Variant report

Variant	rs9888799
Chromosome Location	chr16:59611643-59611644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1482243	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1482259	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1482260	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1564578	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs170181	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17258603	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs173759	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17796442	0.80[EUR][1000 genomes]
rs312135	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs31979	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs31980	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs31981	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs31982	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs31983	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs31984	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs31985	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs31986	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs32002	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35037315	0.80[EUR][1000 genomes]
rs391350	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs399777	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs40286	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6500044	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6500045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6500046	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8053483	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8055541	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8055877	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8056271	0.81[EUR][1000 genomes]
rs8061867	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8062551	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9888883	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9928361	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9936381	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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	nsv906747	chr16:59385832-60172030	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv916423	chr16:59411801-59750824	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv572832	chr16:59578561-59756567	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9888799	ARL2BP	cis	cerebellum	SCAN
rs9888799	MT1L	cis	parietal	SCAN
rs9888799	MT1G	cis	parietal	SCAN
rs9888799	MT1M	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:59608800-59614200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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