Variant report

Variant	rs562486
Chromosome Location	chr15:34341268-34341269
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1529951	0.98[ASN][1000 genomes]
rs1968497	0.98[ASN][1000 genomes]
rs499167	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534155	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539584	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554303	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564262	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579975	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587714	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59502570	0.82[ASN][1000 genomes]
rs668922	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8029344	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035849	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9707955	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs562486	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34337600-34341800	Enhancers	Osteobl	bone
2	chr15:34338800-34341800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:34339400-34341400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:34339600-34341800	Enhancers	HMEC	breast
5	chr15:34340000-34341400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:34340000-34341400	Flanking Active TSS	HSMMtube	muscle
7	chr15:34340000-34341800	Flanking Active TSS	NH-A	brain
8	chr15:34340000-34342000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:34340200-34341400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:34340400-34342000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:34340600-34341600	Enhancers	Placenta	Placenta
12	chr15:34340600-34341600	Enhancers	NHLF	lung
13	chr15:34340600-34341800	Enhancers	NHEK	skin
14	chr15:34340800-34341800	Enhancers	Hela-S3	cervix
15	chr15:34340800-34342000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:34341000-34341600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:34341000-34341800	Enhancers	NHDF-Ad	bronchial
18	chr15:34341200-34341600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr15:34341200-34341600	Enhancers	HSMM	muscle
20	chr15:34341200-34341800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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