Variant report

Variant	rs2874488
Chromosome Location	chr3:156585816-156585817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156391139..156393607-chr3:156585246..156587424,3	MCF-7	breast:
2	chr3:156582444..156584129-chr3:156585763..156587355,2	K562	blood:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10212230	0.84[JPT][hapmap]
rs10936040	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs10936043	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs11914959	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12634915	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs12638253	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs13070271	0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13088978	0.84[JPT][hapmap]
rs1319418	0.89[CEU][hapmap];0.90[TSI][hapmap]
rs1320011	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1384538	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs1574980	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17382070	0.81[ASN][1000 genomes]
rs1995425	0.84[JPT][hapmap]
rs2054880	0.83[JPT][hapmap]
rs2060015	0.82[ASN][1000 genomes]
rs2321290	0.81[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2321291	0.94[CEU][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2321292	0.84[JPT][hapmap]
rs2321293	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2321455	0.84[JPT][hapmap]
rs2874494	0.83[JPT][hapmap]
rs2874495	0.84[JPT][hapmap]
rs343994	0.84[JPT][hapmap]
rs344073	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs344079	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs344080	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs344082	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs344084	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs344087	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34667021	0.84[ASN][1000 genomes]
rs3910072	0.81[ASN][1000 genomes]
rs416600	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4234316	0.95[CEU][hapmap]
rs4315647	1.00[CEU][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs4458324	0.82[AMR][1000 genomes]
rs453219	1.00[CEU][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680311	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680312	0.84[JPT][hapmap]
rs4680313	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4680314	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680317	0.84[JPT][hapmap]
rs6441101	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762708	0.94[CEU][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6765353	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780427	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs6780475	0.85[EUR][1000 genomes]
rs6783162	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6784421	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6803064	0.84[JPT][hapmap]
rs7615304	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs7622309	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7637701	0.84[JPT][hapmap]
rs7638330	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638625	0.81[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs873337	0.94[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs9814813	0.84[CHD][hapmap]
rs9826073	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9837038	0.81[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9844054	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs9847187	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9862338	0.86[EUR][1000 genomes]
rs9863643	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9865905	0.84[JPT][hapmap]
rs9867621	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9870137	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9871817	0.83[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9876010	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs9876148	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs987724	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs9878585	0.84[JPT][hapmap]
rs9882009	0.85[EUR][1000 genomes]
rs9883439	0.94[CEU][hapmap];0.90[EUR][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	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2874488	LINC00886	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156585600-156586400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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