Variant report

Variant	rs12140289
Chromosome Location	chr1:71796914-71796915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1009311	0.84[EUR][1000 genomes]
rs11209756	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11209757	0.85[ASN][1000 genomes]
rs11209761	0.91[ASN][1000 genomes]
rs11209762	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11811835	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12118599	0.83[EUR][1000 genomes]
rs12119958	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12131265	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs12729268	0.80[EUR][1000 genomes]
rs12737582	0.91[ASN][1000 genomes]
rs12744775	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12749022	0.85[AFR][1000 genomes]
rs1367767	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1395289	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1546809	0.83[ASN][1000 genomes]
rs2066373	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2639330	0.83[ASN][1000 genomes]
rs2639331	0.81[ASN][1000 genomes]
rs2694954	0.83[ASN][1000 genomes]
rs2790675	0.83[ASN][1000 genomes]
rs2796187	0.81[ASN][1000 genomes]
rs2796188	0.81[ASN][1000 genomes]
rs2796189	0.81[ASN][1000 genomes]
rs2796190	0.81[ASN][1000 genomes]
rs2796192	0.83[ASN][1000 genomes]
rs2796199	0.88[JPT][hapmap]
rs2796203	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7525499	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs952337	0.82[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv916508	chr1:71777392-72046388	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv546474	chr1:71793221-72040354	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12140289	PTGER3	cis	uninvolved skin	skin_eQTL
rs12140289	PTGER3	cis	Skin Sun Exposed Lower leg	GTEx
rs12140289	LRRC7	cis	parietal	SCAN
rs12140289	SRSF11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71796400-71797200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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