Variant report

Variant	rs17819216
Chromosome Location	chr15:56093738-56093739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56033747..56035690-chr15:56092424..56095396,4	MCF-7	breast:
2	chr15:56032752..56035214-chr15:56091096..56094057,2	MCF-7	breast:
3	chr15:55940663..55943471-chr15:56092171..56094031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1104845	0.95[AMR][1000 genomes]
rs1104848	0.87[AMR][1000 genomes]
rs12907101	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17819222	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819228	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1912403	1.00[MEX][hapmap]
rs2899593	1.00[MEX][hapmap]
rs34146683	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34247233	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34685895	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34755247	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35299498	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35472570	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35734155	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35941636	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36132540	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7182185	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72732242	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8033157	0.90[AMR][1000 genomes]
rs933997	0.87[AMR][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	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
2	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
3	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
4	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
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17819216	CYP19A1	cis	cerebellum	SCAN
rs17819216	TMOD3	cis	cerebellum	SCAN
rs17819216	KIAA1370	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56091800-56094000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:56092000-56093800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:56092000-56094200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:56092000-56095000	Weak transcription	HSMMtube	muscle
5	chr15:56092200-56094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:56092400-56095200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:56092400-56095400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:56092600-56094600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:56092800-56094600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:56092800-56095400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:56093600-56095800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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