050	0.82[JPT][hapmap]
rs13087929	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13090538	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes]
rs13094727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs13095983	0.93[EUR][1000 genomes]
rs13097450	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13100815	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17647717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17786132	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2125482	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2361685	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2541	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs3197223	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs34076262	0.92[EUR][1000 genomes]
rs34225441	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34523942	0.94[EUR][1000 genomes]
rs34589064	0.94[EUR][1000 genomes]
rs34630841	0.94[EUR][1000 genomes]
rs34728236	0.99[EUR][1000 genomes];0.97[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	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35456569	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35778847	0.94[EUR][1000 genomes]
rs35802497	0.94[EUR][1000 genomes]
rs35944878	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36020562	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36064160	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36075665	0.94[EUR][1000 genomes]
rs36092070	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36121690	0.94[EUR][1000 genomes]
rs3729577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731487	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731489	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731497	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731515	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731550	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4130522	0.93[EUR][1000 genomes]
rs4131361	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4131362	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs4511915	0.91[CEU][hapmap];1.00[CHB][hapmap];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	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6442111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6775179	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6782166	0.93[EUR][1000 genomes]
rs6787500	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6791930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793150	0.93[EUR][1000 genomes]
rs6793223	0.92[EUR][1000 genomes]
rs6793239	0.93[EUR][1000 genomes]
rs6794644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6796343	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6796490	0.88[CEU][hapmap]
rs6800492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6801801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6804986	0.92[EUR][1000 genomes]
rs6806112	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs71323391	0.95[EUR][1000 genomes];0.83[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7614532	0.94[EUR][1000 genomes]
rs7621785	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs7624450	0.94[EUR][1000 genomes]
rs7632297	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7644414	0.85[EUR][1000 genomes]
rs7645425	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7647817	0.89[EUR][1000 genomes];0.90[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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs936426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs936427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9818937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9819094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9825637	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.92[EUR][1000 genomes]
rs9830016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9831531	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9833309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9834095	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9837228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9847953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9850672	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9853804	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862131	0.83[EUR][1000 genomes];0.83[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:37)

SNP	Gene	Cis/trans	Tissue	Source
rs7636461	CDC25A	cis	Artery Tibial	GTEx
rs7636461	ZNF589	cis	Stomach	GTEx
rs7636461	NME6	cis	Muscle Skeletal	GTEx
rs7636461	ZNF589	cis	Nerve Tibial	GTEx
rs7636461	ZNF589	cis	Brain Pons	GTEx
rs7636461	MRPS18AP1	cis	Nerve Tibial	GTEx
rs7636461	NME6	cis	Esophagus Muscularis	GTEx
rs7636461	FCF1P2	cis	Artery Tibial	GTEx
rs7636461	CDC25A	cis	Thyroid	GTEx
rs7636461	ZNF589	cis	Artery Aorta	GTEx
rs7636461	ZNF589	cis	Cerebellum	GTEx
rs7636461	ZNF589	cis	Frontal Cortex	GTEx
rs7636461	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs7636461	ZNF589	cis	Temporal Cortex	GTEx
rs7636461	CDC25A	cis	Adipose Subcutaneous	GTEx
rs7636461	MRPS18AP1	cis	Artery Tibial	GTEx
rs7636461	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs7636461	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs7636461	ZNF589	cis	Esophagus Mucosa	GTEx
rs7636461	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7636461	MRPS18AP1	cis	Artery Aorta	GTEx
rs7636461	ZNF589	cis	Esophagus Muscularis	GTEx
rs7636461	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs7636461	NME6	cis	Artery Tibial	GTEx
rs7636461	MRPS18AP1	cis	lung	GTEx
rs7636461	MRPS18AP1	cis	Stomach	GTEx
rs7636461	ZNF589	cis	Artery Tibial	GTEx
rs7636461	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs7636461	ZNF589	cis	Thyroid	GTEx
rs7636461	NME6	cis	Nerve Tibial	GTEx
rs7636461	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs7636461	MRPS18AP1	cis	Thyroid	GTEx
rs7636461	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs7636461	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs7636461	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs7636461	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs7636461	CDC25A	cis	Muscle Skeletal	GTEx

Chromatin state (count:19 , 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	chr3:48265400-48274000	Weak transcription	Hela-S3	cervix
4	chr3:48265600-48274400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:48265800-48273400	Weak transcription	Esophagus	oesophagus
6	chr3:48265800-48277600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:48266000-48274200	Weak transcription	Spleen	Spleen
8	chr3:48268000-48273400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:48268600-48274000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:48268600-48274400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:48268800-48273600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:48268800-48274000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:48269000-48274000	Weak transcription	Thymus	Thymus
14	chr3:48269000-48274000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:48269200-48271000	Weak transcription	GM12878-XiMat	blood
16	chr3:48269200-48271800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:48269200-48273000	Weak transcription	Primary B cells from cord blood	blood
18	chr3:48269600-48274200	Weak transcription	Fetal Thymus	thymus
19	chr3:48270800-48271200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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