Variant report

Variant	rs731393
Chromosome Location	chr11:119840052-119840053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10750167	0.89[ASN][1000 genomes]
rs10790357	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10790359	0.92[ASN][1000 genomes]
rs10790360	0.92[ASN][1000 genomes]
rs10892504	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217601	0.90[ASN][1000 genomes]
rs1787024	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1944504	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1944505	1.00[ASN][1000 genomes]
rs4245210	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4938741	0.90[ASN][1000 genomes]
rs601052	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs602030	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs615539	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs621150	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs626466	0.97[ASN][1000 genomes]
rs636518	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs651055	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6589784	0.92[ASN][1000 genomes]
rs662318	0.83[ASN][1000 genomes]
rs677027	0.83[ASN][1000 genomes]
rs677428	0.83[ASN][1000 genomes]
rs678914	0.80[ASN][1000 genomes]
rs731392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342270	0.86[ASN][1000 genomes]
rs7944850	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7951479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951593	0.92[ASN][1000 genomes]
rs949096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv832285	chr11:119789595-119957724	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs731393	CCDC84	cis	cerebellum	SCAN
rs731393	APOA5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119836200-119841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:119836200-119841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:119836200-119845600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:119836400-119841800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:119837000-119841000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:119837400-119844200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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