Variant report

Variant	rs9855123
Chromosome Location	chr3:49229457-49229458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr3:49229177-49229458	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
C3orf84	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10049462	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10154895	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10865954	0.89[ASN][1000 genomes]
rs11130182	0.83[ASN][1000 genomes]
rs11130184	0.92[ASN][1000 genomes]
rs11552724	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11706052	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710247	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11712006	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713297	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11715581	0.87[ASN][1000 genomes]
rs11716334	0.92[ASN][1000 genomes]
rs11718982	0.88[EUR][1000 genomes]
rs11719220	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719457	0.81[EUR][1000 genomes]
rs11720460	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12487580	0.85[ASN][1000 genomes]
rs12490393	0.87[ASN][1000 genomes]
rs12493001	0.94[ASN][1000 genomes]
rs12629759	0.92[ASN][1000 genomes]
rs12636030	0.94[ASN][1000 genomes]
rs12637576	0.92[ASN][1000 genomes]
rs12715434	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064784	0.85[ASN][1000 genomes]
rs13068038	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072554	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077498	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080725	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086240	0.81[EUR][1000 genomes]
rs13087930	0.81[EUR][1000 genomes]
rs13090839	0.81[EUR][1000 genomes]
rs13096406	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2334958	0.81[ASN][1000 genomes]
rs3212	0.85[ASN][1000 genomes]
rs34326553	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34343820	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34504524	0.84[EUR][1000 genomes]
rs34509487	0.81[EUR][1000 genomes]
rs34566463	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34580506	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34784192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34889065	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35060561	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35102816	0.84[EUR][1000 genomes]
rs35108630	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35185152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35283189	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35673421	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3923475	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279134	0.85[ASN][1000 genomes]
rs4308307	0.87[ASN][1000 genomes]
rs4364202	0.83[ASN][1000 genomes]
rs4499638	0.92[ASN][1000 genomes]
rs4513485	0.85[ASN][1000 genomes]
rs4521268	0.85[ASN][1000 genomes]
rs4536858	0.92[ASN][1000 genomes]
rs4955410	0.89[ASN][1000 genomes]
rs4955418	0.92[ASN][1000 genomes]
rs4955419	0.87[ASN][1000 genomes]
rs4955420	0.87[ASN][1000 genomes]
rs5030795	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55713230	0.92[ASN][1000 genomes]
rs55921200	0.83[EUR][1000 genomes]
rs56306491	0.87[EUR][1000 genomes]
rs56318350	0.81[EUR][1000 genomes]
rs61583136	0.89[ASN][1000 genomes]
rs62262517	0.83[ASN][1000 genomes]
rs66991555	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67286839	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6770112	0.89[ASN][1000 genomes]
rs6779394	0.89[ASN][1000 genomes]
rs67831908	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784111	0.94[ASN][1000 genomes]
rs6790914	0.92[ASN][1000 genomes]
rs6794924	0.92[ASN][1000 genomes]
rs6795025	0.81[ASN][1000 genomes]
rs71324939	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73084135	0.92[EUR][1000 genomes]
rs7615235	0.82[ASN][1000 genomes]
rs7626445	0.85[ASN][1000 genomes]
rs9311439	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9814987	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9826525	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9828310	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835439	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837237	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837625	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840050	0.85[ASN][1000 genomes]
rs9847839	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850917	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9862483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880088	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880309	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9990153	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9855123	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9855123	WDR6	cis	Esophagus Mucosa	GTEx
rs9855123	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9855123	WDR6	cis	Adipose Subcutaneous	GTEx
rs9855123	WDR6	cis	Artery Tibial	GTEx
rs9855123	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49216200-49236400	Weak transcription	Esophagus	oesophagus
2	chr3:49228400-49230200	Enhancers	Fetal Heart	heart
3	chr3:49228600-49229600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49228600-49229600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49228600-49229600	Enhancers	HepG2	liver
6	chr3:49228600-49230200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:49228800-49236400	Weak transcription	Right Atrium	heart
8	chr3:49229000-49230200	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links