Variant report

Variant	rs7612459
Chromosome Location	chr3:48943496-48943497
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48935231..48938102-chr3:48943156..48945841,3	K562	blood:

Variant related genes	Relation type
ENSG00000178537	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10780033	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130176	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1134591	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11705737	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11705888	0.84[EUR][1000 genomes]
rs11708022	0.81[ASN][1000 genomes]
rs11709246	0.86[ASN][1000 genomes]
rs11712982	0.88[ASN][1000 genomes]
rs11713694	0.83[ASN][1000 genomes]
rs11717978	0.90[ASN][1000 genomes]
rs11719457	0.90[ASN][1000 genomes]
rs11920534	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11924597	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12491743	0.85[EUR][1000 genomes]
rs12493289	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12637037	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13064784	0.83[EUR][1000 genomes]
rs13064883	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13064911	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13072911	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13073997	0.85[ASN][1000 genomes]
rs13076394	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13078308	0.87[EUR][1000 genomes]
rs13086240	0.88[ASN][1000 genomes]
rs13087930	0.90[ASN][1000 genomes]
rs13090839	0.88[ASN][1000 genomes]
rs13094900	0.83[ASN][1000 genomes]
rs13315711	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13316620	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28642807	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34477108	0.90[ASN][1000 genomes]
rs34504524	0.83[ASN][1000 genomes]
rs34509487	0.90[ASN][1000 genomes]
rs3774628	0.82[EUR][1000 genomes]
rs4072859	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974078	0.83[ASN][1000 genomes]
rs4974079	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4974080	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974082	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974084	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974085	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4974087	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4974091	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55674449	0.83[ASN][1000 genomes]
rs56318350	0.90[ASN][1000 genomes]
rs6414613	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442130	0.81[EUR][1000 genomes]
rs6446196	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446198	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6446205	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6446252	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446253	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67060340	0.85[ASN][1000 genomes]
rs67332931	0.86[ASN][1000 genomes]
rs6768433	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6781790	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6786665	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6789285	0.93[EUR][1000 genomes]
rs6791234	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6795025	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71324924	0.86[ASN][1000 genomes]
rs7372149	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7373778	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7373790	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7430198	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430501	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7431710	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431857	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7432989	0.87[EUR][1000 genomes]
rs7615235	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7615675	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7616815	0.81[EUR][1000 genomes]
rs7621015	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7623023	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7626445	0.90[EUR][1000 genomes]
rs7627404	0.90[EUR][1000 genomes]
rs7628719	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7636057	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7639332	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7643368	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647093	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7649458	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8926	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9311430	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311432	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311433	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311434	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9681717	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9682444	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9754878	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9755490	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9830636	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9835307	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9840050	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9840684	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9846123	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9850134	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867373	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876848	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9879971	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9884022	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][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	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs7612459	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7612459	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7612459	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7612459	NICN1-AS1	cis	Thyroid	GTEx
rs7612459	WDR6	cis	Nerve Tibial	GTEx
rs7612459	NCKIPSD	cis	Whole Blood	GTEx
rs7612459	NCKIPSD	cis	Muscle Skeletal	GTEx
rs7612459	WDR6	cis	Muscle Skeletal	GTEx
rs7612459	WDR6	cis	Artery Tibial	GTEx
rs7612459	CCDC36	cis	Artery Tibial	GTEx
rs7612459	WDR6	cis	Esophagus Muscularis	GTEx
rs7612459	WDR6	cis	Adipose Subcutaneous	GTEx
rs7612459	AMT	cis	Muscle Skeletal	GTEx
rs7612459	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7612459	WDR6	cis	lung	GTEx
rs7612459	ARIH2	cis	Thyroid	GTEx
rs7612459	AMT	cis	Thyroid	GTEx
rs7612459	CCDC36	cis	Esophagus Muscularis	GTEx
rs7612459	WDR6	cis	Whole Blood	GTEx
rs7612459	NCKIPSD	cis	Nerve Tibial	GTEx
rs7612459	WDR6	cis	Esophagus Mucosa	GTEx
rs7612459	WDR6	cis	Heart Left Ventricle	GTEx
rs7612459	NICN1	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48936600-48954800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:48936600-48954800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:48936800-48948600	Weak transcription	Right Atrium	heart
4	chr3:48942400-48954600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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