Variant report

Variant	rs12498074
Chromosome Location	chr3:48388253-48388254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48341909..48344364-chr3:48387381..48390289,2	MCF-7	breast:
2	chr3:48387745..48390068-chr3:48395716..48398672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172113	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11130165	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130166	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11706939	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12185901	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486935	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486944	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13069884	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13082217	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13082269	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13087050	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13094496	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1471217	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17593974	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017858	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017859	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34008503	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35460860	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62263035	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62263037	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62263038	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779517	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6804828	0.93[EUR][1000 genomes]
rs71323399	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs12498074	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs12498074	CDC25A	cis	Thyroid	GTEx
rs12498074	ZNF589	cis	Nerve Tibial	GTEx
rs12498074	MRPS18AP1	cis	Artery Tibial	GTEx
rs12498074	ZNF589	cis	Esophagus Muscularis	GTEx
rs12498074	CDC25A	cis	Adipose Subcutaneous	GTEx
rs12498074	MRPS18AP1	cis	Artery Aorta	GTEx
rs12498074	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs12498074	ZNF589	cis	Artery Tibial	GTEx
rs12498074	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs12498074	ZNF589	cis	Esophagus Mucosa	GTEx
rs12498074	MRPS18AP1	cis	Thyroid	GTEx
rs12498074	CDC25A	cis	Muscle Skeletal	GTEx
rs12498074	NME6	cis	Nerve Tibial	GTEx
rs12498074	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12498074	ZNF589	cis	Artery Aorta	GTEx
rs12498074	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs12498074	MRPS18AP1	cis	lung	GTEx
rs12498074	ZNF589	cis	Thyroid	GTEx
rs12498074	NME6	cis	Esophagus Muscularis	GTEx
rs12498074	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48387800-48388400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:48387800-48388800	Weak transcription	NHEK	skin
3	chr3:48387800-48390000	Enhancers	Placenta	Placenta
4	chr3:48387800-48391600	Weak transcription	HSMMtube	muscle
5	chr3:48388000-48389400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:48388000-48389800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:48388200-48389000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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