Variant report

Variant	rs2146114
Chromosome Location	chr1:152390621-152390622
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152385310..152387718-chr1:152390033..152392534,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143536	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10888487	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11205007	0.86[AMR][1000 genomes]
rs11579061	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12059943	1.00[YRI][hapmap]
rs16842865	1.00[YRI][hapmap]
rs1923492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1923497	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1923500	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1951523	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2146115	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2146118	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4240876	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4240877	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4240878	0.81[EUR][1000 genomes]
rs4240879	0.83[EUR][1000 genomes]
rs4240880	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4240881	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845432	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845434	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4845763	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]
rs561260	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6587667	1.00[YRI][hapmap]
rs6587669	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6676954	0.89[AFR][1000 genomes]
rs6679896	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554630	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs941933	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2146114	SPRR2E	cis	parietal	SCAN
rs2146114	LYSMD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152390600-152391200	Enhancers	Esophagus	oesophagus

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