Variant report

Variant	rs12423043
Chromosome Location	chr12:83082111-83082112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10862497	0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11115342	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11115348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11115353	0.88[EUR][1000 genomes]
rs11115355	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11609532	0.92[EUR][1000 genomes]
rs11610988	0.80[EUR][1000 genomes]
rs11613168	0.80[EUR][1000 genomes]
rs11614435	0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs11615763	0.80[EUR][1000 genomes]
rs11615765	0.80[EUR][1000 genomes]
rs12305736	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12307168	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12422405	0.82[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426166	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12579483	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs13377925	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17009812	0.84[EUR][1000 genomes]
rs17009851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009854	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17009856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009882	0.82[EUR][1000 genomes]
rs17009885	0.82[EUR][1000 genomes]
rs17009891	0.80[EUR][1000 genomes]
rs17009893	0.80[EUR][1000 genomes]
rs17009899	0.80[EUR][1000 genomes]
rs1922576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1922579	0.91[EUR][1000 genomes]
rs4620789	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4882428	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55657485	0.92[EUR][1000 genomes]
rs56298822	0.95[EUR][1000 genomes]
rs56396658	0.92[EUR][1000 genomes]
rs61485473	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539683	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7134747	0.84[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134766	0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135486	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72615654	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294890	0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7303469	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7313778	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73354481	0.84[EUR][1000 genomes]
rs74106267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv899349	chr12:82931646-83114286	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3348300	chr12:83079532-83086951	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83079400-83082200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:83079400-83082400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:83079400-83084200	Active TSS	Fetal Intestine Large	intestine
4	chr12:83079600-83082200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:83079600-83082200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr12:83079600-83082200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:83079600-83082200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:83079600-83082200	Active TSS	Muscle Satellite Cultured Cells	--
9	chr12:83079600-83082200	Active TSS	Esophagus	oesophagus
10	chr12:83079600-83082200	Active TSS	Pancreas	Pancrea
11	chr12:83079600-83082200	Active TSS	Stomach Mucosa	stomach
12	chr12:83079600-83082200	Active TSS	HSMM	muscle
13	chr12:83079600-83082400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:83079600-83082400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:83079600-83082400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:83079600-83082400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:83079600-83082400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr12:83079600-83082400	Active TSS	Right Ventricle	heart
19	chr12:83079600-83082600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:83079600-83082600	Active TSS	Left Ventricle	heart
21	chr12:83079600-83082800	Active TSS	Colonic Mucosa	Colon
22	chr12:83079600-83082800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:83079600-83082800	Active TSS	Right Atrium	heart
24	chr12:83079600-83082800	Active TSS	NHDF-Ad	bronchial
25	chr12:83079600-83083200	Active TSS	Psoas Muscle	Psoas
26	chr12:83079600-83083600	Active TSS	Stomach Smooth Muscle	stomach
27	chr12:83079600-83083800	Active TSS	Brain Substantia Nigra	brain
28	chr12:83079600-83083800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:83079600-83083800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr12:83079600-83084000	Active TSS	Brain Angular Gyrus	brain
31	chr12:83079600-83084000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:83079600-83084000	Active TSS	Colon Smooth Muscle	Colon
33	chr12:83079600-83084200	Active TSS	Brain Anterior Caudate	brain
34	chr12:83079600-83084200	Active TSS	Brain Cingulate Gyrus	brain
35	chr12:83079600-83084200	Active TSS	Rectal Smooth Muscle	rectum
36	chr12:83079600-83084400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr12:83079600-83084400	Active TSS	Fetal Stomach	stomach
38	chr12:83079600-83084400	Active TSS	GM12878-XiMat	blood
39	chr12:83079600-83084600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:83079600-83084600	Active TSS	Brain Hippocampus Middle	brain
41	chr12:83079800-83082200	Active TSS	Gastric	stomach
42	chr12:83079800-83082200	Active TSS	Lung	lung
43	chr12:83079800-83082200	Active TSS	Ovary	ovary
44	chr12:83079800-83082200	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr12:83079800-83082400	Active TSS	Fetal Heart	heart
46	chr12:83079800-83082600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:83079800-83082800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:83079800-83082800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr12:83080000-83082200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:83080000-83082200	Active TSS	Cortex derived primary cultured neurospheres	brain

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