Variant report

Variant	rs7953233
Chromosome Location	chr12:47223717-47223718
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10881002	0.82[EUR][1000 genomes]
rs10881004	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183620	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs11183625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11183630	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183643	0.83[ASN][1000 genomes]
rs2263486	0.89[ASN][1000 genomes]
rs2263487	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465208	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2465210	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2465211	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2465213	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3989940	0.83[ASN][1000 genomes]
rs4374015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4491335	0.83[EUR][1000 genomes]
rs4495962	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7298017	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7953233	AMIGO2	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47219800-47224000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr12:47219800-47224200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:47219800-47224200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:47219800-47224400	Weak transcription	Right Ventricle	heart
5	chr12:47220000-47224600	Weak transcription	Pancreas	Pancrea
6	chr12:47220200-47224000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:47220200-47224200	Weak transcription	NHEK	skin
8	chr12:47220200-47224400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:47220200-47224400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:47220600-47224200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:47220600-47224800	Weak transcription	HSMM	muscle
12	chr12:47221200-47224000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:47221600-47224200	Enhancers	Liver	Liver
14	chr12:47222200-47224200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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