Variant report

Variant	rs3109166
Chromosome Location	chr4:80552199-80552200
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10022663	0.82[EUR][1000 genomes]
rs1031005	0.83[EUR][1000 genomes]
rs11098770	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs11941782	0.82[EUR][1000 genomes]
rs12643491	0.83[EUR][1000 genomes]
rs13104009	0.83[EUR][1000 genomes]
rs13112067	0.82[EUR][1000 genomes]
rs13112577	0.82[EUR][1000 genomes]
rs1371989	0.83[EUR][1000 genomes]
rs1371993	0.83[EUR][1000 genomes]
rs1440853	0.83[EUR][1000 genomes]
rs1837646	0.81[EUR][1000 genomes]
rs1866835	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2165386	0.83[EUR][1000 genomes]
rs2582681	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2709847	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3111790	1.00[ASN][1000 genomes]
rs3943669	0.83[EUR][1000 genomes]
rs4389603	0.83[EUR][1000 genomes]
rs4975056	0.83[EUR][1000 genomes]
rs60613746	0.94[ASN][1000 genomes]
rs62297619	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62297620	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62297622	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6812760	0.83[EUR][1000 genomes]
rs6850999	0.83[EUR][1000 genomes]
rs7665378	0.97[ASN][1000 genomes]
rs7687586	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7688923	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894054	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs894055	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9307545	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9307551	0.83[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	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879507	chr4:80365765-80552199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv879508	chr4:80398708-80552199	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1005152	chr4:80549659-80814456	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3109166	LINC00989	cis	Adipose Subcutaneous	GTEx
rs3109166	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs3109166	LINC00989	cis	Muscle Skeletal	GTEx
rs3109166	LINC00989	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80545000-80555400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:80545400-80555200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:80547000-80552800	Weak transcription	K562	blood
4	chr4:80551400-80553000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:80551800-80552800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:80551800-80553000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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