Variant report

Variant	rs55912234
Chromosome Location	chr5:178168172-178168173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10043035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11249566	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11747232	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11747390	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11750409	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11750784	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13167549	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173130	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13186580	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34601045	0.81[EUR][1000 genomes]
rs34645905	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34651317	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34981103	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34981407	0.81[EUR][1000 genomes]
rs35579651	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35850587	0.81[EUR][1000 genomes]
rs55818572	0.81[AMR][1000 genomes]
rs56027952	0.81[AMR][1000 genomes]
rs56070635	0.81[AMR][1000 genomes]
rs62392854	0.86[EUR][1000 genomes]
rs66947564	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71611460	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55912234	ZNF354A	cis	Artery Tibial	GTEx
rs55912234	ZNF354A	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178165600-178170400	Enhancers	Adipose Nuclei	Adipose
2	chr5:178166600-178168200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:178166600-178169000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:178166600-178224000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:178166800-178168400	Enhancers	Placenta	Placenta
6	chr5:178166800-178169200	Enhancers	Placenta Amnion	Placenta Amnion

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