Variant report

Variant	rs17578259
Chromosome Location	chr3:25232823-25232824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10510558	0.84[EUR][1000 genomes]
rs10510559	0.84[EUR][1000 genomes]
rs10510560	0.84[EUR][1000 genomes]
rs10510561	0.84[EUR][1000 genomes]
rs13060347	0.85[EUR][1000 genomes]
rs13061437	0.93[EUR][1000 genomes]
rs13068143	0.84[EUR][1000 genomes]
rs13068891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs13074533	0.82[EUR][1000 genomes]
rs13082318	0.82[EUR][1000 genomes]
rs13085280	0.84[EUR][1000 genomes]
rs13087573	0.84[EUR][1000 genomes]
rs13087919	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13088163	0.84[AMR][1000 genomes]
rs13088581	0.87[EUR][1000 genomes]
rs13090740	0.84[EUR][1000 genomes]
rs13092896	0.84[EUR][1000 genomes]
rs13093059	0.84[EUR][1000 genomes]
rs13096074	0.86[EUR][1000 genomes]
rs1561115	0.86[EUR][1000 genomes]
rs1601161	0.84[EUR][1000 genomes]
rs1601162	0.84[EUR][1000 genomes]
rs17015971	0.87[EUR][1000 genomes]
rs17015978	0.84[EUR][1000 genomes]
rs17016060	0.83[EUR][1000 genomes]
rs17016078	0.84[EUR][1000 genomes]
rs17016133	0.81[EUR][1000 genomes]
rs17517792	0.85[EUR][1000 genomes]
rs17517931	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1992059	0.82[EUR][1000 genomes]
rs1992060	0.86[EUR][1000 genomes]
rs34112261	0.90[EUR][1000 genomes]
rs34283888	0.91[EUR][1000 genomes]
rs34370374	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34403304	0.86[EUR][1000 genomes]
rs34537630	0.84[EUR][1000 genomes]
rs34820979	0.81[EUR][1000 genomes]
rs34960742	0.89[EUR][1000 genomes]
rs34985047	0.84[EUR][1000 genomes]
rs35045659	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35069077	0.85[EUR][1000 genomes]
rs35180299	0.81[EUR][1000 genomes]
rs35336027	0.84[EUR][1000 genomes]
rs35383710	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35508620	0.82[EUR][1000 genomes]
rs35646412	0.82[EUR][1000 genomes]
rs35888700	0.84[EUR][1000 genomes]
rs57402663	0.84[EUR][1000 genomes]
rs61228958	0.84[EUR][1000 genomes]
rs66807073	0.84[EUR][1000 genomes]
rs66939282	0.84[EUR][1000 genomes]
rs67093028	0.89[EUR][1000 genomes]
rs67150539	0.84[EUR][1000 genomes]
rs67681308	0.82[EUR][1000 genomes]
rs6779499	0.84[EUR][1000 genomes]
rs67880640	0.86[EUR][1000 genomes]
rs67912541	0.84[EUR][1000 genomes]
rs6792184	0.84[EUR][1000 genomes]
rs68073275	0.84[EUR][1000 genomes]
rs71311526	0.88[EUR][1000 genomes]
rs71622827	0.93[EUR][1000 genomes]
rs73042375	0.81[EUR][1000 genomes]
rs73042380	0.84[EUR][1000 genomes]
rs73044294	0.86[EUR][1000 genomes]
rs73045965	0.86[EUR][1000 genomes]
rs73050342	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7427426	0.84[EUR][1000 genomes]
rs7432016	0.84[EUR][1000 genomes]
rs9830836	0.89[EUR][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	nsv949035	chr3:25194301-26084890	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
2	nsv508213	chr3:25206150-25326196	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17578259	NR1D2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25232200-25233400	Enhancers	Fetal Stomach	stomach
2	chr3:25232800-25233200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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