Variant report

Variant	rs4573843
Chromosome Location	chr14:35391769-35391770
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	chr14:35343366..35345021-chr14:35390010..35392504,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198604	Chromatin interaction
ENSG00000258738	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11156867	0.95[ASN][1000 genomes]
rs11156868	0.95[ASN][1000 genomes]
rs11850317	0.95[ASN][1000 genomes]
rs12050171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050267	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12050404	0.80[ASN][1000 genomes]
rs12050447	0.80[ASN][1000 genomes]
rs12161905	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12588755	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12878219	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12883971	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12886251	0.96[ASN][1000 genomes]
rs12887885	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12888272	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12890056	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12890307	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12891343	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12892056	0.87[ASN][1000 genomes]
rs12893021	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12894365	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12894820	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12895051	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12897044	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17102904	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17102923	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1967723	0.96[ASN][1000 genomes]
rs2273156	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2383688	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2383689	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28373355	0.96[ASN][1000 genomes]
rs34678475	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34927714	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35090385	0.89[ASN][1000 genomes]
rs35106382	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35337462	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35797365	0.87[ASN][1000 genomes]
rs35830406	0.95[ASN][1000 genomes]
rs35875778	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35962127	0.86[ASN][1000 genomes]
rs36008567	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36024417	0.86[ASN][1000 genomes]
rs56686328	0.80[ASN][1000 genomes]
rs56950244	0.82[ASN][1000 genomes]
rs60803103	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712312	0.80[ASN][1000 genomes]
rs7140843	0.95[ASN][1000 genomes]
rs71409556	0.91[ASN][1000 genomes]
rs71421920	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7143827	0.95[ASN][1000 genomes]
rs7144646	0.87[ASN][1000 genomes]
rs7145608	0.80[ASN][1000 genomes]
rs7153068	0.80[ASN][1000 genomes]
rs761505	0.95[ASN][1000 genomes]
rs761506	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs799664	0.80[ASN][1000 genomes]
rs8011422	0.95[ASN][1000 genomes]
rs8014327	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8016566	0.90[ASN][1000 genomes]
rs8018409	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8019179	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1045939	chr14:35311074-35494703	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv901602	chr14:35367889-35571651	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv901603	chr14:35371697-35435651	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv901604	chr14:35381137-35485748	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4573843	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL
rs4573843	PPP2R3C	cis	Whole Blood	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35381000-35398600	Weak transcription	Primary T cells from cord blood	blood
2	chr14:35381400-35412200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr14:35384600-35398200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr14:35384800-35398600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:35387400-35397000	Weak transcription	Fetal Intestine Small	intestine
6	chr14:35389600-35411400	Weak transcription	Aorta	Aorta
7	chr14:35390000-35412600	Weak transcription	Ovary	ovary
8	chr14:35390200-35395400	Weak transcription	NH-A	brain
9	chr14:35390200-35395600	Weak transcription	A549	lung
10	chr14:35390200-35400600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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