Variant report

Variant	rs6450679
Chromosome Location	chr5:29251129-29251130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10044016	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10044024	0.99[ASN][1000 genomes]
rs10050443	0.99[ASN][1000 genomes]
rs10054250	0.97[ASN][1000 genomes]
rs10062606	0.97[ASN][1000 genomes]
rs10069328	0.97[ASN][1000 genomes]
rs10069894	0.97[ASN][1000 genomes]
rs10073570	0.97[ASN][1000 genomes]
rs10440631	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10440642	0.96[ASN][1000 genomes]
rs10454837	0.99[ASN][1000 genomes]
rs10454851	0.99[ASN][1000 genomes]
rs10940787	0.99[ASN][1000 genomes]
rs10940788	0.99[ASN][1000 genomes]
rs10940790	0.99[ASN][1000 genomes]
rs11959636	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13163013	0.84[ASN][1000 genomes]
rs4273618	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4317332	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4331913	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4346778	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4351155	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4370285	0.95[ASN][1000 genomes]
rs4370286	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4370287	0.97[ASN][1000 genomes]
rs4467718	0.97[ASN][1000 genomes]
rs4476737	0.97[ASN][1000 genomes]
rs4577702	0.97[ASN][1000 genomes]
rs4593279	0.97[ASN][1000 genomes]
rs4620035	0.97[ASN][1000 genomes]
rs4632809	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4632810	0.99[ASN][1000 genomes]
rs5023619	0.97[ASN][1000 genomes]
rs55891773	0.99[ASN][1000 genomes]
rs55893778	0.98[ASN][1000 genomes]
rs56009220	0.95[ASN][1000 genomes]
rs56009779	0.95[ASN][1000 genomes]
rs56097252	0.82[ASN][1000 genomes]
rs56104054	0.99[ASN][1000 genomes]
rs56171187	0.99[ASN][1000 genomes]
rs56252458	0.99[ASN][1000 genomes]
rs56359525	0.99[ASN][1000 genomes]
rs56403354	0.99[ASN][1000 genomes]
rs59639762	0.99[ASN][1000 genomes]
rs6450678	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6450680	0.99[ASN][1000 genomes]
rs66793982	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6862626	0.99[ASN][1000 genomes]
rs6881646	0.99[ASN][1000 genomes]
rs72743470	0.99[ASN][1000 genomes]
rs72743471	0.99[ASN][1000 genomes]
rs72743472	0.99[ASN][1000 genomes]
rs72743475	0.92[ASN][1000 genomes]
rs72743476	0.99[ASN][1000 genomes]
rs72743478	0.99[ASN][1000 genomes]
rs72743484	0.95[ASN][1000 genomes]
rs7341031	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7701380	0.99[ASN][1000 genomes]
rs7717789	0.99[ASN][1000 genomes]
rs7732794	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3528360	chr5:29069255-29548659	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv3528361	chr5:29069255-29548659	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1016603	chr5:29102713-29843965	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv537712	chr5:29102713-29843965	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1031329	chr5:29177677-29760923	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv537713	chr5:29177677-29760923	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv880414	chr5:29194872-29495564	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv881552	chr5:29219030-29466930	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1024756	chr5:29220387-29501672	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv880722	chr5:29249544-29466930	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6450679	SNORD59B	trans	parietal	SCAN
rs6450679	RNASEN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:29250400-29254800	Weak transcription	Hela-S3	cervix

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