Variant report

Variant	rs12566320
Chromosome Location	chr1:57592675-57592676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11206975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11206981	1.00[CEU][hapmap]
rs12032549	1.00[CEU][hapmap]
rs12090414	1.00[JPT][hapmap]
rs12406184	0.87[EUR][1000 genomes]
rs12408256	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562392	1.00[CEU][hapmap]
rs12562394	1.00[CEU][hapmap]
rs12562609	1.00[CEU][hapmap]
rs12562930	1.00[CEU][hapmap]
rs12563280	1.00[CEU][hapmap]
rs12564278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564961	1.00[CEU][hapmap]
rs12566131	1.00[CEU][hapmap]
rs12567335	1.00[CEU][hapmap]
rs12567531	1.00[CEU][hapmap]
rs12567904	1.00[CEU][hapmap]
rs12568148	1.00[CEU][hapmap]
rs12568862	1.00[CEU][hapmap]
rs17115023	1.00[CEU][hapmap]
rs17115030	1.00[CEU][hapmap]
rs17115105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115108	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115222	1.00[CEU][hapmap]
rs17115397	1.00[CEU][hapmap]
rs17115580	1.00[CEU][hapmap]
rs17115587	1.00[CEU][hapmap]
rs17420013	1.00[CEU][hapmap]
rs17420216	1.00[CEU][hapmap]
rs17421219	1.00[CEU][hapmap]
rs17421839	1.00[CEU][hapmap]
rs17422039	1.00[CEU][hapmap]
rs17455073	1.00[CEU][hapmap]
rs17455469	1.00[CEU][hapmap]
rs17455616	1.00[CEU][hapmap]
rs17455728	1.00[CEU][hapmap]
rs17455840	1.00[CEU][hapmap]
rs502701	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs519401	0.88[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs553508	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs556204	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs561258	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs61765323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61765326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61765327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61765328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697173	1.00[CEU][hapmap]
rs728719	1.00[CEU][hapmap]

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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12566320	PEG3	trans	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57577200-57595600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57583600-57593000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:57588200-57596800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:57589400-57608600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:57589800-57592800	Enhancers	NHEK	skin
7	chr1:57590600-57601400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:57590800-57597000	Weak transcription	NHDF-Ad	bronchial
9	chr1:57591000-57595400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:57591200-57597000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:57592400-57592800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:57592400-57593400	Enhancers	Fetal Heart	heart
13	chr1:57592600-57596600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:57592600-57596800	Weak transcription	HMEC	breast
15	chr1:57592600-57597000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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