Variant report

Variant	rs12744775
Chromosome Location	chr1:71774506-71774507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009311	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11209756	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11209757	0.92[ASN][1000 genomes]
rs11209761	1.00[ASN][1000 genomes]
rs11209762	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811835	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118599	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12119958	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12131265	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap]
rs12139565	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12140289	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12729268	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12737582	1.00[ASN][1000 genomes]
rs12749022	0.83[AFR][1000 genomes]
rs1367767	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395289	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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	0.91[EUR][1000 genomes];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	0.87[ASN][1000 genomes]
rs2790675	0.87[ASN][1000 genomes]
rs2796187	0.86[ASN][1000 genomes]
rs2796188	0.86[ASN][1000 genomes]
rs2796189	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	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs952337	0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv830159	chr1:71772308-71909860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12744775	PTGER3	cis	Skin Sun Exposed Lower leg	GTEx
rs12744775	LRRC7	cis	parietal	SCAN
rs12744775	PTGER3	cis	uninvolved skin	skin_eQTL
rs12744775	SRSF11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71770600-71781200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:71773400-71774800	Weak transcription	Pancreas	Pancrea
3	chr1:71773600-71774600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:71773600-71777000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:71773600-71777000	Weak transcription	NHDF-Ad	bronchial
6	chr1:71773600-71778000	Weak transcription	HUVEC	blood vessel
7	chr1:71773800-71776800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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