Variant report

Variant	rs56892402
Chromosome Location	chr16:79716625-79716626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:79712002..79713952-chr16:79716097..79718110,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11150187	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11150188	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11150189	0.92[EUR][1000 genomes]
rs11150190	0.96[EUR][1000 genomes]
rs11150191	0.92[EUR][1000 genomes]
rs11644082	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11644758	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11644799	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11644836	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11645076	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11646791	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11864901	0.91[EUR][1000 genomes]
rs12149234	0.81[AMR][1000 genomes]
rs12444166	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12449109	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12449161	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345901	0.83[EUR][1000 genomes]
rs1424231	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16950982	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16950997	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17689024	0.85[EUR][1000 genomes]
rs17689159	0.85[EUR][1000 genomes]
rs17689455	0.85[EUR][1000 genomes]
rs17689625	0.84[EUR][1000 genomes]
rs17767383	0.84[EUR][1000 genomes]
rs17767419	0.85[EUR][1000 genomes]
rs17767491	0.85[EUR][1000 genomes]
rs17767742	0.84[EUR][1000 genomes]
rs17767904	0.84[EUR][1000 genomes]
rs28773265	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813580	0.84[EUR][1000 genomes]
rs3813582	0.84[EUR][1000 genomes]
rs4243177	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4490016	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4888043	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4889009	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4889012	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4889014	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4889015	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56738967	0.85[EUR][1000 genomes]
rs57652769	0.83[EUR][1000 genomes]
rs58722186	0.83[EUR][1000 genomes]
rs59617251	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6564688	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7187128	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188445	0.91[EUR][1000 genomes]
rs7189954	0.82[EUR][1000 genomes]
rs7190187	0.91[EUR][1000 genomes]
rs7195321	0.91[EUR][1000 genomes]
rs7200841	0.84[EUR][1000 genomes]
rs7202240	0.85[EUR][1000 genomes]
rs7202770	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7203756	0.84[EUR][1000 genomes]
rs73575076	0.84[EUR][1000 genomes]
rs73575079	0.85[EUR][1000 genomes]
rs73575083	0.83[EUR][1000 genomes]
rs73575085	0.84[EUR][1000 genomes]
rs73575086	0.84[EUR][1000 genomes]
rs73575095	0.84[EUR][1000 genomes]
rs74037508	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74037509	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7500666	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8047723	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8048539	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8048928	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8053589	0.93[EUR][1000 genomes]
rs9927134	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv833295	chr16:79568878-79726768	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv906992	chr16:79649394-79769790	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518748	chr16:79716333-79729031	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56892402	RP11-345M22.2	cis	Skin Sun Exposed Lower leg	GTEx
rs56892402	RP11-345M22.2	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79708400-79720400	Weak transcription	Ovary	ovary
2	chr16:79714800-79721400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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