Variant report

Variant	rs12466112
Chromosome Location	chr2:72438759-72438760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1000523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1003672	0.92[ASN][1000 genomes]
rs10175915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178847	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181899	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193543	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10204415	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs10205108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10209861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10221767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10865390	0.92[ASN][1000 genomes]
rs11126362	0.85[ASN][1000 genomes]
rs11126363	0.92[ASN][1000 genomes]
rs1123199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1159763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1159766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11681809	0.92[ASN][1000 genomes]
rs12463825	0.89[EUR][1000 genomes]
rs12466026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382986	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13387630	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391463	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13392314	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13404369	0.92[ASN][1000 genomes]
rs13409641	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13410366	1.00[YRI][hapmap]
rs13416674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13417114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13418637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13423761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13430254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194235	1.00[CHB][hapmap]
rs194237	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs194238	0.92[ASN][1000 genomes]
rs194241	0.92[ASN][1000 genomes]
rs194242	0.85[ASN][1000 genomes]
rs194243	0.85[ASN][1000 genomes]
rs2041563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2041564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2080044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109960	0.87[CEU][hapmap]
rs2109963	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2159823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28278	0.85[ASN][1000 genomes]
rs41386	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs41387	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41388	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41389	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41390	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41391	0.85[ASN][1000 genomes]
rs41392	1.00[CHB][hapmap]
rs41393	0.85[ASN][1000 genomes]
rs41394	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41396	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41398	0.85[ASN][1000 genomes]
rs41399	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs41400	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41401	1.00[CHB][hapmap]
rs41402	1.00[CHB][hapmap]
rs41403	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41405	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41406	1.00[CHB][hapmap]
rs41407	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs41408	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs41409	0.80[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs41415	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs41416	0.87[CEU][hapmap];0.85[ASN][1000 genomes]
rs41417	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs41420	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4852285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4852859	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852860	0.92[ASN][1000 genomes]
rs4852861	0.85[ASN][1000 genomes]
rs4852862	0.92[ASN][1000 genomes]
rs55764675	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55877105	0.85[ASN][1000 genomes]
rs55970539	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56045434	0.81[EUR][1000 genomes]
rs56143801	0.81[EUR][1000 genomes]
rs56299443	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147579	0.85[ASN][1000 genomes]
rs62147589	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147626	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147629	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147636	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149273	0.88[EUR][1000 genomes]
rs6546752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6546753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6546755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6719255	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6751276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6760895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs719117	0.88[EUR][1000 genomes]
rs7565922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs768042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs768043	0.85[ASN][1000 genomes]
rs9309463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12466112	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72432800-72441600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:72432800-72456600	Weak transcription	Psoas Muscle	Psoas
3	chr2:72433000-72441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:72433000-72460600	Weak transcription	Pancreas	Pancrea
5	chr2:72433200-72440200	Weak transcription	Left Ventricle	heart
6	chr2:72433200-72442200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:72433200-72450000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:72433200-72450000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:72433200-72466000	Weak transcription	Right Ventricle	heart
10	chr2:72433200-72468600	Weak transcription	Right Atrium	heart
11	chr2:72433400-72450200	Weak transcription	Brain Anterior Caudate	brain
12	chr2:72433600-72439000	Weak transcription	Small Intestine	intestine
13	chr2:72433600-72442000	Weak transcription	Fetal Stomach	stomach
14	chr2:72436600-72439000	Enhancers	A549	lung
15	chr2:72437400-72439400	Enhancers	NHEK	skin
16	chr2:72437400-72439800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:72437600-72438800	Enhancers	Gastric	stomach
18	chr2:72437600-72438800	Enhancers	NH-A	brain
19	chr2:72437600-72439000	Enhancers	Stomach Mucosa	stomach
20	chr2:72437600-72439400	Enhancers	Fetal Intestine Large	intestine
21	chr2:72437600-72439400	Enhancers	Fetal Intestine Small	intestine
22	chr2:72437600-72439800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:72437800-72439600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:72437800-72440200	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:72437800-72440400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:72437800-72440600	Enhancers	Osteobl	bone
27	chr2:72438000-72439000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:72438000-72440200	Weak transcription	Colonic Mucosa	Colon
29	chr2:72438200-72442200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:72438200-72446400	Weak transcription	Fetal Heart	heart
31	chr2:72438400-72439200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:72438400-72440200	Weak transcription	Esophagus	oesophagus
33	chr2:72438400-72449800	Weak transcription	HMEC	breast
34	chr2:72438600-72438800	Flanking Active TSS	NHDF-Ad	bronchial
35	chr2:72438600-72439200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:72438600-72439600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:72438600-72440600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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