Variant report

Variant	rs1473393
Chromosome Location	chr4:160656799-160656800
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10020770	0.89[AMR][1000 genomes]
rs10032251	0.86[AMR][1000 genomes]
rs11100255	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13104739	0.86[AMR][1000 genomes]
rs13150115	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1457815	0.89[AMR][1000 genomes]
rs1473392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902829	0.89[AMR][1000 genomes]
rs1902830	0.89[AMR][1000 genomes]
rs1976456	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2088981	0.98[EUR][1000 genomes]
rs2088982	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2088983	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2348620	0.83[EUR][1000 genomes]
rs28493940	0.84[EUR][1000 genomes]
rs4280694	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61217796	0.83[EUR][1000 genomes]
rs62338507	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6536465	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848125	0.86[AMR][1000 genomes]
rs6848849	0.83[AMR][1000 genomes]
rs7663113	0.80[AMR][1000 genomes]
rs7667063	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690659	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7698008	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs868962	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9991303	0.86[AMR][1000 genomes]
rs9993565	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1015469	chr4:160389277-160841619	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537316	chr4:160389277-160841619	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv595813	chr4:160574450-160665365	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv4574	chr4:160652259-160686024	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1473393	RAPGEF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160656200-160657000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:160656200-160658400	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr4:160656400-160658000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:160656600-160658000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr4:160656600-160658200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr4:160656600-160658200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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