Variant report

Variant	rs4680313
Chromosome Location	chr3:156619137-156619138
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	chr3:156533681..156536272-chr3:156616712..156620558,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11914959	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320011	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1574980	0.93[EUR][1000 genomes]
rs2321291	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2321293	0.91[EUR][1000 genomes]
rs2874488	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs344073	0.85[EUR][1000 genomes]
rs344079	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs344080	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs344082	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs344084	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs344087	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs416600	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs453219	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680311	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4680314	0.95[EUR][1000 genomes]
rs6441101	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6762708	0.88[EUR][1000 genomes]
rs6765353	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6780475	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6783162	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7622309	0.88[EUR][1000 genomes]
rs7638330	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs873337	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826073	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862338	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863643	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9870137	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9876148	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9882009	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9883439	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680313	LINC00886	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156611600-156621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:156612000-156621200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:156616600-156621000	Weak transcription	Osteobl	bone
4	chr3:156617000-156620200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:156617800-156621200	Weak transcription	HSMMtube	muscle
6	chr3:156618400-156620200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:156618400-156620400	Weak transcription	HSMM	muscle
8	chr3:156618600-156627800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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