Variant report

Variant	rs7745458
Chromosome Location	chr6:48898009-48898010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10447401	0.88[AMR][1000 genomes]
rs10447402	0.88[AMR][1000 genomes]
rs10948471	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10948473	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10948474	0.88[AMR][1000 genomes]
rs10948479	0.87[AMR][1000 genomes]
rs11966408	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12164014	0.88[AMR][1000 genomes]
rs12193009	0.88[AMR][1000 genomes]
rs12194577	0.87[AMR][1000 genomes]
rs12196232	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12209867	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1543321	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546857	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1938220	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2011289	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2011294	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2205870	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2396888	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2396892	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4129112	0.87[AMR][1000 genomes]
rs4129113	0.87[AMR][1000 genomes]
rs4145251	0.88[AMR][1000 genomes]
rs4145253	0.87[AMR][1000 genomes]
rs4314496	0.88[AMR][1000 genomes]
rs4326233	0.88[AMR][1000 genomes]
rs4327693	0.86[AMR][1000 genomes]
rs4352681	0.86[AMR][1000 genomes]
rs4382258	0.84[AMR][1000 genomes]
rs4383815	0.85[AMR][1000 genomes]
rs4397213	0.86[AMR][1000 genomes]
rs4410717	0.88[AMR][1000 genomes]
rs4437467	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4440458	0.86[AMR][1000 genomes]
rs4489146	0.88[AMR][1000 genomes]
rs4506042	0.86[AMR][1000 genomes]
rs4512222	0.88[AMR][1000 genomes]
rs4527706	0.85[AMR][1000 genomes]
rs4537126	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4537140	0.88[AMR][1000 genomes]
rs4554314	0.88[AMR][1000 genomes]
rs4569963	0.86[AMR][1000 genomes]
rs4571562	0.86[AMR][1000 genomes]
rs4580868	0.88[AMR][1000 genomes]
rs4590266	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4601115	0.86[AMR][1000 genomes]
rs4616992	0.85[AMR][1000 genomes]
rs62412795	0.83[AMR][1000 genomes]
rs62636144	0.87[AMR][1000 genomes]
rs6458640	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6458643	0.88[AMR][1000 genomes]
rs6458644	0.88[AMR][1000 genomes]
rs6458645	0.88[AMR][1000 genomes]
rs6458646	0.88[AMR][1000 genomes]
rs6458647	0.88[AMR][1000 genomes]
rs6458651	0.87[AMR][1000 genomes]
rs6458655	0.86[AMR][1000 genomes]
rs6458656	0.86[AMR][1000 genomes]
rs6458657	0.86[AMR][1000 genomes]
rs6900450	0.85[AMR][1000 genomes]
rs6902329	0.85[AMR][1000 genomes]
rs6902574	0.88[AMR][1000 genomes]
rs6910198	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6917596	0.88[AMR][1000 genomes]
rs6929991	0.88[AMR][1000 genomes]
rs6930005	0.88[AMR][1000 genomes]
rs6931955	0.86[AMR][1000 genomes]
rs6932586	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6940183	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7453585	0.84[AMR][1000 genomes]
rs760683	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs760684	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7747751	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7749289	0.88[AMR][1000 genomes]
rs7753993	0.86[AMR][1000 genomes]
rs7754368	0.87[AMR][1000 genomes]
rs7755153	0.88[AMR][1000 genomes]
rs7757406	0.85[AMR][1000 genomes]
rs7765075	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7767717	0.88[AMR][1000 genomes]
rs7772150	0.86[AMR][1000 genomes]
rs7772532	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7772533	0.88[AMR][1000 genomes]
rs7773546	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7774112	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7774894	0.88[AMR][1000 genomes]
rs9349467	0.88[AMR][1000 genomes]
rs9357585	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357587	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357596	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9357598	0.88[AMR][1000 genomes]
rs9367338	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9367343	0.88[AMR][1000 genomes]
rs9369821	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9369836	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9369842	0.88[AMR][1000 genomes]
rs9369845	0.88[AMR][1000 genomes]
rs9369847	0.88[AMR][1000 genomes]
rs9369848	0.88[AMR][1000 genomes]
rs9369851	0.88[AMR][1000 genomes]
rs9369854	0.88[AMR][1000 genomes]
rs9381721	0.88[AMR][1000 genomes]
rs9381724	0.88[AMR][1000 genomes]
rs9381727	0.84[AMR][1000 genomes]
rs9395420	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9395439	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9395448	0.88[AMR][1000 genomes]
rs9688726	0.88[AMR][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	nsv949690	chr6:48595821-49289855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv603037	chr6:48804862-48995221	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7745458	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs7745458	MUT	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:48832200-48944000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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