Variant report

Variant	rs6551298
Chromosome Location	chr3:88270375-88270376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs11128021	0.80[EUR][1000 genomes]
rs12493327	0.82[EUR][1000 genomes]
rs12631689	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714702	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060704	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13063511	0.81[ASN][1000 genomes]
rs13067183	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13067419	0.81[EUR][1000 genomes]
rs13317261	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28672845	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28694532	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3890707	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4241551	0.81[EUR][1000 genomes]
rs4257571	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4337654	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4374552	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4384978	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4414876	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4429658	0.81[EUR][1000 genomes]
rs4432672	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4434168	0.81[EUR][1000 genomes]
rs4485742	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4488864	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4501136	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4507280	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4518156	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4555548	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4580585	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4596173	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4616670	0.80[EUR][1000 genomes]
rs4858935	0.87[EUR][1000 genomes]
rs4858936	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858937	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858938	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858995	0.81[EUR][1000 genomes]
rs4858998	0.81[ASN][1000 genomes]
rs4858999	0.81[ASN][1000 genomes]
rs4859001	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859002	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859004	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859005	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55744603	0.82[EUR][1000 genomes]
rs55923163	0.80[EUR][1000 genomes]
rs55936434	0.80[EUR][1000 genomes]
rs60377014	0.80[EUR][1000 genomes]
rs6419867	0.81[ASN][1000 genomes]
rs6551271	0.80[EUR][1000 genomes]
rs6551272	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6551273	0.81[ASN][1000 genomes]
rs6551274	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551275	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551277	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551278	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551280	0.85[EUR][1000 genomes]
rs6551282	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551283	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551284	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551285	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551286	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6551288	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6551289	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6551291	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551292	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551293	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6551294	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6551296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6551297	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6762453	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6767258	0.83[ASN][1000 genomes]
rs6771031	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6778708	0.96[EUR][1000 genomes]
rs6781333	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6782507	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6785359	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6785560	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786788	0.81[EUR][1000 genomes]
rs6791133	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792208	0.81[EUR][1000 genomes]
rs6793783	0.81[EUR][1000 genomes]
rs6801046	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6804818	0.81[EUR][1000 genomes]
rs6805957	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73132515	0.80[EUR][1000 genomes]
rs7427047	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7427296	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7427335	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7427704	0.83[ASN][1000 genomes]
rs7428357	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7429120	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430158	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7431074	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7432509	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7432559	0.84[AFR][1000 genomes]
rs7432838	0.85[EUR][1000 genomes]
rs7433285	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7615585	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7617691	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7618080	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7620830	0.80[EUR][1000 genomes]
rs7626777	0.81[EUR][1000 genomes]
rs7628689	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7630028	0.81[EUR][1000 genomes]
rs7630240	0.82[EUR][1000 genomes]
rs7632123	0.88[EUR][1000 genomes]
rs7635996	0.81[EUR][1000 genomes]
rs7639420	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7641173	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7650707	0.83[EUR][1000 genomes]
rs7651641	0.83[ASN][1000 genomes]
rs7652528	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7653652	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9310072	0.81[EUR][1000 genomes]
rs9310077	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9809661	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9813894	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9814057	0.88[EUR][1000 genomes]
rs9831230	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9841834	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9843550	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9847355	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9848258	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9849248	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9849353	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854138	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9856990	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861398	0.81[ASN][1000 genomes]
rs9865335	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9865578	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9865703	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9865710	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9866843	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9868310	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9868977	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873182	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876807	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9881255	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1013031	chr3:88256289-88347505	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6551298	C3orf38	Cis_1M	lymphoblastoid	RTeQTL
rs6551298	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88253400-88278200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:88268600-88274400	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:88268600-88274400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:88269400-88270800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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