Variant report

Variant	rs425463
Chromosome Location	chr5:79901952-79901953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12517451	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs1643665	0.89[ASN][1000 genomes]
rs1650697	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs2115014	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs372069	0.80[ASN][1000 genomes]
rs380691	0.82[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs384925	0.80[ASN][1000 genomes]
rs431443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443611	0.80[ASN][1000 genomes]
rs836788	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836805	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs861365	0.80[ASN][1000 genomes]
rs863901	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs425463	MSH3	cis	Whole Blood	GTEx
rs425463	MSH3	cis	cerebellum	SCAN
rs425463	MSH3	cis	parietal	SCAN
rs425463	MSH3	cis	Artery Aorta	GTEx
rs425463	MSH3	cis	Adipose Subcutaneous	GTEx
rs425463	MSH3	cis	Thyroid	GTEx

Chromatin state (count:2 , 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
2	chr5:79901600-79902200	Enhancers	GM12878-XiMat	blood

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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

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