Variant report

Variant	rs2146115
Chromosome Location	chr1:152443495-152443496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10888487	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11205007	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11579061	0.81[AMR][1000 genomes]
rs1923492	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1923497	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923500	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1951523	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2146114	0.94[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2146118	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2203891	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240876	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4240877	0.94[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4240878	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240879	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240880	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4240881	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476589	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845432	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845434	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4845763	0.94[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs561260	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587669	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6679896	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs941933	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2146115	LYSMD1	cis	parietal	SCAN
rs2146115	SPRR2E	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152443400-152443600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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