Variant report

Variant	rs4845763
Chromosome Location	chr1:152388138-152388139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10888487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205007	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11579061	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923497	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1923500	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1951523	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2146114	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2146115	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2146118	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2203891	0.81[EUR][1000 genomes]
rs4240876	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240878	0.85[EUR][1000 genomes]
rs4240879	0.87[EUR][1000 genomes]
rs4240880	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4240881	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845432	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845434	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs561260	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56890884	0.83[AFR][1000 genomes]
rs57180647	0.86[AFR][1000 genomes]
rs57443269	0.86[AFR][1000 genomes]
rs57945463	0.86[AFR][1000 genomes]
rs59794640	0.83[AFR][1000 genomes]
rs60680249	0.86[AFR][1000 genomes]
rs61323779	0.86[AFR][1000 genomes]
rs6587669	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679896	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs941933	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	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
5	nsv516541	chr1:152376710-152390452	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4845763	LYSMD1	cis	parietal	SCAN
rs4845763	SPRR2E	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152384800-152388200	Weak transcription	Spleen	Spleen
2	chr1:152387000-152390600	Weak transcription	Esophagus	oesophagus

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