Variant report

Variant	rs17689159
Chromosome Location	chr16:79742390-79742391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11150187	0.83[EUR][1000 genomes]
rs11150188	0.90[EUR][1000 genomes]
rs11150189	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11150190	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11150191	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11642757	0.82[EUR][1000 genomes]
rs11644082	0.84[EUR][1000 genomes]
rs11644758	0.85[EUR][1000 genomes]
rs11644799	0.85[EUR][1000 genomes]
rs11644836	0.90[EUR][1000 genomes]
rs11645076	0.85[EUR][1000 genomes]
rs11646791	0.90[EUR][1000 genomes]
rs11864901	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11865979	0.88[EUR][1000 genomes]
rs12149203	0.88[EUR][1000 genomes]
rs12444166	0.90[EUR][1000 genomes]
rs12449109	0.85[EUR][1000 genomes]
rs12449161	0.87[EUR][1000 genomes]
rs1345901	0.82[EUR][1000 genomes]
rs1424231	0.83[EUR][1000 genomes]
rs16950982	0.90[EUR][1000 genomes]
rs16950997	0.83[EUR][1000 genomes]
rs17689024	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17689455	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17689625	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17767383	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17767419	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17767491	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17767742	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17767904	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28773265	0.83[EUR][1000 genomes]
rs3813580	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813582	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4575545	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56738967	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56892402	0.85[EUR][1000 genomes]
rs57652769	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58722186	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59617251	0.83[EUR][1000 genomes]
rs7187128	0.85[EUR][1000 genomes]
rs7188445	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7190187	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7195321	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7202240	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7202770	0.82[EUR][1000 genomes]
rs7203756	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73575076	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73575079	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73575083	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73575085	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73575086	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73575095	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74037508	0.85[EUR][1000 genomes]
rs74037509	0.84[EUR][1000 genomes]
rs8047723	0.83[EUR][1000 genomes]
rs8048928	0.83[EUR][1000 genomes]
rs8053589	0.88[AMR][1000 genomes];0.91[EUR][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	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	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
3	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
4	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
5	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17689159	RP11-345M22.2	cis	Skin Sun Exposed Lower leg	GTEx
rs17689159	RP11-345M22.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79738800-79744400	Weak transcription	Fetal Intestine Small	intestine
2	chr16:79739600-79742400	Enhancers	NHDF-Ad	bronchial
3	chr16:79739800-79742600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr16:79741400-79742400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr16:79741600-79742400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:79741600-79742400	Enhancers	Aorta	Aorta
7	chr16:79741600-79742400	Enhancers	Duodenum Mucosa	Duodenum
8	chr16:79741600-79742400	Enhancers	Small Intestine	intestine
9	chr16:79741600-79742400	Enhancers	Stomach Mucosa	stomach
10	chr16:79741800-79742400	Enhancers	Esophagus	oesophagus
11	chr16:79742000-79749400	Weak transcription	Pancreas	Pancrea

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