Variant report

Variant	rs1988660
Chromosome Location	chr15:56059700-56059701
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	chr15:56033924..56036726-chr15:56059253..56062733,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11071205	0.84[AMR][1000 genomes]
rs11071206	0.81[AMR][1000 genomes]
rs11071207	0.84[AMR][1000 genomes]
rs11071208	0.84[AMR][1000 genomes]
rs11071209	0.84[AMR][1000 genomes]
rs11630006	0.84[AMR][1000 genomes]
rs11630082	0.82[AMR][1000 genomes]
rs11635384	0.82[AMR][1000 genomes]
rs11635386	0.82[AMR][1000 genomes]
rs2018522	0.84[AMR][1000 genomes]
rs34795841	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58587583	0.84[AMR][1000 genomes]
rs60285843	0.84[AMR][1000 genomes]
rs6493819	0.84[AMR][1000 genomes]
rs7167653	0.84[AMR][1000 genomes]
rs7175125	0.81[AMR][1000 genomes]
rs7176575	0.84[AMR][1000 genomes]
rs7177532	0.84[AMR][1000 genomes]
rs7178078	0.84[AMR][1000 genomes]
rs7178119	0.84[AMR][1000 genomes]
rs7179170	0.84[AMR][1000 genomes]
rs7179377	0.84[AMR][1000 genomes]
rs7181910	0.81[AMR][1000 genomes]
rs8029451	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	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
rs1988660	PRTG	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56057400-56069400	Weak transcription	Right Atrium	heart
2	chr15:56057400-56078800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:56058200-56060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:56059000-56062600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:56059200-56060000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:56059200-56060600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:56059400-56060400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:56059400-56060400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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