Variant report

Variant	rs2830538
Chromosome Location	chr21:28172706-28172707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs229037	0.81[ASN][1000 genomes]
rs229039	0.81[ASN][1000 genomes]
rs2830542	0.85[ASN][1000 genomes]
rs3017433	0.87[ASN][1000 genomes]
rs419895	0.87[ASN][1000 genomes]
rs458819	0.81[AMR][1000 genomes]
rs461995	0.81[AMR][1000 genomes]
rs464293	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2830538	VANGL1	trans	cerebellum	SCAN
rs2830538	ATP5J	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28168400-28174600	Enhancers	Hela-S3	cervix
2	chr21:28168400-28176400	Weak transcription	Left Ventricle	heart
3	chr21:28168800-28173600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr21:28168800-28174000	Weak transcription	HSMM	muscle
5	chr21:28169400-28173600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr21:28169600-28173200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr21:28170800-28181000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr21:28171400-28174200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr21:28171600-28173000	Enhancers	Rectal Smooth Muscle	rectum
10	chr21:28171600-28173200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr21:28171600-28173400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr21:28171600-28173600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr21:28171600-28173800	Enhancers	Fetal Muscle Leg	muscle
14	chr21:28171800-28173200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr21:28171800-28173200	Weak transcription	Brain Anterior Caudate	brain
16	chr21:28171800-28173400	Enhancers	Colon Smooth Muscle	Colon
17	chr21:28171800-28173400	Enhancers	NHLF	lung
18	chr21:28171800-28173800	Enhancers	Fetal Stomach	stomach
19	chr21:28171800-28174400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr21:28171800-28174400	Enhancers	Fetal Lung	lung
21	chr21:28172000-28172800	Weak transcription	Brain Substantia Nigra	brain
22	chr21:28172000-28173400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr21:28172000-28173800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr21:28172200-28172800	Enhancers	Fetal Heart	heart
25	chr21:28172200-28173200	Enhancers	Osteobl	bone
26	chr21:28172400-28172800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr21:28172400-28172800	Enhancers	Lung	lung
28	chr21:28172400-28173000	Enhancers	Stomach Smooth Muscle	stomach
29	chr21:28172400-28173000	Enhancers	Spleen	Spleen
30	chr21:28172400-28173200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr21:28172400-28173200	Enhancers	NHDF-Ad	bronchial
32	chr21:28172400-28173400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr21:28172400-28173400	Enhancers	Adipose Nuclei	Adipose
34	chr21:28172400-28174000	Enhancers	HSMMtube	muscle
35	chr21:28172400-28174800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr21:28172400-28175000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr21:28172600-28172800	Enhancers	Placenta	Placenta
38	chr21:28172600-28172800	Flanking Active TSS	Ovary	ovary
39	chr21:28172600-28173200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr21:28172600-28173800	Enhancers	Brain Hippocampus Middle	brain

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