Variant report

Variant	rs17109739
Chromosome Location	chr14:80148281-80148282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1030127	0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs10483933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11848654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap]
rs17109747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17109760	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17109764	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17109772	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17109775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17109778	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes]
rs178377	1.00[ASW][hapmap]
rs178386	1.00[ASW][hapmap]
rs2160920	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61993165	0.81[EUR][1000 genomes]
rs61993166	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61995221	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61995222	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61995223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61995224	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61995225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045241	chr14:79885361-80734201	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1039622	chr14:79908702-80266601	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17109739	MAG	trans	brain	seeQTL
rs17109739	CYB5R2	trans	brain	seeQTL
rs17109739	RHOU	trans	brain	seeQTL
rs17109739	ADAMTS4	trans	brain	seeQTL
rs17109739	ELOVL1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:80147200-80152600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr14:80148000-80148800	Enhancers	Brain Germinal Matrix	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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