Variant report

Variant	rs11162526
Chromosome Location	chr1:79144319-79144320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10873993	1.00[ASN][1000 genomes]
rs10873994	1.00[ASN][1000 genomes]
rs11162527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11162543	1.00[ASN][1000 genomes]
rs12066013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081949	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628313	1.00[ASN][1000 genomes]
rs17394028	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17394244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1751524	1.00[ASN][1000 genomes]
rs55802282	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs60222720	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673963	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74092102	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526675	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536070	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11162526	MSH4	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79117600-79153000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:79126600-79148000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:79138600-79148200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:79143600-79144600	Enhancers	Dnd41	blood
5	chr1:79143600-79151200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:79143800-79144600	Flanking Active TSS	GM12878-XiMat	blood
7	chr1:79144000-79144400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr1:79144000-79144400	Enhancers	Placenta	Placenta
9	chr1:79144000-79144400	Enhancers	Ovary	ovary
10	chr1:79144000-79144400	Enhancers	HSMM	muscle
11	chr1:79144000-79144600	Enhancers	Esophagus	oesophagus
12	chr1:79144200-79144400	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:79144200-79148000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:79144200-79148000	Weak transcription	Osteobl	bone

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