Variant report

Variant	rs7489188
Chromosome Location	chr12:20680357-20680358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11613220	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12832108	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4762764	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4762968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4762973	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6487099	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134968	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7303852	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7484304	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7487227	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7953905	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7977362	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20673800-20680800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:20673800-20694200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:20673800-20704200	Weak transcription	Fetal Intestine Large	intestine
4	chr12:20674000-20680600	Weak transcription	Fetal Lung	lung
5	chr12:20674000-20681000	Weak transcription	Ovary	ovary
6	chr12:20675000-20680400	Weak transcription	Fetal Stomach	stomach
7	chr12:20675000-20680400	Weak transcription	Left Ventricle	heart
8	chr12:20675600-20680400	Enhancers	Osteobl	bone
9	chr12:20677200-20680600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:20677200-20681200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:20677400-20680400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:20677400-20681000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:20677400-20681400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:20678000-20681000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:20678400-20680400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:20679400-20681600	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:20679800-20680400	Active TSS	Colon Smooth Muscle	Colon
18	chr12:20679800-20680800	Active TSS	A549	lung
19	chr12:20679800-20681600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:20680000-20681200	Active TSS	Aorta	Aorta
21	chr12:20680000-20681600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:20680000-20681600	Enhancers	NHDF-Ad	bronchial
23	chr12:20680200-20680400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:20680200-20680400	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr12:20680200-20680400	Active TSS	Brain Substantia Nigra	brain
26	chr12:20680200-20680600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:20680200-20680600	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr12:20680200-20680600	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr12:20680200-20680800	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr12:20680200-20680800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr12:20680200-20681000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr12:20680200-20681000	Active TSS	Stomach Smooth Muscle	stomach
33	chr12:20680200-20681400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr12:20680200-20681400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:20680200-20681600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:20680200-20681600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr12:20680200-20681600	Enhancers	Brain Germinal Matrix	brain
38	chr12:20680200-20681800	Strong transcription	Hela-S3	cervix

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