Variant report

Variant	rs12046339
Chromosome Location	chr1:71245703-71245704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10443262	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1108801	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209697	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12022025	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12033260	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039590	0.82[CHD][hapmap]
rs12729410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1327451	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1327453	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1327460	0.92[CHB][hapmap];0.95[JPT][hapmap]
rs1343786	0.83[ASN][1000 genomes]
rs1409985	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1889599	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2225025	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2257598	0.84[EUR][1000 genomes]
rs2421783	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421790	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34289107	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34384777	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650085	1.00[ASN][1000 genomes]
rs7530345	0.92[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs7533733	0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs871577	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3452325	chr1:71243992-71249701	Active TSS Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
2	esv3452326	chr1:71244085-71249601	Flanking Active TSS Enhancers Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
3	esv3452327	chr1:71244085-71249601	Enhancers Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	inside rSNPs	diseases
4	esv18463	chr1:71244106-71249573	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
5	nsv546457	chr1:71245142-71246574	Enhancers Weak transcription Active TSS Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
6	nsv546458	chr1:71245142-71246843	Weak transcription Enhancers Flanking Active TSS Active TSS	lncRNA	n/a	inside rSNPs	diseases
7	nsv546459	chr1:71245142-71247531	Flanking Active TSS Enhancers Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
8	nsv546460	chr1:71245142-71248283	Flanking Active TSS Enhancers Active TSS Weak transcription	lncRNA	n/a	inside rSNPs	diseases
9	nsv546461	chr1:71245142-71249139	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
10	nsv546462	chr1:71245142-71249485	Enhancers Weak transcription Active TSS Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
11	nsv546463	chr1:71245423-71246843	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
12	nsv546464	chr1:71245423-71247822	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
13	nsv546465	chr1:71245423-71249139	Enhancers Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	inside rSNPs	diseases
14	nsv546466	chr1:71245423-71249485	Flanking Active TSS Enhancers Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
15	nsv546467	chr1:71245703-71249485	Enhancers Flanking Active TSS Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12046339	PTGER3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71243000-71247000	Enhancers	NHDF-Ad	bronchial
2	chr1:71244800-71245800	Enhancers	HSMM	muscle
3	chr1:71245200-71246200	Weak transcription	Osteobl	bone
4	chr1:71245400-71246200	Enhancers	NHLF	lung
5	chr1:71245600-71245800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:71245600-71245800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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