Variant report

Variant	rs6446246
Chromosome Location	chr3:51039817-51039818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11130258	0.83[AMR][1000 genomes]
rs11923336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13092850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13325937	1.00[AMR][1000 genomes]
rs2262848	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2355701	0.91[ASW][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2459450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2608994	1.00[AMR][1000 genomes]
rs2608996	1.00[AMR][1000 genomes]
rs2609004	1.00[AMR][1000 genomes]
rs2609014	1.00[AMR][1000 genomes]
rs2609015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2609027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2609030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675775	1.00[AMR][1000 genomes]
rs2675781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675797	1.00[AMR][1000 genomes]
rs2675798	1.00[AMR][1000 genomes]
rs2675815	1.00[AMR][1000 genomes]
rs2675823	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675824	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675826	0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675833	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4401355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4423762	1.00[AMR][1000 genomes]
rs4440121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688717	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56198179	1.00[EUR][1000 genomes]
rs56307672	1.00[EUR][1000 genomes]
rs56341000	1.00[EUR][1000 genomes]
rs56367927	0.83[AFR][1000 genomes]
rs57164594	1.00[EUR][1000 genomes]
rs57577112	1.00[EUR][1000 genomes]
rs57756789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58225351	0.83[AFR][1000 genomes]
rs58911362	1.00[EUR][1000 genomes]
rs59749820	1.00[EUR][1000 genomes]
rs59944295	1.00[EUR][1000 genomes]
rs60132317	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60209025	1.00[EUR][1000 genomes]
rs60420261	1.00[EUR][1000 genomes]
rs60455882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446242	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446244	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781959	0.91[ASW][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap]
rs6799213	0.80[YRI][hapmap]
rs6805545	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6807662	1.00[AMR][1000 genomes]
rs7373700	0.91[ASW][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833247	1.00[EUR][1000 genomes]
rs73833251	1.00[AMR][1000 genomes]
rs73833935	1.00[EUR][1000 genomes]
rs73833947	1.00[EUR][1000 genomes]
rs73833949	1.00[EUR][1000 genomes]
rs73833952	1.00[EUR][1000 genomes]
rs73833954	1.00[EUR][1000 genomes]
rs7433944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642578	1.00[EUR][1000 genomes]
rs7650772	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7653228	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311462	0.91[ASW][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap]
rs9818443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821597	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854588	1.00[AMR][1000 genomes]
rs9868870	0.83[LWK][hapmap]

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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6446246	PRPF6	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51038800-51041000	Enhancers	HepG2	liver
2	chr3:51039000-51041000	Enhancers	Liver	Liver

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