Variant report

Variant	rs2675833
Chromosome Location	chr3:50862213-50862214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1038415	0.91[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs107457	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130258	0.90[AFR][1000 genomes];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	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1552255	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552256	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17051012	1.00[EUR][1000 genomes]
rs17051016	1.00[EUR][1000 genomes]
rs17051017	1.00[EUR][1000 genomes]
rs17051404	1.00[EUR][1000 genomes]
rs1843073	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2129069	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2262848	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2355337	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2355701	0.91[ASW][hapmap];0.86[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2608996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2609004	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];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[YRI][hapmap];1.00[AMR][1000 genomes]
rs2675779	0.91[ASW][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap]
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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2675815	0.91[ASW][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];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]
rs407164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs421689	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234694	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234695	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4267639	0.82[ASW][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4340700	1.00[YRI][hapmap];0.83[AFR][1000 genomes];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]
rs4688704	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4688717	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55852678	1.00[EUR][1000 genomes]
rs56112107	1.00[EUR][1000 genomes]
rs56198179	1.00[EUR][1000 genomes]
rs56341000	1.00[EUR][1000 genomes]
rs56413944	1.00[EUR][1000 genomes]
rs57756789	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57987466	1.00[EUR][1000 genomes]
rs58854038	1.00[EUR][1000 genomes]
rs58911362	1.00[EUR][1000 genomes]
rs59065723	1.00[EUR][1000 genomes]
rs59337835	1.00[EUR][1000 genomes]
rs59340349	1.00[EUR][1000 genomes]
rs59749820	1.00[EUR][1000 genomes]
rs59944295	1.00[EUR][1000 genomes]
rs60132317	0.90[AFR][1000 genomes];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]
rs609678	1.00[EUR][1000 genomes]
rs61032466	1.00[EUR][1000 genomes]
rs61455710	1.00[EUR][1000 genomes]
rs621975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs628865	1.00[ASW][hapmap];0.96[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446223	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446246	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]
rs650473	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs665943	1.00[EUR][1000 genomes]
rs6768539	1.00[EUR][1000 genomes]
rs6789552	1.00[EUR][1000 genomes]
rs6807662	1.00[AMR][1000 genomes]
rs7373700	0.91[ASW][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833231	1.00[EUR][1000 genomes]
rs73833232	1.00[EUR][1000 genomes]
rs73833239	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]
rs73835533	1.00[EUR][1000 genomes]
rs73835535	1.00[EUR][1000 genomes]
rs73835537	1.00[EUR][1000 genomes]
rs73835538	1.00[EUR][1000 genomes]
rs7433944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611428	0.82[LWK][hapmap]
rs7642578	1.00[EUR][1000 genomes]
rs7650772	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652715	0.83[LWK][hapmap]
rs7653228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311462	0.91[ASW][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap]
rs936714	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9818443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821597	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9825283	0.91[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9840476	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851304	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854588	1.00[AMR][1000 genomes]
rs9857033	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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
rs2675833	PRPF6	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50856000-50863200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:50856200-50863400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:50857200-50862600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:50857200-50867600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:50860400-50868000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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