Variant report

Variant	rs12472557
Chromosome Location	chr2:134528080-134528081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1110673	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474261	0.81[ASN][1000 genomes]
rs1348838	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374401	0.86[ASN][1000 genomes]
rs1596918	0.87[ASN][1000 genomes]
rs2321298	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2321301	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3936142	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4056124	0.87[ASN][1000 genomes]
rs4270397	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4343520	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467329	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4505578	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547575	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4549152	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4553871	0.81[ASN][1000 genomes]
rs4558640	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4560170	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4954077	0.82[ASN][1000 genomes]
rs6414015	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6430446	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6430447	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6430452	0.87[ASN][1000 genomes]
rs6430457	0.81[ASN][1000 genomes]
rs6711922	0.82[ASN][1000 genomes]
rs6726492	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6730129	0.81[ASN][1000 genomes]
rs6743076	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745752	0.86[ASN][1000 genomes]
rs6752406	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs744128	0.87[ASN][1000 genomes]
rs749825	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558993	0.80[ASN][1000 genomes]
rs7570764	0.82[ASN][1000 genomes]
rs7571025	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580128	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586665	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595524	0.80[ASN][1000 genomes]
rs7598780	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605721	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9283451	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12472557	LOC440905	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134523600-134532400	Weak transcription	Right Ventricle	heart
2	chr2:134524000-134529400	Weak transcription	Adipose Nuclei	Adipose
3	chr2:134524000-134530800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:134524000-134531200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:134524200-134531600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:134524400-134531000	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:134524600-134531200	Weak transcription	Brain Substantia Nigra	brain
8	chr2:134524600-134531600	Weak transcription	Fetal Stomach	stomach
9	chr2:134524600-134537200	Weak transcription	NHLF	lung
10	chr2:134524800-134531400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:134524800-134531600	Weak transcription	Left Ventricle	heart
12	chr2:134524800-134531800	Weak transcription	Ovary	ovary
13	chr2:134526200-134531200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:134526400-134531200	Weak transcription	Fetal Heart	heart
15	chr2:134526400-134531400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:134526400-134531600	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:134526600-134531400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:134527000-134531000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:134527000-134531000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:134527000-134532000	Weak transcription	Esophagus	oesophagus
21	chr2:134527000-134532000	Weak transcription	Right Atrium	heart
22	chr2:134527600-134530800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:134528000-134530600	Weak transcription	Fetal Lung	lung

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