Variant report

Variant	rs873337
Chromosome Location	chr3:156634710-156634711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156623940..156626208-chr3:156631962..156634745,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11914959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070271	0.81[TSI][hapmap]
rs1319418	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap]
rs1320011	0.94[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs1574980	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2321291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2321293	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs237250	0.81[JPT][hapmap]
rs2874488	0.94[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs344073	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs344079	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs344080	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs344082	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs344084	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs344087	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs416600	0.86[EUR][1000 genomes]
rs4234316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4315647	0.94[CEU][hapmap];0.93[TSI][hapmap]
rs453219	0.94[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs4680311	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs4680313	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680314	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441101	0.90[EUR][1000 genomes]
rs6762708	0.88[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6765353	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6780475	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6783162	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616633	0.80[MEX][hapmap]
rs7622309	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7638330	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs9826073	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862338	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863643	0.90[EUR][1000 genomes]
rs9870137	0.94[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs9876148	0.94[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs9882009	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9883439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv592120	chr3:156626091-156691604	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs873337	LINC00886	cis	Adipose Subcutaneous	GTEx
rs873337	LEKR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156628600-156636600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:156628600-156636600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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