Variant report

Variant	rs17689455
Chromosome Location	chr16:79746335-79746336
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr16:79746227-79746489	HepG2	liver:	n/a	n/a
2	FOXA1	chr16:79746179-79746449	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:79744125..79746553-chr16:79748554..79750825,2	K562	blood:

Variant related genes	Relation type
ENSG00000260876	TF binding region

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

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

rs_ID	r²[population]
rs11150187	0.82[EUR][1000 genomes]
rs11150188	0.90[EUR][1000 genomes]
rs11150189	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11150190	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11150191	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11642757	0.83[EUR][1000 genomes]
rs11644082	0.83[EUR][1000 genomes]
rs11644758	0.84[EUR][1000 genomes]
rs11644799	0.85[EUR][1000 genomes]
rs11644836	0.89[EUR][1000 genomes]
rs11645076	0.85[EUR][1000 genomes]
rs11646791	0.90[EUR][1000 genomes]
rs11864901	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11865979	0.87[EUR][1000 genomes]
rs12149203	0.87[EUR][1000 genomes]
rs12444166	0.89[EUR][1000 genomes]
rs12449109	0.85[EUR][1000 genomes]
rs12449161	0.87[EUR][1000 genomes]
rs1345901	0.81[EUR][1000 genomes]
rs1424231	0.82[EUR][1000 genomes]
rs16950982	0.90[EUR][1000 genomes]
rs16950997	0.82[EUR][1000 genomes]
rs17689024	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17689159	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17689625	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767383	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17767419	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17767491	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767742	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767904	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28773265	0.82[EUR][1000 genomes]
rs3813580	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813582	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575545	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56738967	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56892402	0.85[EUR][1000 genomes]
rs57652769	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58722186	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59617251	0.82[EUR][1000 genomes]
rs7187128	0.85[EUR][1000 genomes]
rs7188445	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7190187	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7195321	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7202240	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202770	0.81[EUR][1000 genomes]
rs7203756	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575076	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73575079	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575083	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575085	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575086	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73575095	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74037508	0.85[EUR][1000 genomes]
rs74037509	0.84[EUR][1000 genomes]
rs8047723	0.82[EUR][1000 genomes]
rs8048928	0.82[EUR][1000 genomes]
rs8053589	0.87[AMR][1000 genomes];0.90[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
rs17689455	RP11-345M22.2	cis	Adipose Subcutaneous	GTEx
rs17689455	RP11-345M22.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79742000-79749400	Weak transcription	Pancreas	Pancrea
2	chr16:79742400-79747800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr16:79742400-79748600	Weak transcription	Stomach Mucosa	stomach
4	chr16:79742400-79749400	Weak transcription	Aorta	Aorta
5	chr16:79744400-79747200	Enhancers	Fetal Intestine Small	intestine
6	chr16:79745000-79747000	Enhancers	Fetal Intestine Large	intestine
7	chr16:79746000-79746400	Enhancers	Liver	Liver
8	chr16:79746000-79746800	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr16:79746000-79746800	Enhancers	Small Intestine	intestine
10	chr16:79746000-79747000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr16:79746200-79749800	Enhancers	Duodenum Mucosa	Duodenum

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