Variant report

Variant	rs9399525
Chromosome Location	chr6:145313726-145313727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1011291	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1111809	0.87[EUR][1000 genomes]
rs11155384	0.85[EUR][1000 genomes]
rs11752326	0.97[EUR][1000 genomes]
rs12175554	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13194942	0.85[EUR][1000 genomes]
rs13200093	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13213543	0.90[EUR][1000 genomes]
rs13216473	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13216871	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1338704	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1338705	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1416297	0.85[EUR][1000 genomes]
rs1572675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074550	0.90[EUR][1000 genomes]
rs2050719	0.89[EUR][1000 genomes]
rs2185145	0.85[EUR][1000 genomes]
rs2211068	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328623	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6570662	0.86[EUR][1000 genomes]
rs6570663	0.85[EUR][1000 genomes]
rs6932709	0.97[EUR][1000 genomes]
rs7742978	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7768827	0.91[EUR][1000 genomes]
rs7769009	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7773947	0.85[EUR][1000 genomes]
rs9322016	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9322017	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9373439	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373440	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373441	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9376878	0.85[EUR][1000 genomes]
rs9376883	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9376884	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9376885	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9376886	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9376887	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9386096	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9386097	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9390263	0.90[EUR][1000 genomes]
rs9390268	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9390269	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390270	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9390271	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9399523	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399526	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9403636	0.81[EUR][1000 genomes]
rs9403645	0.90[EUR][1000 genomes]
rs9403649	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9403650	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9403651	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403652	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403653	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403655	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9497135	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv1850377	chr6:145199259-145319640	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv886742	chr6:145269757-145376903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9399525	PLAGL1	cis	cerebellum	SCAN
rs9399525	MTHFSD	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145311000-145314600	Weak transcription	HUVEC	blood vessel
2	chr6:145311000-145315000	Weak transcription	NHDF-Ad	bronchial
3	chr6:145311400-145315000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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