Variant report

Variant	rs4889015
Chromosome Location	chr16:79718730-79718731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11150187	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11150188	0.82[EUR][1000 genomes]
rs11150189	0.81[EUR][1000 genomes]
rs11150190	0.83[EUR][1000 genomes]
rs11150191	0.80[EUR][1000 genomes]
rs11644082	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11644758	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11644799	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11644836	0.81[EUR][1000 genomes]
rs11645076	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11646791	0.82[EUR][1000 genomes]
rs12149234	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12444166	0.81[EUR][1000 genomes]
rs12449109	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12449161	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1424231	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16950982	0.82[EUR][1000 genomes]
rs16950997	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28773265	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4243177	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4490016	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4888043	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4889009	0.88[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4889012	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4889014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889016	0.87[ASN][1000 genomes]
rs56225749	0.86[ASN][1000 genomes]
rs56892402	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59617251	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6564688	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7187128	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7200841	0.89[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7202770	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs74037508	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74037509	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7500666	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8047723	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8048539	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8048928	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8053589	0.81[EUR][1000 genomes]
rs9927134	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889015	RP11-345M22.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:3 , 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
3	chr16:79718600-79720000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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