Variant report

Variant	rs4886413
Chromosome Location	chr15:75262310-75262311
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11072514	0.82[AMR][1000 genomes]
rs1133323	0.80[AMR][1000 genomes]
rs11630087	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630592	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11636892	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639413	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11856413	0.80[AMR][1000 genomes]
rs12901190	0.84[AMR][1000 genomes]
rs12903370	0.82[AMR][1000 genomes]
rs12904326	0.80[AMR][1000 genomes]
rs12909335	0.80[AMR][1000 genomes]
rs12912343	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912839	0.80[AMR][1000 genomes]
rs2044157	0.84[AMR][1000 genomes]
rs2415251	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34063670	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34307821	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34799293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35556055	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35882241	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56338926	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62029217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495664	0.80[AMR][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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1612	chr15:75247725-75281284	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv977735	chr15:75257534-75268830	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886413	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs4886413	SCAMP5	cis	Artery Tibial	GTEx
rs4886413	SCAMP2	cis	Whole Blood	GTEx
rs4886413	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs4886413	SCAMP5	cis	lung	GTEx
rs4886413	COX5A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75257600-75270800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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