Variant report

Variant	rs1017559
Chromosome Location	chr4:85379704-85379705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11725830	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11726182	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12642415	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12642612	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12644117	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12650684	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13125585	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13142585	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1444953	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1444956	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444957	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1444975	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1444978	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1822836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867546	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1867547	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2028765	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28399961	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61714578	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs752399	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs752401	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752402	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs752403	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs763540	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654114	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658460	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7660161	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7684261	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7690203	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs977463	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs988422	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs988423	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	nsv829997	chr4:85244076-85409405	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv829998	chr4:85299693-85473450	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1017559	SPP1	cis	cerebellum	SCAN
rs1017559	C4orf22	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85377800-85387400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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