Variant report

Variant	rs2169299
Chromosome Location	chr12:41586051-41586052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10748266	0.86[EUR][1000 genomes]
rs10748267	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10785150	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10879830	0.81[EUR][1000 genomes]
rs10879831	0.84[EUR][1000 genomes]
rs10879858	0.87[EUR][1000 genomes]
rs1346905	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1367601	0.85[EUR][1000 genomes]
rs1367602	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1431102	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1431103	0.86[EUR][1000 genomes]
rs1431104	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1431105	0.86[EUR][1000 genomes]
rs1431106	0.86[EUR][1000 genomes]
rs1431107	0.85[EUR][1000 genomes]
rs1431108	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1431109	0.86[EUR][1000 genomes]
rs1431110	0.87[EUR][1000 genomes]
rs1461094	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527086	0.85[EUR][1000 genomes]
rs1864611	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1864612	0.86[EUR][1000 genomes]
rs1864613	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2116133	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2116134	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2116135	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2163415	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405768	0.85[EUR][1000 genomes]
rs2567034	0.82[EUR][1000 genomes]
rs281829	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs281831	0.89[EUR][1000 genomes]
rs281832	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs281837	0.91[EUR][1000 genomes]
rs281839	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs281840	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs281841	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs281843	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2897227	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3847980	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847981	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858726	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911712	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4767999	0.81[EUR][1000 genomes]
rs6582240	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7296581	0.86[EUR][1000 genomes]
rs7303285	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7487688	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs776560	0.87[EUR][1000 genomes]
rs776561	0.87[EUR][1000 genomes]
rs776562	0.88[EUR][1000 genomes]
rs776567	0.92[EUR][1000 genomes]
rs7954881	0.95[EUR][1000 genomes]
rs7980599	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs975602	0.86[EUR][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	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41585200-41587200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:41585200-41588000	Enhancers	Colon Smooth Muscle	Colon
3	chr12:41585400-41586800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:41585400-41599000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:41586000-41586200	Enhancers	Esophagus	oesophagus

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