Variant report

Variant	rs12372457
Chromosome Location	chr12:20567648-20567649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10505865	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10732533	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10732534	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743370	0.89[ASN][1000 genomes]
rs10743372	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743373	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743374	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10770650	0.85[ASN][1000 genomes]
rs10770651	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10770652	0.86[ASN][1000 genomes]
rs10770653	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10770654	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10770655	0.80[EUR][1000 genomes]
rs10770656	0.83[ASN][1000 genomes]
rs10841501	0.89[ASN][1000 genomes]
rs10841509	0.80[ASN][1000 genomes]
rs10841510	0.83[ASN][1000 genomes]
rs10841512	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841513	0.86[ASN][1000 genomes]
rs10841515	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10841516	0.86[ASN][1000 genomes]
rs11045206	0.83[ASN][1000 genomes]
rs11045207	0.83[ASN][1000 genomes]
rs11045211	0.82[ASN][1000 genomes]
rs11045218	0.83[ASN][1000 genomes]
rs11045220	0.83[ASN][1000 genomes]
rs11045221	0.83[ASN][1000 genomes]
rs11045222	0.82[ASN][1000 genomes]
rs11045223	0.85[ASN][1000 genomes]
rs11045224	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11045225	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11045226	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11045227	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11045228	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11045230	0.86[ASN][1000 genomes]
rs12297116	0.85[ASN][1000 genomes]
rs12370745	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12370763	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1348583	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1444628	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444629	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444630	0.95[ASN][1000 genomes]
rs1444634	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444635	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444641	0.94[ASN][1000 genomes]
rs1444643	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444644	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444645	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444646	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1838447	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1838448	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4762955	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5014033	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5014034	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5014035	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5014036	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5014037	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5014038	0.81[EUR][1000 genomes]
rs5014039	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5014040	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60977432	0.83[ASN][1000 genomes]
rs6487083	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487084	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487085	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487086	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7136586	0.85[ASN][1000 genomes]
rs71450706	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7310385	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7314448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954501	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957567	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7967538	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935258	0.86[ASN][1000 genomes]
rs978349	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9805045	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv1042315	chr12:20531641-20629866	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20550400-20568200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:20553200-20571200	Weak transcription	Psoas Muscle	Psoas
3	chr12:20556400-20573200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:20556600-20582400	Weak transcription	Osteobl	bone
5	chr12:20558200-20568800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:20558600-20588000	Weak transcription	HUVEC	blood vessel
7	chr12:20559800-20577800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:20562800-20573400	Weak transcription	Fetal Kidney	kidney
9	chr12:20563400-20568000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:20563400-20568000	Weak transcription	Adipose Nuclei	Adipose
11	chr12:20563400-20568000	Weak transcription	NHDF-Ad	bronchial
12	chr12:20563400-20570400	Weak transcription	Fetal Intestine Large	intestine
13	chr12:20563400-20573000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:20564000-20568400	Weak transcription	Right Atrium	heart
15	chr12:20564800-20573800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:20565200-20570800	Strong transcription	Hela-S3	cervix
17	chr12:20566000-20568000	Weak transcription	Pancreas	Pancrea
18	chr12:20566200-20567800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:20566600-20568000	Weak transcription	Aorta	Aorta
20	chr12:20566600-20569200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:20566600-20570400	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:20566600-20572800	Weak transcription	Left Ventricle	heart
23	chr12:20566800-20572200	Weak transcription	Right Ventricle	heart
24	chr12:20566800-20576200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:20567200-20573200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:20567200-20574400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:20567400-20568800	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:20567600-20567800	Enhancers	Fetal Stomach	stomach
29	chr12:20567600-20568400	Enhancers	Fetal Lung	lung

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