Variant report

Variant	rs4888542
Chromosome Location	chr16:76784687-76784688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11859422	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11863986	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11865787	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12051146	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12051456	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12325148	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28482984	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28628577	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35944588	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924497	0.96[EUR][1000 genomes]
rs4128626	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243128	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4243129	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243130	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4420546	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4493053	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4497706	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4531755	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4594278	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4887875	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4887877	0.82[AMR][1000 genomes]
rs4888541	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4888547	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4888548	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4888551	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4888554	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4888555	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4888556	0.84[EUR][1000 genomes]
rs55633617	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55708680	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55789571	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55802409	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55881077	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55924867	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56041502	0.90[EUR][1000 genomes]
rs56046613	0.95[EUR][1000 genomes]
rs56331902	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56861109	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56879922	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56902504	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57674440	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57687945	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57724103	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58184388	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58949128	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60056123	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61217580	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564365	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66521224	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66757454	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66822431	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66886305	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66897320	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66973227	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67017862	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67048634	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67141892	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67536114	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67537070	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67587326	0.85[ASN][1000 genomes]
rs67593505	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67607703	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67616652	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67876318	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs68127547	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190230	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190330	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7191013	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7192137	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7198483	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7205513	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7498325	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8049894	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8061558	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8063471	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9933879	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063069	chr16:76462850-77214064	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv542963	chr16:76462850-77214064	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv573047	chr16:76540798-76881625	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2422474	chr16:76544108-77125562	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1056946	chr16:76599511-77084651	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
6	nsv833288	chr16:76621358-76785197	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1060132	chr16:76640155-77057830	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
8	nsv573051	chr16:76650543-76798980	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv906947	chr16:76682263-77160626	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
10	nsv827755	chr16:76687126-76786702	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv2754946	chr16:76710087-76850338	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv869201	chr16:76714549-77233646	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
13	esv2830265	chr16:76722500-76844155	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1066043	chr16:76730435-76795452	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1065850	chr16:76766096-76889490	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1063345	chr16:76766096-76891460	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv457539	chr16:76777664-77081676	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
18	nsv573073	chr16:76777664-77081676	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
19	esv2761915	chr16:76782108-76874387	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4888542	PLEKHO1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:76781200-76784800	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr16:76782200-76785400	Enhancers	Fetal Lung	lung
3	chr16:76784000-76786400	Weak transcription	Brain Germinal Matrix	brain
4	chr16:76784600-76785600	Weak transcription	Fetal Brain Male	brain

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