Variant report

Variant	rs672561
Chromosome Location	chr1:78987302-78987303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10489787	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12058120	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12082394	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12094298	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12725125	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12740498	0.97[ASN][1000 genomes]
rs12748050	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs1322931	0.89[YRI][hapmap]
rs1322933	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1322934	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1322935	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28832602	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33994937	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34012602	0.95[ASN][1000 genomes]
rs34077564	0.97[ASN][1000 genomes]
rs34490913	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34528585	0.97[ASN][1000 genomes]
rs34572897	0.97[ASN][1000 genomes]
rs34852041	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35123627	0.97[ASN][1000 genomes]
rs35324676	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35978825	0.97[ASN][1000 genomes]
rs3766346	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766347	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766348	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766351	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4650581	1.00[JPT][hapmap]
rs540757	0.81[ASW][hapmap];0.87[LWK][hapmap]
rs61769118	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700362	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67351117	1.00[ASN][1000 genomes]
rs72673924	0.97[ASN][1000 genomes]
rs72673925	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	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	nsv870807	chr1:78867347-79032598	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78977600-78987600	Weak transcription	NHDF-Ad	bronchial
2	chr1:78977600-78993200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:78977800-78987800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:78986600-78987600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:78986800-78988000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:78986800-78988000	Weak transcription	Osteobl	bone
7	chr1:78987000-78988000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links