Variant report

Variant	rs13065289
Chromosome Location	chr3:160375002-160375003
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10936207	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10936208	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10936209	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11709300	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714916	0.82[ASN][1000 genomes]
rs13095931	0.84[EUR][1000 genomes]
rs1317085	0.82[EUR][1000 genomes]
rs17236586	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2178452	0.82[EUR][1000 genomes]
rs2204817	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2367209	0.82[ASN][1000 genomes]
rs28544045	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28730907	0.85[EUR][1000 genomes]
rs34362576	0.85[EUR][1000 genomes]
rs34949451	0.84[EUR][1000 genomes]
rs35308461	0.83[EUR][1000 genomes]
rs35480231	0.83[EUR][1000 genomes]
rs35664264	0.82[EUR][1000 genomes]
rs35867836	0.83[EUR][1000 genomes]
rs36118017	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3946273	0.81[EUR][1000 genomes]
rs4679659	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4679660	0.85[EUR][1000 genomes]
rs4679909	0.82[EUR][1000 genomes]
rs4679910	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60028768	0.83[EUR][1000 genomes]
rs62272215	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272216	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62272217	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62272218	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62272219	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62272220	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6773389	0.85[EUR][1000 genomes]
rs6773962	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774379	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6774566	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6776873	0.85[EUR][1000 genomes]
rs6777739	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6779581	0.85[EUR][1000 genomes]
rs6779671	0.85[EUR][1000 genomes]
rs6787452	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6797760	0.85[EUR][1000 genomes]
rs6798462	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6801373	0.85[EUR][1000 genomes]
rs7632884	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv2757019	chr3:160351021-160380161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2759194	chr3:160351021-160380161	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13065289	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160372600-160376000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:160372600-160385200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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