Variant report

Variant	rs2616160
Chromosome Location	chr8:20684477-20684478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12056930	0.87[ASN][1000 genomes]
rs1441799	0.95[ASN][1000 genomes]
rs17494497	0.91[ASN][1000 genomes]
rs2260948	0.96[ASN][1000 genomes]
rs2410669	0.98[ASN][1000 genomes]
rs2583676	1.00[ASN][1000 genomes]
rs2583677	1.00[ASN][1000 genomes]
rs2583678	1.00[ASN][1000 genomes]
rs2583679	0.95[ASN][1000 genomes]
rs2583680	0.96[ASN][1000 genomes]
rs2583681	0.96[ASN][1000 genomes]
rs2583684	0.84[ASN][1000 genomes]
rs2616150	1.00[ASN][1000 genomes]
rs2616152	0.96[ASN][1000 genomes]
rs2616155	0.96[ASN][1000 genomes]
rs2616158	0.98[ASN][1000 genomes]
rs2616159	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616162	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616163	0.98[ASN][1000 genomes]
rs2616165	1.00[ASN][1000 genomes]
rs2616169	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6981033	0.96[ASN][1000 genomes]
rs6985254	0.87[ASN][1000 genomes]
rs7001823	0.87[ASN][1000 genomes]
rs7008802	0.91[ASN][1000 genomes]
rs7460973	0.89[ASN][1000 genomes]
rs7823871	0.87[ASN][1000 genomes]
rs7827868	0.91[ASN][1000 genomes]
rs964189	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032450	chr8:20514995-21033577	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv539524	chr8:20514995-21033577	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1033319	chr8:20606592-20718378	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv831257	chr8:20610436-20767433	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1021366	chr8:20624387-20726669	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv539525	chr8:20624387-20726669	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1020160	chr8:20652610-20825810	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv539526	chr8:20652610-20825810	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1024612	chr8:20665835-20837761	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv539527	chr8:20665835-20837761	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv1803225	chr8:20684287-20693912	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2616160	LGI3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20683000-20684600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr8:20683800-20684600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr8:20684400-20689800	Weak transcription	Fetal Heart	heart

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