Variant report

Variant	rs650555
Chromosome Location	chr6:145400233-145400234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1007379	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11155401	0.96[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13192528	0.80[EUR][1000 genomes]
rs2328639	0.81[EUR][1000 genomes]
rs2761089	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2788713	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2788720	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs477572	0.86[EUR][1000 genomes]
rs480110	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs499988	0.82[EUR][1000 genomes]
rs510141	0.83[EUR][1000 genomes]
rs512985	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs514258	0.84[EUR][1000 genomes]
rs515224	0.84[EUR][1000 genomes]
rs519680	0.84[EUR][1000 genomes]
rs521471	0.82[EUR][1000 genomes]
rs522959	0.81[EUR][1000 genomes]
rs524563	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526564	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs529733	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs539661	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs540319	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs544904	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs559299	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs561083	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs565687	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs572490	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs584911	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs605757	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs607623	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs608041	0.83[ASN][1000 genomes]
rs609639	0.86[EUR][1000 genomes]
rs620561	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs621529	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs623736	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs625054	0.82[EUR][1000 genomes]
rs625717	0.84[ASN][1000 genomes]
rs627131	0.84[ASN][1000 genomes]
rs630099	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs632526	0.84[EUR][1000 genomes]
rs635627	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs636367	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs637348	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs647744	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648664	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs649933	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs666199	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669469	0.86[EUR][1000 genomes]
rs669890	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs674575	0.83[EUR][1000 genomes]
rs680108	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs683944	0.86[EUR][1000 genomes]
rs6939640	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1022965	chr6:145374851-145635385	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015500	chr6:145388558-145421503	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv830834	chr6:145392073-145556294	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs650555	PLAGL1	cis	cerebellum	SCAN
rs650555	EPM2A	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145399200-145401600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:145399600-145401800	Weak transcription	HSMMtube	muscle

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