Variant report

Variant	rs836790
Chromosome Location	chr5:79901151-79901152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1238951	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1643656	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1650660	0.85[EUR][1000 genomes]
rs1650684	0.80[EUR][1000 genomes]
rs1650687	0.81[EUR][1000 genomes]
rs1650690	0.84[CEU][hapmap]
rs1650716	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1650723	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1677697	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1677705	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs32958	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6151616	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6151636	0.83[EUR][1000 genomes]
rs836789	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs836791	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs836792	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs836803	0.83[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv513244	chr5:79900666-79904808	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs836790	MSH3	cis	cerebellum	SCAN
rs836790	MSH3	cis	parietal	SCAN
rs836790	DP58	cis	multi-tissue	Pritchard
rs836790	DHFR	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79899400-79910200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

Quick Search:

Input of quick search could be:

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

what's new

Quick links