Variant report

Variant	rs1378661
Chromosome Location	chr3:160424299-160424300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160411890..160413956-chr3:160423439..160425541,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10433459	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11707740	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12638557	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062999	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13091372	0.83[ASN][1000 genomes]
rs13092981	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1378659	0.92[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1455872	0.83[ASW][hapmap];0.81[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1543234	0.80[ASN][1000 genomes]
rs1568573	0.90[JPT][hapmap];0.86[LWK][hapmap];0.80[ASN][1000 genomes]
rs16831361	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17217147	0.84[EUR][1000 genomes]
rs2366967	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34275580	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35355599	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7633816	0.85[CEU][hapmap]
rs7651855	0.92[CEU][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs7651941	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs959826	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9820796	0.81[CEU][hapmap]
rs9835634	0.81[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1378661	PPM1L	cis	cerebellum	SCAN
rs1378661	IFT80	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160418800-160424800	Weak transcription	Hela-S3	cervix

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