Variant report

Variant	rs12523473
Chromosome Location	chr5:59566119-59566120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10051717	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs10059334	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[ASN][1000 genomes]
rs10074696	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10077172	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs10079009	0.90[EUR][1000 genomes]
rs10471474	0.94[ASN][1000 genomes]
rs10471475	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12516794	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12520400	0.87[ASN][1000 genomes]
rs1862614	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4235479	0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4328990	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs4404639	0.94[ASN][1000 genomes]
rs4700370	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5024245	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60399456	0.97[ASN][1000 genomes]
rs62370659	0.94[ASN][1000 genomes]
rs62371960	0.90[ASN][1000 genomes]
rs6449459	0.88[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs6864705	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs6882437	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72755103	0.87[ASN][1000 genomes]
rs7710822	0.92[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7714765	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728100	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[ASN][1000 genomes]
rs7734400	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9291685	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9291686	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv4847	chr5:59523591-59569307	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3376670	chr5:59565291-59567158	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12523473	PNMAL1	trans	lymphoblastoid	seeQTL
rs12523473	SLC2A4	trans	cerebellum	SCAN
rs12523473	ELOVL7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59559600-59584800	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59561600-59576600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:59565400-59567400	Weak transcription	Aorta	Aorta
4	chr5:59565600-59569600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr5:59566000-59566200	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr5:59566000-59567400	Weak transcription	Primary monocytes fromperipheralblood	blood

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