Variant report

Variant	rs11699876
Chromosome Location	chr20:24686375-24686376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11087477	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11698370	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11698382	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11699163	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11699367	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11699717	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12625030	0.95[CEU][hapmap]
rs13041502	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13043903	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13045365	1.00[ASW][hapmap]
rs34025307	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34084123	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34489305	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34751858	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35449981	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4140548	0.95[CEU][hapmap]
rs57130956	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57927783	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59210731	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6036878	0.95[CEU][hapmap]
rs6049859	0.94[CEU][hapmap]
rs6049860	0.95[CEU][hapmap]
rs6049868	0.95[CEU][hapmap]
rs6049869	0.95[CEU][hapmap]
rs6049871	0.95[CEU][hapmap]
rs6049872	0.84[CEU][hapmap]
rs6049874	0.95[CEU][hapmap]
rs6049888	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60746501	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs729540	0.95[CEU][hapmap]
rs735186	0.95[CEU][hapmap]
rs742807	0.95[CEU][hapmap]
rs880502	0.95[CEU][hapmap]
rs926708	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv523138	chr20:24683554-24686375	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11699876	TMEM90B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24675800-24689200	Weak transcription	Right Atrium	heart
2	chr20:24685800-24687000	Enhancers	HSMM	muscle
3	chr20:24685800-24688800	Weak transcription	Fetal Thymus	thymus
4	chr20:24685800-24695000	Weak transcription	Thymus	Thymus

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