Variant report

Variant	rs3858726
Chromosome Location	chr12:41588568-41588569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10748266	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10748267	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10785150	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10785174	0.80[AMR][1000 genomes]
rs10879830	0.82[EUR][1000 genomes]
rs10879831	0.85[EUR][1000 genomes]
rs10879858	0.89[EUR][1000 genomes]
rs1346905	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1367600	0.80[AMR][1000 genomes]
rs1367601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1367602	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405548	0.80[AMR][1000 genomes]
rs1431102	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1431103	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1431104	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1431105	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1431106	0.87[EUR][1000 genomes]
rs1431107	0.86[EUR][1000 genomes]
rs1431108	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1431109	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1431110	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1431114	0.80[AMR][1000 genomes]
rs1431115	0.80[AMR][1000 genomes]
rs1461094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527086	0.86[EUR][1000 genomes]
rs1852461	0.80[AMR][1000 genomes]
rs1864611	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1864612	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1864613	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1870704	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2060053	0.80[AMR][1000 genomes]
rs2060054	0.80[AMR][1000 genomes]
rs2060055	0.80[AMR][1000 genomes]
rs2116133	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2116134	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2116135	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2163415	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2169299	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405768	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2567034	0.83[EUR][1000 genomes]
rs281829	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs281831	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs281832	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs281837	0.92[EUR][1000 genomes]
rs281839	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs281840	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs281841	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs281843	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2897227	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3847980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847981	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911712	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4238081	0.81[EUR][1000 genomes]
rs4767999	0.82[EUR][1000 genomes]
rs6582240	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7296581	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7303285	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7304286	0.80[AMR][1000 genomes]
rs7487688	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs776560	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs776561	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs776562	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs776567	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7954881	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7963760	0.81[EUR][1000 genomes]
rs7980599	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs975602	0.83[AMR][1000 genomes];0.87[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:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41585400-41599000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:41586800-41590600	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:41587800-41589400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:41588400-41589600	Weak transcription	Colon Smooth Muscle	Colon

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