Variant report

Variant	rs1483480
Chromosome Location	chr3:88857169-88857170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11128061	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13321295	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1483479	0.91[EUR][1000 genomes]
rs17026511	0.82[AMR][1000 genomes]
rs4241402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241403	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301012	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4377496	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4558761	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855790	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855806	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4855811	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4855816	0.80[EUR][1000 genomes]
rs6551368	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6551371	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6551372	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6773197	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792929	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6805311	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7434092	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7615019	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621168	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625470	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7630500	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7643228	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9284815	0.80[AMR][1000 genomes]
rs9827227	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830958	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9851828	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9869106	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9870254	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][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	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv877157	chr3:88690163-88974863	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1483480	EPHA3	cis	parietal	SCAN
rs1483480	C3orf38	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88855800-88858000	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:88855800-88859600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:88856000-88857200	Enhancers	Fetal Intestine Small	intestine
4	chr3:88856000-88857400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:88856000-88858400	Enhancers	Fetal Intestine Large	intestine
6	chr3:88856000-88859400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:88856400-88857400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:88856400-88857400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:88856400-88857400	Enhancers	NHDF-Ad	bronchial
10	chr3:88856600-88857200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr3:88856600-88857400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:88856600-88857400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:88856600-88857400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:88856600-88857400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:88856600-88857400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:88856600-88857600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:88856600-88858200	Enhancers	HMEC	breast
18	chr3:88856800-88857200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:88856800-88857200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:88856800-88857200	Enhancers	Fetal Heart	heart
21	chr3:88856800-88857200	Flanking Active TSS	NH-A	brain
22	chr3:88856800-88857200	Flanking Active TSS	NHEK	skin
23	chr3:88856800-88857200	Enhancers	Osteobl	bone
24	chr3:88856800-88857400	Enhancers	Hela-S3	cervix
25	chr3:88857000-88857200	Enhancers	Fetal Lung	lung

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