Variant report

Variant	rs55653648
Chromosome Location	chr5:178114512-178114513
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10516147	0.83[EUR][1000 genomes]
rs12187838	0.85[EUR][1000 genomes]
rs4419608	0.84[EUR][1000 genomes]
rs4626352	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv1023697	chr5:178070594-178126328	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537972	chr5:178070594-178126328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv5155	chr5:178075100-178132799	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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
7	esv1837537	chr5:178103405-178122284	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv1840322	chr5:178103405-178122284	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1843063	chr5:178105326-178117482	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3468608	chr5:178110146-178115244	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
11	esv3468606	chr5:178110871-178114719	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
12	esv3468609	chr5:178110871-178114719	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
13	esv1847742	chr5:178111284-178117482	Flanking Active TSS Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
14	nsv600437	chr5:178111284-178120334	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv1844379	chr5:178111284-178122284	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv600446	chr5:178111743-178120334	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv1834677	chr5:178112220-178118951	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
18	nsv600451	chr5:178112451-178120334	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55653648	ZNF354A	cis	Whole Blood	GTEx
rs55653648	ZNF354A	cis	lung	GTEx
rs55653648	ZNF354A	cis	Thyroid	GTEx
rs55653648	CLK4	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178112000-178115400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr5:178113200-178115200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr5:178113400-178115000	Weak transcription	Monocytes-CD14+_RO01746	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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