Variant report

Variant	rs12599770
Chromosome Location	chr16:79783234-79783235
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:79782700..79785427-chr16:79803858..79806131,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260876	Chromatin interaction
ENSG00000261390	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10871377	0.90[ASN][1000 genomes]
rs10871378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11150194	0.90[ASN][1000 genomes]
rs11150195	0.90[ASN][1000 genomes]
rs11150196	0.93[ASN][1000 genomes]
rs11150197	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11150198	0.92[ASN][1000 genomes]
rs11640485	0.90[ASN][1000 genomes]
rs11646174	0.88[ASN][1000 genomes]
rs11648369	0.87[ASN][1000 genomes]
rs11649483	0.88[ASN][1000 genomes]
rs11864576	0.90[ASN][1000 genomes]
rs11864742	0.90[ASN][1000 genomes]
rs12373096	0.90[ASN][1000 genomes]
rs12598937	0.90[ASN][1000 genomes]
rs12716880	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12921991	0.88[ASN][1000 genomes]
rs12935201	0.90[ASN][1000 genomes]
rs3813578	0.90[ASN][1000 genomes]
rs4243178	0.87[ASN][1000 genomes]
rs4243179	0.90[ASN][1000 genomes]
rs4257219	0.86[JPT][hapmap]
rs4296269	0.86[JPT][hapmap]
rs4325577	0.93[ASN][1000 genomes]
rs4327063	0.81[JPT][hapmap]
rs4360949	0.88[ASN][1000 genomes]
rs4387616	0.92[CHB][hapmap]
rs4395087	0.89[ASN][1000 genomes]
rs4411509	0.86[JPT][hapmap]
rs4420544	0.88[ASN][1000 genomes]
rs4426362	0.82[ASN][1000 genomes]
rs4435267	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs4485383	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4547344	0.86[JPT][hapmap]
rs4567730	0.85[CHB][hapmap]
rs4632143	0.89[ASN][1000 genomes]
rs4889017	0.90[ASN][1000 genomes]
rs4889018	0.90[ASN][1000 genomes]
rs4889020	0.90[ASN][1000 genomes]
rs4889021	0.93[ASN][1000 genomes]
rs4889022	0.92[ASN][1000 genomes]
rs6564694	0.90[ASN][1000 genomes]
rs6564701	0.81[JPT][hapmap]
rs6564702	0.81[JPT][hapmap]
rs7186075	0.90[ASN][1000 genomes]
rs7190488	0.90[ASN][1000 genomes]
rs7196084	0.90[ASN][1000 genomes]
rs8045678	0.81[JPT][hapmap]
rs8049118	0.81[ASN][1000 genomes]
rs8049124	0.81[ASN][1000 genomes]
rs8054169	0.86[ASN][1000 genomes]
rs8056945	0.85[ASN][1000 genomes]
rs8060072	0.81[JPT][hapmap]
rs8062324	0.88[JPT][hapmap]
rs9673780	0.88[JPT][hapmap]
rs9673947	0.88[JPT][hapmap]
rs9921624	0.81[JPT][hapmap]
rs9927598	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2755409	chr16:79776699-79816299	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12599770	RP11-345M22.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79772600-79785600	Weak transcription	Fetal Lung	lung
2	chr16:79782000-79783600	Enhancers	Primary T cells from cord blood	blood
3	chr16:79782400-79783400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:79782600-79785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:79782800-79783600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr16:79782800-79784400	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr16:79783200-79784000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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