Variant report

Variant	rs4516787
Chromosome Location	chr4:56010165-56010166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10012589	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10012701	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10013228	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10020668	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10517343	0.92[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12331471	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12331507	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12331538	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12331597	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12498317	0.84[CEU][hapmap];0.97[GIH][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12505096	0.84[CEU][hapmap];1.00[GIH][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1551641	0.91[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1551642	0.87[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1551643	0.92[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1551644	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1551645	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17711320	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17773813	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1903068	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2239702	0.92[GIH][hapmap]
rs28411232	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28517654	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28584303	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28680424	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28838369	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36146043	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236106	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73236109	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73236111	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312655	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9312656	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9312657	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9312658	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9992737	0.87[AFR][1000 genomes]
rs9997685	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][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	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv980205	chr4:56009143-56011119	Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4516787	SPATA18	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55999600-56020600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links