Variant report

Variant	rs7746139
Chromosome Location	chr6:49051477-49051478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10447401	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10447402	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10948473	0.80[EUR][1000 genomes]
rs10948474	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10948479	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12164014	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12173388	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12193009	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194577	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12198427	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36178489	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129112	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4129113	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4145251	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4145253	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4272220	0.80[AMR][1000 genomes]
rs4272221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4289650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4295467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4305722	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4314496	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4326233	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4327693	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4352681	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4382258	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4383815	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4397213	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4403253	0.81[ASN][1000 genomes]
rs4410717	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4440458	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4449619	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4489146	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4506042	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4510676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4512222	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4523088	0.82[AMR][1000 genomes]
rs4527706	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4537140	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4554314	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4569963	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4571562	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4580868	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4601115	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4601116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4607434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4616992	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458643	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458644	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458645	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458646	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458647	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458651	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458655	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458656	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458657	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458669	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458670	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6458671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458676	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6900450	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6901713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6902329	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6902574	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6917596	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6927013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927493	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6929991	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6930005	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6931955	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6938215	0.81[ASN][1000 genomes]
rs7449972	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7453585	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7749289	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7753993	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7754368	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7755153	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7757406	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7767717	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7772150	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7772533	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7774894	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9349467	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357598	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357599	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9367343	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369842	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9369845	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9369847	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9369848	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9369851	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9369854	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9381721	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9381724	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9381727	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9395448	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9395453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9688726	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv603049	chr6:48931959-49169337	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885880	chr6:48975662-49102186	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7746139	CENPQ	cis	Esophagus Muscularis	GTEx
rs7746139	MUT	cis	Nerve Tibial	GTEx
rs7746139	CENPQ	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49040400-49089600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:49051200-49052000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:49051400-49052000	Enhancers	H9 Cell Line	embryonic stem cell

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