Variant report

Variant	rs1561115
Chromosome Location	chr3:25260453-25260454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10510558	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10510559	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10510560	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10510561	0.96[EUR][1000 genomes]
rs13068143	0.94[EUR][1000 genomes]
rs13068891	0.85[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs13074533	0.94[EUR][1000 genomes]
rs13082318	0.94[EUR][1000 genomes]
rs13085280	0.96[EUR][1000 genomes]
rs13087573	0.96[EUR][1000 genomes]
rs13087919	0.86[EUR][1000 genomes]
rs13088581	0.99[EUR][1000 genomes]
rs13090740	0.96[EUR][1000 genomes]
rs13092896	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13093059	0.96[EUR][1000 genomes]
rs13096074	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1436239	0.85[EUR][1000 genomes]
rs1601161	0.96[EUR][1000 genomes]
rs1601162	0.96[EUR][1000 genomes]
rs17015971	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17015978	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17016060	0.95[EUR][1000 genomes]
rs17016078	0.96[EUR][1000 genomes]
rs17016133	0.93[EUR][1000 genomes]
rs17578259	0.86[EUR][1000 genomes]
rs1992059	0.94[EUR][1000 genomes]
rs1992060	0.98[EUR][1000 genomes]
rs34197182	0.83[EUR][1000 genomes]
rs34403304	0.98[EUR][1000 genomes]
rs34537630	0.96[EUR][1000 genomes]
rs34820979	0.93[EUR][1000 genomes]
rs34985047	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35180299	0.93[EUR][1000 genomes]
rs35264689	0.89[EUR][1000 genomes]
rs35336027	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35508620	0.94[EUR][1000 genomes]
rs35646412	0.95[EUR][1000 genomes]
rs35888700	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56062751	0.87[EUR][1000 genomes]
rs57402663	0.96[EUR][1000 genomes]
rs61228958	0.96[EUR][1000 genomes]
rs66807073	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66939282	0.96[EUR][1000 genomes]
rs67150539	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67681308	0.94[EUR][1000 genomes]
rs6779499	0.97[EUR][1000 genomes]
rs67880640	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67912541	0.96[EUR][1000 genomes]
rs6792184	0.97[EUR][1000 genomes]
rs68073275	0.96[EUR][1000 genomes]
rs73042375	0.91[EUR][1000 genomes]
rs73042380	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73044294	0.98[EUR][1000 genomes]
rs73045965	0.98[EUR][1000 genomes]
rs7427426	0.96[EUR][1000 genomes]
rs7432016	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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	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
rs1561115	NR1D2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25259600-25260600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:25260200-25265600	Weak transcription	Fetal Heart	heart

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