Variant report

Variant	rs28489579
Chromosome Location	chr15:50686778-50686779
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	chr15:50646659..50649812-chr15:50686170..50691655,5	MCF-7	breast:
2	chr15:50684853..50686825-chr15:50690971..50693142,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs1056682	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11634585	0.81[EUR][1000 genomes]
rs12905221	0.81[EUR][1000 genomes]
rs12911017	0.84[EUR][1000 genomes]
rs17431095	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17431150	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17431171	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1806843	0.89[ASN][1000 genomes]
rs2555486	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28817272	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28820353	0.97[ASN][1000 genomes]
rs34174311	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34565064	0.81[EUR][1000 genomes]
rs35541701	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35628775	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35831049	0.83[EUR][1000 genomes]
rs4775880	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55941574	0.84[EUR][1000 genomes]
rs55948407	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs606118	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66904653	0.83[EUR][1000 genomes]
rs7164848	0.81[EUR][1000 genomes]
rs7182201	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs720599	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28489579	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs28489579	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs28489579	GABPB1-AS1	cis	Thyroid	GTEx
rs28489579	GABPB1-AS1	cis	lung	GTEx
rs28489579	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs28489579	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs28489579	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs28489579	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs28489579	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs28489579	CTD-3110H11.1	cis	Thyroid	GTEx
rs28489579	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs28489579	CTD-3110H11.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50677000-50690400	Weak transcription	Right Atrium	heart
2	chr15:50683800-50703800	Weak transcription	K562	blood
3	chr15:50684800-50690000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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