Variant report

Variant	rs593445
Chromosome Location	chr18:8422588-8422589
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12957274	0.95[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12968293	0.95[EUR][1000 genomes]
rs16953484	0.81[EUR][1000 genomes]
rs593102	0.94[EUR][1000 genomes]
rs637785	0.95[EUR][1000 genomes]
rs638153	0.95[EUR][1000 genomes]
rs652669	0.95[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs658901	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9956121	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	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv909361	chr18:8364598-8446393	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv458022	chr18:8417484-8471457	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv576429	chr18:8417484-8471457	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs593445	PPP4R1	cis	cerebellum	SCAN
rs593445	ANKRD12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8412600-8423000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:8417000-8423000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:8417400-8423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:8420600-8423000	Weak transcription	HepG2	liver
5	chr18:8422400-8423600	Enhancers	Adipose Nuclei	Adipose
6	chr18:8422400-8426000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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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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