Variant report

Variant	rs1558982
Chromosome Location	chr12:46088738-46088739
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11183170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183184	0.88[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs11183201	1.00[YRI][hapmap]
rs12314770	0.82[GIH][hapmap];0.88[YRI][hapmap]
rs12582799	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468993	0.82[GIH][hapmap]
rs1558983	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863127	0.80[CHD][hapmap];1.00[YRI][hapmap]
rs2193749	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs2216470	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2216471	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247930	1.00[YRI][hapmap]
rs35115	0.82[GIH][hapmap];1.00[YRI][hapmap]
rs35117	1.00[YRI][hapmap]
rs35121	1.00[YRI][hapmap]
rs35125	1.00[YRI][hapmap]
rs4768657	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582574	1.00[YRI][hapmap]
rs7138997	0.82[GIH][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs7958600	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979218	0.85[YRI][hapmap]
rs7979398	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978689	0.92[EUR][1000 genomes];0.94[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	nsv899052	chr12:46068394-46175469	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	esv32607	chr12:46087430-46097227	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1558982	SLC38A1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46083800-46090400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:46083800-46090800	Weak transcription	Right Ventricle	heart
3	chr12:46088000-46089800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr12:46088400-46097400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:46088600-46089400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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