Variant report

Variant	rs11209761
Chromosome Location	chr1:71764175-71764176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009311	0.84[ASN][1000 genomes]
rs11209756	0.87[ASN][1000 genomes]
rs11209757	0.92[ASN][1000 genomes]
rs11209762	1.00[ASN][1000 genomes]
rs11811835	1.00[ASN][1000 genomes]
rs12118599	0.84[ASN][1000 genomes]
rs12119958	0.87[ASN][1000 genomes]
rs12131265	0.82[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs12139565	0.82[ASN][1000 genomes]
rs12140289	0.91[ASN][1000 genomes]
rs12729268	0.84[ASN][1000 genomes]
rs12737582	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744775	1.00[ASN][1000 genomes]
rs1367767	1.00[ASN][1000 genomes]
rs1395289	1.00[ASN][1000 genomes]
rs1418449	0.82[ASN][1000 genomes]
rs1546809	0.87[ASN][1000 genomes]
rs1573061	0.84[ASN][1000 genomes]
rs1954285	0.84[ASN][1000 genomes]
rs2066371	0.84[ASN][1000 genomes]
rs2066373	0.87[ASN][1000 genomes]
rs2639329	0.84[ASN][1000 genomes]
rs2639330	0.87[ASN][1000 genomes]
rs2639331	0.86[ASN][1000 genomes]
rs2639335	0.84[ASN][1000 genomes]
rs2639338	0.84[ASN][1000 genomes]
rs2694954	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2790675	0.87[ASN][1000 genomes]
rs2796187	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2796188	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2796189	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2796190	0.86[ASN][1000 genomes]
rs2796192	0.87[ASN][1000 genomes]
rs2796199	0.88[JPT][hapmap]
rs2796201	0.84[ASN][1000 genomes]
rs2796202	0.84[ASN][1000 genomes]
rs2796203	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4397614	0.84[ASN][1000 genomes]
rs4425938	0.84[ASN][1000 genomes]
rs7525499	0.97[ASN][1000 genomes]
rs952337	0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949599	chr1:71655652-72327802	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1005726	chr1:71701840-71953242	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1848377	chr1:71718838-71964514	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv531880	chr1:71724941-71964501	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11209761	LRRC7	cis	parietal	SCAN
rs11209761	PTGER3	cis	uninvolved skin	skin_eQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71762400-71764400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:71762800-71764200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:71763200-71764200	Weak transcription	HMEC	breast
4	chr1:71763800-71764800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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